LMU BioDB 2017 - User contributions [en]

JASPAR the Friendly Ghost Final Deliverables

2017-12-15T23:57:15Z

Ebachour: /* Team Signatures */ added my sig!!!

==Group Report==
[[Media:JASPAR Final Paper.pdf|JASPAR the Friendly Ghost Group Report]]

==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1_Individual_Assessment_and_Reflection|Antonio Porras]] | [[Ebachour_Week_15|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]

==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
[[Media:Api.txt|JASPAR team's code (as well as hAPI's code)]] | December 15, 2017 
==README that summarizes the functionality of your team's new feature==
[[Media:README.txt|Readme.txt]] | December 15, 2017 
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to the microarray results files==
#[[Aporras1 Week 8]]
#[[Aporras1 Week 10]]
#[[Aporras1 Week 14]]
#[[Aporras1 Week 15]]

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}
===Team Signatures===
*[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 20:49, 13 December 2017 (PST) 
*[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:48, 15 December 2017 (PST)
*[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:55, 15 December 2017 (PST)
*[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 15:57, 15 December 2017 (PST)

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

Template:Ebachour

2017-12-15T23:45:46Z

Ebachour: added week 15

Ebachour Week 15

2017-12-15T23:44:20Z

Ebachour: /* Reflection on the Process */ Finished reflection

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017 
[[Media:README.txt|JASPAR The Friendly Ghost Group Readme]] | December 15, 2017 
[[Media:Api.txt|JASPAR The Friendly Ghost Group Code]] | December 15, 2017 

==Individual Assessment and Reflection / Electronic Journal==

=== Statement of Work ===

There were a number of steps that the coders team members completed throughout this assignment. Before the coders moved their focus to the bulk of the GRNsight part of this project, they were asked to gain some background knowledge on the field of web development. They read “Chapter 6: How Are Apps Made?” in Paul Ford’s What is Code? which is an article from 2015 that covers most of the bases of the software development industry. They were asked to thoroughly read this chapter and then present to their class what it entailed. This chapter was specific to all of the tools that the coders used in development, highlighting some important tools at the time. After covering all of the background knowledge, the coders then began the introduction phase to the new project. Often when being assigned to a new project, software engineers are given an introduction to the code base so that they may understand how everything functions within the project before they begin their work. This project was no different, as the professor gave a quick introduction along with a manual which illustrated the relevant folders within the code bank that would be used for this feature. After JASPAR’s fellow team members forked GRNsight, the JASPAR team start by setting up a local version of GRNsight and making sure that everything was properly functioning. After this step, they began to acquaint themselves with GRNsight and understand their job in the implementation of this new feature. At this point, as as displayed in Figure C, the coders moved from the immersion phase (green) and into the intermediate phase (yellow).

The intermediate phase was where most of the progress was made towards finishing their part of the feature. They started by creating the branch that would be solely for JASPAR team progress, as well as the new files that would contain their soon-to-be-written code. At this point the coders were all setup on the GRNsight side and were ready to move to learning about the JASPAR database and how it worked. The majority of this part was spent reading the JASPAR database documentation which clearly states how the database API calls work; specifically URL, return values, and headers. JASPAR was effective in laying out their different API calls and explaining what each call did. This made it much easier for the coders to decipher which of the calls was best for retrieving the information that they needed (JASPAR API).
After studying JASPAR, and deciding which calls were to be use, the coders then moved on to implementing the first of the API calls. The first call used the inputted gene symbol to search the JASPAR database and retrieve a list of search results, from which they retrieved the matrix ID from the first result. The second call retrieves the object of gene information associated with that gene symbol. It used the matrix ID that was retrieved from the first call and returned the object with all of the information that JASPAR has for this gene, if any at all. At this point, as they were testing their code, they were getting something called an “Access-Control-Allow-Origin” error which is usually caused by an APIs lack of support for Cross-Origin Resource Sharing(CORS), but when they went and checked the websites overview page, they found that the API specifically stated that they supported CORS (API Overview). After reading this on the API Overview page of JASPAR, the coders began to believe that this error was due to miscoding of the getJasparInfo() function, but after studying the code and testing the API calls through the JASPAR interface, they realized that this issue was not due to the structure of their code, but in fact was due to JASPAR and the fact that they don’t support CORS. At this point, the JASPAR team met with the professor and decided that the best solution would be to implement a relay controller that would handle all traffic from JASPAR to GRNsight. Once the relay controller was done being integrated with the server-side of GRNsight, the API calls began working properly, which corresponded with the end of the intermediate phase of this project (Figure C).

The next phase of the project was the finishing touches (red) phase, which was where the coders spent most of their time interacting with the other teams working on this feature, to make sure that all of the pieces were working together properly (Figure C). The first step was to make sure that the JASPAR information, that the biologists on the integration team were requiring for the final page, was properly being organized and returned so that the information was useful on the page. This required taking the object returned from the second API call and properly “filing” the relevant fields into their spots within the master object. At this point, all that was left to do was to pass the information onto the page design and integration team so that they knew what to expect when calling the JASPAR function, so that they could properly put it on the page, which then marked the end of the coders work on this GRNsight feature, as displayed in Figure C.

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
*: Our team worked pretty well together to finish both the paper and the powerpoint together, but this was mainly due to good leadership from Quinn. He kept us up to date and he is the only reason this assignment was even remotely tolerable.
* What worked and what didn't work?
*: Everything worked really well. We had good communication and, although arranging meetup times was difficult, we still met three times out of class to work on the presentation.
* Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#: For the code specifically, everything was very well done, very clean and readable.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#: Quinn did a very good job of making our team page. I didn't really have much of a part in it but it looks really good.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*#: Yes we completed every single task. Even though they were all just very repetitive.

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
**: I learned a lot from the Computer Science portions of the class because it was building on my knowledge base of frameworks and software design and engineering.
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
**: I don't like biology, not because the subject isn't of interest (it is), but because of the way things are done in the Biology department. I just find it much more preferable to learn how I do in my major classes.
** With your hands (technical skills)?
**: Maybe I can type faster after all of the writing you guys made me do.

=Acknowledgements=
Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
I worked with my homework partner in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:29, 15 December 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 15. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{Template:Ebachour}}

Ebachour Week 15

2017-12-15T23:41:25Z

Ebachour: /* Assessment of Project */ Finished assessment of the project

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017 
[[Media:README.txt|JASPAR The Friendly Ghost Group Readme]] | December 15, 2017 
[[Media:Api.txt|JASPAR The Friendly Ghost Group Code]] | December 15, 2017 

==Individual Assessment and Reflection / Electronic Journal==

=== Statement of Work ===

There were a number of steps that the coders team members completed throughout this assignment. Before the coders moved their focus to the bulk of the GRNsight part of this project, they were asked to gain some background knowledge on the field of web development. They read “Chapter 6: How Are Apps Made?” in Paul Ford’s What is Code? which is an article from 2015 that covers most of the bases of the software development industry. They were asked to thoroughly read this chapter and then present to their class what it entailed. This chapter was specific to all of the tools that the coders used in development, highlighting some important tools at the time. After covering all of the background knowledge, the coders then began the introduction phase to the new project. Often when being assigned to a new project, software engineers are given an introduction to the code base so that they may understand how everything functions within the project before they begin their work. This project was no different, as the professor gave a quick introduction along with a manual which illustrated the relevant folders within the code bank that would be used for this feature. After JASPAR’s fellow team members forked GRNsight, the JASPAR team start by setting up a local version of GRNsight and making sure that everything was properly functioning. After this step, they began to acquaint themselves with GRNsight and understand their job in the implementation of this new feature. At this point, as as displayed in Figure C, the coders moved from the immersion phase (green) and into the intermediate phase (yellow).

The intermediate phase was where most of the progress was made towards finishing their part of the feature. They started by creating the branch that would be solely for JASPAR team progress, as well as the new files that would contain their soon-to-be-written code. At this point the coders were all setup on the GRNsight side and were ready to move to learning about the JASPAR database and how it worked. The majority of this part was spent reading the JASPAR database documentation which clearly states how the database API calls work; specifically URL, return values, and headers. JASPAR was effective in laying out their different API calls and explaining what each call did. This made it much easier for the coders to decipher which of the calls was best for retrieving the information that they needed (JASPAR API).
After studying JASPAR, and deciding which calls were to be use, the coders then moved on to implementing the first of the API calls. The first call used the inputted gene symbol to search the JASPAR database and retrieve a list of search results, from which they retrieved the matrix ID from the first result. The second call retrieves the object of gene information associated with that gene symbol. It used the matrix ID that was retrieved from the first call and returned the object with all of the information that JASPAR has for this gene, if any at all. At this point, as they were testing their code, they were getting something called an “Access-Control-Allow-Origin” error which is usually caused by an APIs lack of support for Cross-Origin Resource Sharing(CORS), but when they went and checked the websites overview page, they found that the API specifically stated that they supported CORS (API Overview). After reading this on the API Overview page of JASPAR, the coders began to believe that this error was due to miscoding of the getJasparInfo() function, but after studying the code and testing the API calls through the JASPAR interface, they realized that this issue was not due to the structure of their code, but in fact was due to JASPAR and the fact that they don’t support CORS. At this point, the JASPAR team met with the professor and decided that the best solution would be to implement a relay controller that would handle all traffic from JASPAR to GRNsight. Once the relay controller was done being integrated with the server-side of GRNsight, the API calls began working properly, which corresponded with the end of the intermediate phase of this project (Figure C).

The next phase of the project was the finishing touches (red) phase, which was where the coders spent most of their time interacting with the other teams working on this feature, to make sure that all of the pieces were working together properly (Figure C). The first step was to make sure that the JASPAR information, that the biologists on the integration team were requiring for the final page, was properly being organized and returned so that the information was useful on the page. This required taking the object returned from the second API call and properly “filing” the relevant fields into their spots within the master object. At this point, all that was left to do was to pass the information onto the page design and integration team so that they knew what to expect when calling the JASPAR function, so that they could properly put it on the page, which then marked the end of the coders work on this GRNsight feature, as displayed in Figure C.

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
*: Our team worked pretty well together to finish both the paper and the powerpoint together, but this was mainly due to good leadership from Quinn. He kept us up to date and he is the only reason this assignment was even remotely tolerable.
* What worked and what didn't work?
*: Everything worked really well. We had good communication and, although arranging meetup times was difficult, we still met three times out of class to work on the presentation.
* Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#: For the code specifically, everything was very well done, very clean and readable.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#: Quinn did a very good job of making our team page. I didn't really have much of a part in it but it looks really good.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*#: Yes we completed every single task. Even though they were all just very repetitive.

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

=Acknowledgements=
Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
I worked with my homework partner in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:29, 15 December 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 15. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{Template:Ebachour}}

Ebachour Week 15

2017-12-15T23:33:11Z

Ebachour: /* Statement of Work */ fixed

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017 
[[Media:README.txt|JASPAR The Friendly Ghost Group Readme]] | December 15, 2017 
[[Media:Api.txt|JASPAR The Friendly Ghost Group Code]] | December 15, 2017 

==Individual Assessment and Reflection / Electronic Journal==

=== Statement of Work ===

There were a number of steps that the coders team members completed throughout this assignment. Before the coders moved their focus to the bulk of the GRNsight part of this project, they were asked to gain some background knowledge on the field of web development. They read “Chapter 6: How Are Apps Made?” in Paul Ford’s What is Code? which is an article from 2015 that covers most of the bases of the software development industry. They were asked to thoroughly read this chapter and then present to their class what it entailed. This chapter was specific to all of the tools that the coders used in development, highlighting some important tools at the time. After covering all of the background knowledge, the coders then began the introduction phase to the new project. Often when being assigned to a new project, software engineers are given an introduction to the code base so that they may understand how everything functions within the project before they begin their work. This project was no different, as the professor gave a quick introduction along with a manual which illustrated the relevant folders within the code bank that would be used for this feature. After JASPAR’s fellow team members forked GRNsight, the JASPAR team start by setting up a local version of GRNsight and making sure that everything was properly functioning. After this step, they began to acquaint themselves with GRNsight and understand their job in the implementation of this new feature. At this point, as as displayed in Figure C, the coders moved from the immersion phase (green) and into the intermediate phase (yellow).

The intermediate phase was where most of the progress was made towards finishing their part of the feature. They started by creating the branch that would be solely for JASPAR team progress, as well as the new files that would contain their soon-to-be-written code. At this point the coders were all setup on the GRNsight side and were ready to move to learning about the JASPAR database and how it worked. The majority of this part was spent reading the JASPAR database documentation which clearly states how the database API calls work; specifically URL, return values, and headers. JASPAR was effective in laying out their different API calls and explaining what each call did. This made it much easier for the coders to decipher which of the calls was best for retrieving the information that they needed (JASPAR API).
After studying JASPAR, and deciding which calls were to be use, the coders then moved on to implementing the first of the API calls. The first call used the inputted gene symbol to search the JASPAR database and retrieve a list of search results, from which they retrieved the matrix ID from the first result. The second call retrieves the object of gene information associated with that gene symbol. It used the matrix ID that was retrieved from the first call and returned the object with all of the information that JASPAR has for this gene, if any at all. At this point, as they were testing their code, they were getting something called an “Access-Control-Allow-Origin” error which is usually caused by an APIs lack of support for Cross-Origin Resource Sharing(CORS), but when they went and checked the websites overview page, they found that the API specifically stated that they supported CORS (API Overview). After reading this on the API Overview page of JASPAR, the coders began to believe that this error was due to miscoding of the getJasparInfo() function, but after studying the code and testing the API calls through the JASPAR interface, they realized that this issue was not due to the structure of their code, but in fact was due to JASPAR and the fact that they don’t support CORS. At this point, the JASPAR team met with the professor and decided that the best solution would be to implement a relay controller that would handle all traffic from JASPAR to GRNsight. Once the relay controller was done being integrated with the server-side of GRNsight, the API calls began working properly, which corresponded with the end of the intermediate phase of this project (Figure C).

The next phase of the project was the finishing touches (red) phase, which was where the coders spent most of their time interacting with the other teams working on this feature, to make sure that all of the pieces were working together properly (Figure C). The first step was to make sure that the JASPAR information, that the biologists on the integration team were requiring for the final page, was properly being organized and returned so that the information was useful on the page. This required taking the object returned from the second API call and properly “filing” the relevant fields into their spots within the master object. At this point, all that was left to do was to pass the information onto the page design and integration team so that they knew what to expect when calling the JASPAR function, so that they could properly put it on the page, which then marked the end of the coders work on this GRNsight feature, as displayed in Figure C.

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
* What worked and what didn't work?
* What would you do differently if you could do it all over again?
* Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

=Acknowledgements=
Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
I worked with my homework partner in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:29, 15 December 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 15. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{Template:Ebachour}}

Ebachour Week 15

2017-12-15T23:31:38Z

Ebachour: /* Statement of Work */ added my statement of work, everything above was also written in the paper.

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017 
[[Media:README.txt|JASPAR The Friendly Ghost Group Readme]] | December 15, 2017 
[[Media:Api.txt|JASPAR The Friendly Ghost Group Code]] | December 15, 2017 

==Individual Assessment and Reflection / Electronic Journal==

=== Statement of Work ===

There were a number of steps that the coders team members completed throughout this assignment. Before the coders moved their focus to the bulk of the GRNsight part of this project, they were asked to gain some background knowledge on the field of web development. They read “Chapter 6: How Are Apps Made?” in Paul Ford’s What is Code? which is an article from 2015 that covers most of the bases of the software development industry. They were asked to thoroughly read this chapter and then present to their class what it entailed. This chapter was specific to all of the tools that the coders used in development, highlighting some important tools at the time. After covering all of the background knowledge, the coders then began the introduction phase to the new project. Often when being assigned to a new project, software engineers are given an introduction to the code base so that they may understand how everything functions within the project before they begin their work. This project was no different, as the professor gave a quick introduction along with a manual which illustrated the relevant folders within the code bank that would be used for this feature. After JASPAR’s fellow team members forked GRNsight, the JASPAR team start by setting up a local version of GRNsight and making sure that everything was properly functioning. After this step, they began to acquaint themselves with GRNsight and understand their job in the implementation of this new feature. At this point, as as displayed in Figure C, the coders moved from the immersion phase (green) and into the intermediate phase (yellow).
The intermediate phase was where most of the progress was made towards finishing their part of the feature. They started by creating the branch that would be solely for JASPAR team progress, as well as the new files that would contain their soon-to-be-written code. At this point the coders were all setup on the GRNsight side and were ready to move to learning about the JASPAR database and how it worked. The majority of this part was spent reading the JASPAR database documentation which clearly states how the database API calls work; specifically URL, return values, and headers. JASPAR was effective in laying out their different API calls and explaining what each call did. This made it much easier for the coders to decipher which of the calls was best for retrieving the information that they needed (JASPAR API).
After studying JASPAR, and deciding which calls were to be use, the coders then moved on to implementing the first of the API calls. The first call used the inputted gene symbol to search the JASPAR database and retrieve a list of search results, from which they retrieved the matrix ID from the first result. The second call retrieves the object of gene information associated with that gene symbol. It used the matrix ID that was retrieved from the first call and returned the object with all of the information that JASPAR has for this gene, if any at all. At this point, as they were testing their code, they were getting something called an “Access-Control-Allow-Origin” error which is usually caused by an APIs lack of support for Cross-Origin Resource Sharing(CORS), but when they went and checked the websites overview page, they found the following:

(API Overview). After reading this on the API Overview page of JASPAR, the coders began to believe that this error was due to miscoding of the getJasparInfo() function, but after studying the code and testing the API calls through the JASPAR interface, they realized that this issue was not due to the structure of their code, but in fact was due to JASPAR and the fact that they don’t support CORS. At this point, the JASPAR team met with the professor and decided that the best solution would be to implement a relay controller that would handle all traffic from JASPAR to GRNsight. Once the relay controller was done being integrated with the server-side of GRNsight, the API calls began working properly, which corresponded with the end of the intermediate phase of this project (Figure C).
The next phase of the project was the finishing touches (red) phase, which was where the coders spent most of their time interacting with the other teams working on this feature, to make sure that all of the pieces were working together properly (Figure C). The first step was to make sure that the JASPAR information, that the biologists on the integration team were requiring for the final page, was properly being organized and returned so that the information was useful on the page. This required taking the object returned from the second API call and properly “filing” the relevant fields into their spots within the master object. At this point, all that was left to do was to pass the information onto the page design and integration team so that they knew what to expect when calling the JASPAR function, so that they could properly put it on the page, which then marked the end of the coders work on this GRNsight feature, as displayed in Figure C.

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
* What worked and what didn't work?
* What would you do differently if you could do it all over again?
* Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

=Acknowledgements=
Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
I worked with my homework partner in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:29, 15 December 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 15. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{Template:Ebachour}}

Ebachour Week 15

2017-12-15T23:27:58Z

Ebachour: fixed template link

Ebachour Week 15

2017-12-15T21:30:11Z

Ebachour: /* Acknowledgements */ got rid of numbering

Ebachour Week 15

2017-12-15T21:29:26Z

Ebachour: Added references and acknowledgements

Ebachour Week 15

2017-12-15T21:28:28Z

Ebachour: Fixed template

Ebachour Week 15

2017-12-15T21:27:25Z

Ebachour: Starting the Week 15 page

JASPAR the Friendly Ghost Final Deliverables

2017-12-15T21:23:44Z

Ebachour: /* Individual statements of work, assessments, reflections */ change url

==Group Report==
==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1_Individual_Assessment_and_Reflection|Antonio Porras]] | [[Ebachour_Week_15|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]

==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
[[Media:Api.txt|JASPAR team's code (as well as hAPI's code)]] | December 15, 2017 
==README that summarizes the functionality of your team's new feature==
[[Media:README.txt|Readme.txt]] | December 15, 2017 
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to the microarray results files==
#[[Aporras1 Week 8]]
#[[Aporras1 Week 10]]
#[[Aporras1 Week 14]]
#[[Aporras1 Week 15]]

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}
===Team Signatures===
*[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 20:49, 13 December 2017 (PST)

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost Final Deliverables

2017-12-15T21:21:51Z

Ebachour: Adding my code to the final deliverables page

==Group Report==
==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1_Individual_Assessment_and_Reflection|Antonio Porras]] | [[Ebachour_individual_statement|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]

==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
[[Media:Api.txt|JASPAR team's code (as well as hAPI's code)]] | December 15, 2017 
==README that summarizes the functionality of your team's new feature==
[[Media:README.txt|Readme.txt]] | December 15, 2017 
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to the microarray results files==
#[[Aporras1 Week 8]]
#[[Aporras1 Week 10]]
#[[Aporras1 Week 14]]
#[[Aporras1 Week 15]]

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}
===Team Signatures===
*[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 20:49, 13 December 2017 (PST)

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T21:20:21Z

Ebachour: /* Working Deliverables */ adding code

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]]) 
[[Media:README.txt|Readme.txt]] | December 15, 2017 
[[Media:Api.txt|Our code for this feature (also hAPI team's code)]] | December 15, 2017 

==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====
The beginning of this week was spent finishing our feature. We ran into some issues, but we worked it out with King Dondi. Once we were done with the feature, we spent some time making sure that the other teams knew what to expect from JASPAR specifically, so that they could properly put it on the final page product. After we were done with this part of the assignment, we then began to work on the power point presentation. We all worked together at first and then split off to work on our specific parts. We presented, and still didn't celebrate because we had to write an essay. The essay was a lot of repetition and formalities.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:13, 15 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always an advantage.

====Eddie's Reflection====
# What worked?
#* In my opinion, we worked really well as a group to finish the powerpoint ahead of time and start the presentation earlier than some of the other time. This had nothing to do with me, but my teammates were very on top of this whole assignment.
# What didn't work?
#* It was completely unfair how much time we had to spend on this project, especially during the week before and of finals week. And on top of that we are turning in a 40 page paper on our work on the project. Everything worked efficiently within our group and we still struggled with finishing the assignment so it must've been something wrong with the expectations of us for this assignment.
# What will I do next time?
#* I would like to say start earlier, but in all honesty, with all of my other classes and the other assignments that this class was throwing at us, I don't think that was very possible.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:09, 15 December 2017 (PST)

==Acknowledgements==
# A huge thank you to both [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]] for taking the time to teach this course and support us, the students, throughout the semester's challenges.
# The [[JASPAR_the_Friendly_Ghost|JASPAR The Friendly Ghost]] team for working as a cohesive unit.
# The Department of Biology at LMU
# The Department of Computer Science at LMU
# The entire class composed of students who we worked alongside throughout the semester.

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

File:Api.txt

2017-12-15T21:18:53Z

Ebachour: Here is our code in a .txt file

Here is our code in a .txt file

JASPAR the Friendly Ghost

2017-12-15T21:14:51Z

Ebachour: /* Working Deliverables */ added breaks

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]]) 
[[Media:README.txt|Readme.txt]] | December 15, 2017 

==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====
The beginning of this week was spent finishing our feature. We ran into some issues, but we worked it out with King Dondi. Once we were done with the feature, we spent some time making sure that the other teams knew what to expect from JASPAR specifically, so that they could properly put it on the final page product. After we were done with this part of the assignment, we then began to work on the power point presentation. We all worked together at first and then split off to work on our specific parts. We presented, and still didn't celebrate because we had to write an essay. The essay was a lot of repetition and formalities.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:13, 15 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always an advantage.

====Eddie's Reflection====
# What worked?
#* In my opinion, we worked really well as a group to finish the powerpoint ahead of time and start the presentation earlier than some of the other time. This had nothing to do with me, but my teammates were very on top of this whole assignment.
# What didn't work?
#* It was completely unfair how much time we had to spend on this project, especially during the week before and of finals week. And on top of that we are turning in a 40 page paper on our work on the project. Everything worked efficiently within our group and we still struggled with finishing the assignment so it must've been something wrong with the expectations of us for this assignment.
# What will I do next time?
#* I would like to say start earlier, but in all honesty, with all of my other classes and the other assignments that this class was throwing at us, I don't think that was very possible.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:09, 15 December 2017 (PST)

==Acknowledgements==
# A huge thank you to both [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]] for taking the time to teach this course and support us, the students, throughout the semester's challenges.
# The [[JASPAR_the_Friendly_Ghost|JASPAR The Friendly Ghost]] team for working as a cohesive unit.
# The Department of Biology at LMU
# The Department of Computer Science at LMU
# The entire class composed of students who we worked alongside throughout the semester.

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T21:14:22Z

Ebachour: /* Working Deliverables */ Adding readme.txt

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
[[Media:README.txt|Readme.txt]] | December 15, 2017

==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====
The beginning of this week was spent finishing our feature. We ran into some issues, but we worked it out with King Dondi. Once we were done with the feature, we spent some time making sure that the other teams knew what to expect from JASPAR specifically, so that they could properly put it on the final page product. After we were done with this part of the assignment, we then began to work on the power point presentation. We all worked together at first and then split off to work on our specific parts. We presented, and still didn't celebrate because we had to write an essay. The essay was a lot of repetition and formalities.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:13, 15 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always an advantage.

====Eddie's Reflection====
# What worked?
#* In my opinion, we worked really well as a group to finish the powerpoint ahead of time and start the presentation earlier than some of the other time. This had nothing to do with me, but my teammates were very on top of this whole assignment.
# What didn't work?
#* It was completely unfair how much time we had to spend on this project, especially during the week before and of finals week. And on top of that we are turning in a 40 page paper on our work on the project. Everything worked efficiently within our group and we still struggled with finishing the assignment so it must've been something wrong with the expectations of us for this assignment.
# What will I do next time?
#* I would like to say start earlier, but in all honesty, with all of my other classes and the other assignments that this class was throwing at us, I don't think that was very possible.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:09, 15 December 2017 (PST)

==Acknowledgements==
# A huge thank you to both [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]] for taking the time to teach this course and support us, the students, throughout the semester's challenges.
# The [[JASPAR_the_Friendly_Ghost|JASPAR The Friendly Ghost]] team for working as a cohesive unit.
# The Department of Biology at LMU
# The Department of Computer Science at LMU
# The entire class composed of students who we worked alongside throughout the semester.

==References==
===Week 11===
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#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
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#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
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#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
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#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
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#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
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#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
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#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T21:13:10Z

Ebachour: /* Executive Summaries */ Added my executive summary

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====
The beginning of this week was spent finishing our feature. We ran into some issues, but we worked it out with King Dondi. Once we were done with the feature, we spent some time making sure that the other teams knew what to expect from JASPAR specifically, so that they could properly put it on the final page product. After we were done with this part of the assignment, we then began to work on the power point presentation. We all worked together at first and then split off to work on our specific parts. We presented, and still didn't celebrate because we had to write an essay. The essay was a lot of repetition and formalities.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:13, 15 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always an advantage.

====Eddie's Reflection====
# What worked?
#* In my opinion, we worked really well as a group to finish the powerpoint ahead of time and start the presentation earlier than some of the other time. This had nothing to do with me, but my teammates were very on top of this whole assignment.
# What didn't work?
#* It was completely unfair how much time we had to spend on this project, especially during the week before and of finals week. And on top of that we are turning in a 40 page paper on our work on the project. Everything worked efficiently within our group and we still struggled with finishing the assignment so it must've been something wrong with the expectations of us for this assignment.
# What will I do next time?
#* I would like to say start earlier, but in all honesty, with all of my other classes and the other assignments that this class was throwing at us, I don't think that was very possible.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:09, 15 December 2017 (PST)

==Acknowledgements==
# A huge thank you to both [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]] for taking the time to teach this course and support us, the students, throughout the semester's challenges.
# The [[JASPAR_the_Friendly_Ghost|JASPAR The Friendly Ghost]] team for working as a cohesive unit.
# The Department of Biology at LMU
# The Department of Computer Science at LMU
# The entire class composed of students who we worked alongside throughout the semester.

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#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T21:09:33Z

Ebachour: /* Eddie's Reflection */ Adding sig

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always an advantage.

====Eddie's Reflection====
# What worked?
#* In my opinion, we worked really well as a group to finish the powerpoint ahead of time and start the presentation earlier than some of the other time. This had nothing to do with me, but my teammates were very on top of this whole assignment.
# What didn't work?
#* It was completely unfair how much time we had to spend on this project, especially during the week before and of finals week. And on top of that we are turning in a 40 page paper on our work on the project. Everything worked efficiently within our group and we still struggled with finishing the assignment so it must've been something wrong with the expectations of us for this assignment.
# What will I do next time?
#* I would like to say start earlier, but in all honesty, with all of my other classes and the other assignments that this class was throwing at us, I don't think that was very possible.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:09, 15 December 2017 (PST)

==Acknowledgements==
# A huge thank you to both [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]] for taking the time to teach this course and support us, the students, throughout the semester's challenges.
# The [[JASPAR_the_Friendly_Ghost|JASPAR The Friendly Ghost]] team for working as a cohesive unit.
# The Department of Biology at LMU
# The Department of Computer Science at LMU
# The entire class composed of students who we worked alongside throughout the semester.

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T21:08:44Z

Ebachour: /* Weekly Reflections */ Adding my reflection

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always an advantage.

====Eddie's Reflection====
# What worked?
#* In my opinion, we worked really well as a group to finish the powerpoint ahead of time and start the presentation earlier than some of the other time. This had nothing to do with me, but my teammates were very on top of this whole assignment.
# What didn't work?
#* It was completely unfair how much time we had to spend on this project, especially during the week before and of finals week. And on top of that we are turning in a 40 page paper on our work on the project. Everything worked efficiently within our group and we still struggled with finishing the assignment so it must've been something wrong with the expectations of us for this assignment.
# What will I do next time?
#* I would like to say start earlier, but in all honesty, with all of my other classes and the other assignments that this class was throwing at us, I don't think that was very possible.

==Acknowledgements==
# A huge thank you to both [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]] for taking the time to teach this course and support us, the students, throughout the semester's challenges.
# The [[JASPAR_the_Friendly_Ghost|JASPAR The Friendly Ghost]] team for working as a cohesive unit.
# The Department of Biology at LMU
# The Department of Computer Science at LMU
# The entire class composed of students who we worked alongside throughout the semester.

==References==
===Week 11===
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#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
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#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
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#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

File:README.txt

2017-12-15T20:58:17Z

Ebachour: The file is written in MD, but they won't let me upload a MD file so here is a txt file.

The file is written in MD, but they won't let me upload a MD file so here is a txt file.

Ebachour Week 14

2017-12-05T07:46:59Z

Ebachour: /* Electronic Journal */ Added Electronic Journal

=Electronic Journal=
* Simon and worked a lot in class and cracked the code on how to access the JASPAR data relevant using an gene id
* We ran into complication that we think are due to CORS
* We decided that our branch shouldn't really be separate from the gene-database-apis branch, so we decided to merge the two for the sake of ease
** This means that there are now four people working on our branch
* I also did some work on my own, trying to figure out if there was an easy fix for the CORS issue
* I found a local fix which uses a chrome extension to trick (sort of) Jaspar somehow, I'm not sure that I really understand how it works, but it does
* I committed all this code, which works on my own machine, but I still need to confirm with Dondi how this would work for GRNsight.
* I also created the master object that would contain all of the data that we need from all the sources

=Fields to Pull From Each Database=
''' EVERYTHING IN THIS SECTION WAS PULLED FROM QUINN'S JOURNAL PAGE '''

We decided that from JASPAR we will pull:
*Matrix ID ''MA0319.1''
*Class ''Heat shock factors''
*Family ''HSF factors''
*Sequence Logo ''image below''
*Frequency Matrix ''image below''
[[File:Jasper seq log and freq matrix.png]]

Breakdown of what we want from all other databases: 
'''NCBI:'''
*Gene ID ''852806''
*Locus Tag ''YGL073W''
*Also Known As '''EXA3; MAS3'''
*Chromosome Sequence ''Chromosome: VII; NC_001139.9 (368753..371254)''
*Genomic Sequence ''NC_001139.9''
*Protein Sequence ''NP_011442.3''
 
'''Ensembl:'''
*Gene ID ''YGL073W''
*Description/Function ''Trimeric heat shock transcription factor; activates multiple genes in response to highly diverse stresses, including hyperthermia; recognizes variable heat shock elements (HSEs) consisting of inverted NGAAN repeats; monitors translational status of cell at the ribosome through an RQC (Ribosomal Quality Control)-mediated translation-stress signal; involved in diauxic shift; posttranslationally regulated [Source:SGD;Acc:S000003041]''
*DNA Sequence ''>chromosome:R64-1-1:VII:368153:371854:1'' 
<code>''AAAATACTCCACTAAGGCCAGTAGCAACAACACGTTTTCTTGGATGATGCGTTTTCTTGA ACAAACAGTACCGACTAGGACTGTTTCAATGAAGTTGTGTACGGTCTGGTAGTATATCTA TATTCCGTGATGCCTTTGTGGAGGACGTTGAGATGAGACTGAGTCGTACACCATGTTATT CCTGTTTACGGTTAATTGCGCGTCGCGCTTTCTCTAGCAAATATCTCGGTTCGAAGTAAA GCAGGTCCTTCATGTAATGGTAACCTAAGGCAAAGGGTTTGTCATATACCCGTGAAGGCA TTTACACAAGCGCACTTCTAGTCATATGCAGTTCATGCATATTAAGTGAGTGTTATAACG CAAGAGTTATATTTGAAATAGGGTTGTTAAAGAAGGGAGAACCCATTCACCACATTATCT TTGCGAGTGTAAAACTAGATAACTTAAATTTTTAGGAGAGATTTTGCCACTTGGCAGCAA ATACCAAATAGCAGTACTGTTCCGGTAGATAAAGGCAAAGAGTTAGAGGTGTGCTTTACG AACAGCGCTGGAAGGGAAAGGAAACAAAAAAGACAAAAAGACAGCTGTATTGTTGGCGCC ATGAATAATGCTGCAAATACAGGGACGACCAATGAGTCAAACGTGAGCGATGCTCCCCGT ATTGAGCCTTTACCAAGCTTGAATGATGATGACATTGAAAAAATCTTACAACCGAACGAT ATCTTTACGACCGATCGTACCGATGCAAGTACTACATCTTCCACAGCCATTGAAGATATT ATTAACCCCTCATTGGATCCGCAGTCAGCAGCATCGCCGGTTCCTTCTTCCTCTTTTTTC CATGACTCAAGGAAACCTTCCACCAGTACACATTTAGTAAGGAGAGGTACTCCATTGGGA ATTTACCAAACCAATCTATACGGTCACAATAGCAGAGAAAATACTAATCCTAATAGTACA TTATTATCTTCTAAGTTACTCGCGCATCCACCAGTTCCTTATGGGCAAAATCCCGATTTA CTACAACATGCTGTGTACAGGGCACAGCCGTCAAGTGGAACCACTAACGCGCAACCGCGC CAAACCACAAGAAGATATCAATCCCATAAATCACGGCCTGCATTTGTTAATAAACTATGG AGCATGTTAAACGATGATTCTAATACGAAACTTATACAGTGGGCGGAGGATGGAAAATCT TTTATTGTCACGAATAGGGAGGAATTTGTGCACCAAATTTTACCAAAATATTTTAAACAT TCCAATTTCGCTTCCTTTGTAAGACAATTGAACATGTATGGATGGCATAAAGTTCAAGAT GTCAAGTCAGGATCAATTCAAAGTAGTTCAGATGATAAGTGGCAATTTGAAAATGAAAAC TTCATTAGAGGTAGAGAAGATTTGCTGGAAAAAATAATCAGGCAGAAAGGTTCCTCCAAT AACCATAATAGCCCTAGTGGTAACGGTAATCCAGCGAATGGTAGCAACATCCCTCTGGAC AATGCCGCAGGAAGTAATAATAGCAATAATAACATCAGTAGTAGTAATTCATTTTTTAAC AATGGTCATTTATTGCAGGGTAAAACACTAAGATTAATGAACGAAGCGAATCTTGGAGAT AAGAATGATGTCACCGCGATTTTGGGGGAATTAGAGCAAATAAAATATAACCAGATTGCA ATTTCCAAAGATTTACTAAGAATAAACAAAGATAATGAGTTATTATGGCAAGAGAATATG ATGGCCAGGGAAAGACATAGAACCCAACAGCAAGCCTTGGAAAAAATGTTCAGATTCTTG ACATCTATAGTCCCACACTTAGATCCCAAAATGATTATGGACGGGCTGGGAGATCCGAAA GTTAATAATGAAAAGCTAAACAGTGCGAATAACATTGGGTTAAATCGCGACAACACAGGC ACTATAGATGAACTAAAATCCAACGATTCTTTCATAAACGATGATCGTAATTCTTTCACC AATGCTACAACCAACGCCCGTAATAACATGAGTCCCAACAATGATGACAATAGTATTGAC ACCGCTAGCACTAATACCACCAACAGAAAGAAAAATATAGATGAAAACATCAAAAATAAC AACGACATAATTAATGACATTATATTTAATACCAACCTTGCCAACAATCTCAGCAATTAC AATTCCAACAATAATGCTGGCTCGCCAATAAGGCCCTATAAACAAAGATATCTTTTGAAA AATAGAGCCAATTCCTCGACATCGAGTGAGAATCCAAGCCTAACGCCCTTTGATATCGAA TCTAATAATGACCGCAAAATTTCAGAAATTCCTTTTGATGACGAAGAAGAAGAAGAAACG GATTTTAGGCCTTTTACCTCGCGAGATCCTAATAACCAAACGAGTGAAAACACTTTTGAT CCAAACAGATTTACGATGCTCTCTGATGATGATTTAAAAAAAGATTCTCATACCAATGAC AATAAACACAACGAAAGTGATCTTTTTTGGGACAACGTACATAGAAATATAGACGAACAA GATGCAAGACTCCAGAACTTGGAAAATATGGTTCACATACTTTCTCCTGGATATCCTAAT AAGTCGTTCAACAACAAAACTTCCTCGACAAACACTAATTCCAATATGGAAAGTGCTGTC AACGTTAATAGCCCTGGTTTCAACTTACAGGATTATTTAACTGGAGAGTCTAATTCCCCC AATTCTGTTCATTCTGTTCCCTCCAATGGCAGCGGCTCCACACCGTTGCCCATGCCAAAT GATAATGACACCGAGCACGCAAGTACAAGTGTCAATCAAGGCGAAAATGGAAGCGGATTA ACGCCCTTCCTCACGGTAGATGATCACACACTAAACGACAATAACACTAGTGAGGGAAGT ACAAGGGTGTCCCCCGATATAAAGTTCAGCGCCACTGAAAACACTAAAGTGAGTGATAAC CTGCCAAGCTTTAATGACCACAGTTATTCCACCCAGGCCGACACGGCGCCCGAGAACGCT AAGAAAAGATTTGTGGAGGAAATACCGGAACCGGCTATAGTCGAAATACAGGACCCGACA GAGTACAACGATCACCGCCTGCCCAAACGAGCTAAGAAATAGTACACAGGGCAAGGTCAT TAAATAGCGTATATAATCATTTAATATAGTATGTTCTCGAAGCTGATCGCGTAAGGCGCA GAGCGAACTAAAAAAAATACCGGCACCCATGCACCTCACACCGCCGCACGCGAGTGAGGT TGAACTGCACCCGGAAAATGCCAAGTAGATGAGTCGTGAAGAGTTCTCGTTATTCGAGCT AGTGAGAGCCTGAGAAGGGCTTGCCGAGTGAACTGGTGTCACATTGGCCGTTTTAACGCA AGTTGGCGTACTTATATTGACTGTTGGATGAAAGGGTAATCAAGAGAAACGGAAACGGCC TCCTCATCGTTAAGCTCATCAGTATTCATTTCTCCCCTTTCTGCTCCATCGCGTGCTCGA GACTATATTCTTCAGATTATCAAGCAGAAACAGAATTCGCATATTACATAACTTTCACAG GTTGAAGTATAAACCGCTACAGTACACAACCTCGGATAGAATATAGGGAAGAGGCCAATT CCGTGAAAACGATTTAATATTCTTTACAGTTACAAAAAGTATTACCTATTATCCTCTTTT CGGTGTCATTGACAAACCTCTTAGCGACAGAAACTCCCTAGC''</code>
*Gene Location ''Chromosome VII: 368,753-371,254''
*Gene Map 
[[File:Saccharomycescerevisiae HSF1.pdf]]
 
'''UniProt:'''
*Gene ID: ''P10961 (HSF_YEAST)''
*Protein Sequence 
<code>''MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI
INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST
LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW
SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD
VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD
NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA
ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK
VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID
TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK
NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD
PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN
KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN
DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN
LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK''</code>
*Similar Protein: ''N1P1W2'' and ID of Similar Protein: ''P10961''
*Protein Type/Name: ''Heat shock factor protein''
*Species: ''Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)''
 
'''SGD:'''
*Gene ID
**Standard Name ''HSF1''
**Systematic Name ''YGL073W''
**SGD ID ''S000003041''
*Regulation
**Regulators: ''6''
**Targets: ''478''
*Interaction
**Total Interactions: ''85 total interactions for 71 unique genes''
**Physical Interactions:
***''Affinity Capture-MS: 11''
***''Affinity Capture-RNA: 1''
***''Affinity Capture-Western: 4''
***''Biochemical Activity: 11''
***''Co-localization: 3''
***''Reconstituted Complex: 2''
***''Two-hybrid: 3''
**Genetic Interactions:
***''Dosage Rescue: 16''
***''Negative Genetic: 8''
***''Phenotypic Enhancement: 1''
***''Phenotypic Suppression: 5''
***''Synthetic Growth Defect: 2''
***''Synthetic Haploinsufficiency: 1''
***''Synthetic Lethality: 6''
***''Synthetic Rescue: 11''
*Gene Ontology
**Summary: ''Sequence-specific DNA binding transcription factor that induces expression of the Hsp90-family protein chaperones Hsc82p and Hsp82p during the cellular response to heat; also negatively regulates TOR signaling''
**Molecular Function:
***''Manually Curated: DNA binding transcription factor activity (IDA)''
***''High-Throughput: sequence-specific DNA binding (HDA)''
**Biological Process
***''Manually Curated: negative regulation of TOR signaling (IMP), positive regulation of transcription from RNA polymerase II promoter (IMP), regulation of establishment of protein localization to chromosome (IMP), regulation of transcription from RNA polymerase II promoter (IDA), response to heat (IMP)''
**Cellular Component:
***''Manually Curated: nucleus (IDA)''
***''High-Throughput: mitochondrion (HDA)''

=Acknowledgements=
I worked with my homework partner in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:41, 4 December 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 14. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14

{{Template:ebachour}}

Ebachour Week 14

2017-12-05T07:41:11Z

Ebachour: Added logistics that you require

=Electronic Journal=

=Fields to Pull From Each Database=
''' EVERYTHING IN THIS SECTION WAS PULLED FROM QUINN'S JOURNAL PAGE '''

We decided that from JASPAR we will pull:
*Matrix ID ''MA0319.1''
*Class ''Heat shock factors''
*Family ''HSF factors''
*Sequence Logo ''image below''
*Frequency Matrix ''image below''
[[File:Jasper seq log and freq matrix.png]]

Breakdown of what we want from all other databases: 
'''NCBI:'''
*Gene ID ''852806''
*Locus Tag ''YGL073W''
*Also Known As '''EXA3; MAS3'''
*Chromosome Sequence ''Chromosome: VII; NC_001139.9 (368753..371254)''
*Genomic Sequence ''NC_001139.9''
*Protein Sequence ''NP_011442.3''
 
'''Ensembl:'''
*Gene ID ''YGL073W''
*Description/Function ''Trimeric heat shock transcription factor; activates multiple genes in response to highly diverse stresses, including hyperthermia; recognizes variable heat shock elements (HSEs) consisting of inverted NGAAN repeats; monitors translational status of cell at the ribosome through an RQC (Ribosomal Quality Control)-mediated translation-stress signal; involved in diauxic shift; posttranslationally regulated [Source:SGD;Acc:S000003041]''
*DNA Sequence ''>chromosome:R64-1-1:VII:368153:371854:1'' 
<code>''AAAATACTCCACTAAGGCCAGTAGCAACAACACGTTTTCTTGGATGATGCGTTTTCTTGA ACAAACAGTACCGACTAGGACTGTTTCAATGAAGTTGTGTACGGTCTGGTAGTATATCTA TATTCCGTGATGCCTTTGTGGAGGACGTTGAGATGAGACTGAGTCGTACACCATGTTATT CCTGTTTACGGTTAATTGCGCGTCGCGCTTTCTCTAGCAAATATCTCGGTTCGAAGTAAA GCAGGTCCTTCATGTAATGGTAACCTAAGGCAAAGGGTTTGTCATATACCCGTGAAGGCA TTTACACAAGCGCACTTCTAGTCATATGCAGTTCATGCATATTAAGTGAGTGTTATAACG CAAGAGTTATATTTGAAATAGGGTTGTTAAAGAAGGGAGAACCCATTCACCACATTATCT TTGCGAGTGTAAAACTAGATAACTTAAATTTTTAGGAGAGATTTTGCCACTTGGCAGCAA ATACCAAATAGCAGTACTGTTCCGGTAGATAAAGGCAAAGAGTTAGAGGTGTGCTTTACG AACAGCGCTGGAAGGGAAAGGAAACAAAAAAGACAAAAAGACAGCTGTATTGTTGGCGCC ATGAATAATGCTGCAAATACAGGGACGACCAATGAGTCAAACGTGAGCGATGCTCCCCGT ATTGAGCCTTTACCAAGCTTGAATGATGATGACATTGAAAAAATCTTACAACCGAACGAT ATCTTTACGACCGATCGTACCGATGCAAGTACTACATCTTCCACAGCCATTGAAGATATT ATTAACCCCTCATTGGATCCGCAGTCAGCAGCATCGCCGGTTCCTTCTTCCTCTTTTTTC CATGACTCAAGGAAACCTTCCACCAGTACACATTTAGTAAGGAGAGGTACTCCATTGGGA ATTTACCAAACCAATCTATACGGTCACAATAGCAGAGAAAATACTAATCCTAATAGTACA TTATTATCTTCTAAGTTACTCGCGCATCCACCAGTTCCTTATGGGCAAAATCCCGATTTA CTACAACATGCTGTGTACAGGGCACAGCCGTCAAGTGGAACCACTAACGCGCAACCGCGC CAAACCACAAGAAGATATCAATCCCATAAATCACGGCCTGCATTTGTTAATAAACTATGG AGCATGTTAAACGATGATTCTAATACGAAACTTATACAGTGGGCGGAGGATGGAAAATCT TTTATTGTCACGAATAGGGAGGAATTTGTGCACCAAATTTTACCAAAATATTTTAAACAT TCCAATTTCGCTTCCTTTGTAAGACAATTGAACATGTATGGATGGCATAAAGTTCAAGAT GTCAAGTCAGGATCAATTCAAAGTAGTTCAGATGATAAGTGGCAATTTGAAAATGAAAAC TTCATTAGAGGTAGAGAAGATTTGCTGGAAAAAATAATCAGGCAGAAAGGTTCCTCCAAT AACCATAATAGCCCTAGTGGTAACGGTAATCCAGCGAATGGTAGCAACATCCCTCTGGAC AATGCCGCAGGAAGTAATAATAGCAATAATAACATCAGTAGTAGTAATTCATTTTTTAAC AATGGTCATTTATTGCAGGGTAAAACACTAAGATTAATGAACGAAGCGAATCTTGGAGAT AAGAATGATGTCACCGCGATTTTGGGGGAATTAGAGCAAATAAAATATAACCAGATTGCA ATTTCCAAAGATTTACTAAGAATAAACAAAGATAATGAGTTATTATGGCAAGAGAATATG ATGGCCAGGGAAAGACATAGAACCCAACAGCAAGCCTTGGAAAAAATGTTCAGATTCTTG ACATCTATAGTCCCACACTTAGATCCCAAAATGATTATGGACGGGCTGGGAGATCCGAAA GTTAATAATGAAAAGCTAAACAGTGCGAATAACATTGGGTTAAATCGCGACAACACAGGC ACTATAGATGAACTAAAATCCAACGATTCTTTCATAAACGATGATCGTAATTCTTTCACC AATGCTACAACCAACGCCCGTAATAACATGAGTCCCAACAATGATGACAATAGTATTGAC ACCGCTAGCACTAATACCACCAACAGAAAGAAAAATATAGATGAAAACATCAAAAATAAC AACGACATAATTAATGACATTATATTTAATACCAACCTTGCCAACAATCTCAGCAATTAC AATTCCAACAATAATGCTGGCTCGCCAATAAGGCCCTATAAACAAAGATATCTTTTGAAA AATAGAGCCAATTCCTCGACATCGAGTGAGAATCCAAGCCTAACGCCCTTTGATATCGAA TCTAATAATGACCGCAAAATTTCAGAAATTCCTTTTGATGACGAAGAAGAAGAAGAAACG GATTTTAGGCCTTTTACCTCGCGAGATCCTAATAACCAAACGAGTGAAAACACTTTTGAT CCAAACAGATTTACGATGCTCTCTGATGATGATTTAAAAAAAGATTCTCATACCAATGAC AATAAACACAACGAAAGTGATCTTTTTTGGGACAACGTACATAGAAATATAGACGAACAA GATGCAAGACTCCAGAACTTGGAAAATATGGTTCACATACTTTCTCCTGGATATCCTAAT AAGTCGTTCAACAACAAAACTTCCTCGACAAACACTAATTCCAATATGGAAAGTGCTGTC AACGTTAATAGCCCTGGTTTCAACTTACAGGATTATTTAACTGGAGAGTCTAATTCCCCC AATTCTGTTCATTCTGTTCCCTCCAATGGCAGCGGCTCCACACCGTTGCCCATGCCAAAT GATAATGACACCGAGCACGCAAGTACAAGTGTCAATCAAGGCGAAAATGGAAGCGGATTA ACGCCCTTCCTCACGGTAGATGATCACACACTAAACGACAATAACACTAGTGAGGGAAGT ACAAGGGTGTCCCCCGATATAAAGTTCAGCGCCACTGAAAACACTAAAGTGAGTGATAAC CTGCCAAGCTTTAATGACCACAGTTATTCCACCCAGGCCGACACGGCGCCCGAGAACGCT AAGAAAAGATTTGTGGAGGAAATACCGGAACCGGCTATAGTCGAAATACAGGACCCGACA GAGTACAACGATCACCGCCTGCCCAAACGAGCTAAGAAATAGTACACAGGGCAAGGTCAT TAAATAGCGTATATAATCATTTAATATAGTATGTTCTCGAAGCTGATCGCGTAAGGCGCA GAGCGAACTAAAAAAAATACCGGCACCCATGCACCTCACACCGCCGCACGCGAGTGAGGT TGAACTGCACCCGGAAAATGCCAAGTAGATGAGTCGTGAAGAGTTCTCGTTATTCGAGCT AGTGAGAGCCTGAGAAGGGCTTGCCGAGTGAACTGGTGTCACATTGGCCGTTTTAACGCA AGTTGGCGTACTTATATTGACTGTTGGATGAAAGGGTAATCAAGAGAAACGGAAACGGCC TCCTCATCGTTAAGCTCATCAGTATTCATTTCTCCCCTTTCTGCTCCATCGCGTGCTCGA GACTATATTCTTCAGATTATCAAGCAGAAACAGAATTCGCATATTACATAACTTTCACAG GTTGAAGTATAAACCGCTACAGTACACAACCTCGGATAGAATATAGGGAAGAGGCCAATT CCGTGAAAACGATTTAATATTCTTTACAGTTACAAAAAGTATTACCTATTATCCTCTTTT CGGTGTCATTGACAAACCTCTTAGCGACAGAAACTCCCTAGC''</code>
*Gene Location ''Chromosome VII: 368,753-371,254''
*Gene Map 
[[File:Saccharomycescerevisiae HSF1.pdf]]
 
'''UniProt:'''
*Gene ID: ''P10961 (HSF_YEAST)''
*Protein Sequence 
<code>''MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI
INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST
LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW
SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD
VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD
NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA
ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK
VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID
TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK
NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD
PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN
KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN
DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN
LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK''</code>
*Similar Protein: ''N1P1W2'' and ID of Similar Protein: ''P10961''
*Protein Type/Name: ''Heat shock factor protein''
*Species: ''Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)''
 
'''SGD:'''
*Gene ID
**Standard Name ''HSF1''
**Systematic Name ''YGL073W''
**SGD ID ''S000003041''
*Regulation
**Regulators: ''6''
**Targets: ''478''
*Interaction
**Total Interactions: ''85 total interactions for 71 unique genes''
**Physical Interactions:
***''Affinity Capture-MS: 11''
***''Affinity Capture-RNA: 1''
***''Affinity Capture-Western: 4''
***''Biochemical Activity: 11''
***''Co-localization: 3''
***''Reconstituted Complex: 2''
***''Two-hybrid: 3''
**Genetic Interactions:
***''Dosage Rescue: 16''
***''Negative Genetic: 8''
***''Phenotypic Enhancement: 1''
***''Phenotypic Suppression: 5''
***''Synthetic Growth Defect: 2''
***''Synthetic Haploinsufficiency: 1''
***''Synthetic Lethality: 6''
***''Synthetic Rescue: 11''
*Gene Ontology
**Summary: ''Sequence-specific DNA binding transcription factor that induces expression of the Hsp90-family protein chaperones Hsc82p and Hsp82p during the cellular response to heat; also negatively regulates TOR signaling''
**Molecular Function:
***''Manually Curated: DNA binding transcription factor activity (IDA)''
***''High-Throughput: sequence-specific DNA binding (HDA)''
**Biological Process
***''Manually Curated: negative regulation of TOR signaling (IMP), positive regulation of transcription from RNA polymerase II promoter (IMP), regulation of establishment of protein localization to chromosome (IMP), regulation of transcription from RNA polymerase II promoter (IDA), response to heat (IMP)''
**Cellular Component:
***''Manually Curated: nucleus (IDA)''
***''High-Throughput: mitochondrion (HDA)''

=Acknowledgements=
I worked with my homework partner in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:41, 4 December 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 14. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14

{{Template:ebachour}}

Ebachour Week 14

2017-12-05T07:30:05Z

Ebachour: Started Week 14

===Fields to Pull From Each Database===
''' EVERYTHING IN THIS SECTION WAS PULLED FROM QUINN'S JOURNAL PAGE '''

We decided that from JASPAR we will pull:
*Matrix ID ''MA0319.1''
*Class ''Heat shock factors''
*Family ''HSF factors''
*Sequence Logo ''image below''
*Frequency Matrix ''image below''
[[File:Jasper seq log and freq matrix.png]]

Breakdown of what we want from all other databases: 
'''NCBI:'''
*Gene ID ''852806''
*Locus Tag ''YGL073W''
*Also Known As '''EXA3; MAS3'''
*Chromosome Sequence ''Chromosome: VII; NC_001139.9 (368753..371254)''
*Genomic Sequence ''NC_001139.9''
*Protein Sequence ''NP_011442.3''
 
'''Ensembl:'''
*Gene ID ''YGL073W''
*Description/Function ''Trimeric heat shock transcription factor; activates multiple genes in response to highly diverse stresses, including hyperthermia; recognizes variable heat shock elements (HSEs) consisting of inverted NGAAN repeats; monitors translational status of cell at the ribosome through an RQC (Ribosomal Quality Control)-mediated translation-stress signal; involved in diauxic shift; posttranslationally regulated [Source:SGD;Acc:S000003041]''
*DNA Sequence ''>chromosome:R64-1-1:VII:368153:371854:1'' 
<code>''AAAATACTCCACTAAGGCCAGTAGCAACAACACGTTTTCTTGGATGATGCGTTTTCTTGA ACAAACAGTACCGACTAGGACTGTTTCAATGAAGTTGTGTACGGTCTGGTAGTATATCTA TATTCCGTGATGCCTTTGTGGAGGACGTTGAGATGAGACTGAGTCGTACACCATGTTATT CCTGTTTACGGTTAATTGCGCGTCGCGCTTTCTCTAGCAAATATCTCGGTTCGAAGTAAA GCAGGTCCTTCATGTAATGGTAACCTAAGGCAAAGGGTTTGTCATATACCCGTGAAGGCA TTTACACAAGCGCACTTCTAGTCATATGCAGTTCATGCATATTAAGTGAGTGTTATAACG CAAGAGTTATATTTGAAATAGGGTTGTTAAAGAAGGGAGAACCCATTCACCACATTATCT TTGCGAGTGTAAAACTAGATAACTTAAATTTTTAGGAGAGATTTTGCCACTTGGCAGCAA ATACCAAATAGCAGTACTGTTCCGGTAGATAAAGGCAAAGAGTTAGAGGTGTGCTTTACG AACAGCGCTGGAAGGGAAAGGAAACAAAAAAGACAAAAAGACAGCTGTATTGTTGGCGCC ATGAATAATGCTGCAAATACAGGGACGACCAATGAGTCAAACGTGAGCGATGCTCCCCGT ATTGAGCCTTTACCAAGCTTGAATGATGATGACATTGAAAAAATCTTACAACCGAACGAT ATCTTTACGACCGATCGTACCGATGCAAGTACTACATCTTCCACAGCCATTGAAGATATT ATTAACCCCTCATTGGATCCGCAGTCAGCAGCATCGCCGGTTCCTTCTTCCTCTTTTTTC CATGACTCAAGGAAACCTTCCACCAGTACACATTTAGTAAGGAGAGGTACTCCATTGGGA ATTTACCAAACCAATCTATACGGTCACAATAGCAGAGAAAATACTAATCCTAATAGTACA TTATTATCTTCTAAGTTACTCGCGCATCCACCAGTTCCTTATGGGCAAAATCCCGATTTA CTACAACATGCTGTGTACAGGGCACAGCCGTCAAGTGGAACCACTAACGCGCAACCGCGC CAAACCACAAGAAGATATCAATCCCATAAATCACGGCCTGCATTTGTTAATAAACTATGG AGCATGTTAAACGATGATTCTAATACGAAACTTATACAGTGGGCGGAGGATGGAAAATCT TTTATTGTCACGAATAGGGAGGAATTTGTGCACCAAATTTTACCAAAATATTTTAAACAT TCCAATTTCGCTTCCTTTGTAAGACAATTGAACATGTATGGATGGCATAAAGTTCAAGAT GTCAAGTCAGGATCAATTCAAAGTAGTTCAGATGATAAGTGGCAATTTGAAAATGAAAAC TTCATTAGAGGTAGAGAAGATTTGCTGGAAAAAATAATCAGGCAGAAAGGTTCCTCCAAT AACCATAATAGCCCTAGTGGTAACGGTAATCCAGCGAATGGTAGCAACATCCCTCTGGAC AATGCCGCAGGAAGTAATAATAGCAATAATAACATCAGTAGTAGTAATTCATTTTTTAAC AATGGTCATTTATTGCAGGGTAAAACACTAAGATTAATGAACGAAGCGAATCTTGGAGAT AAGAATGATGTCACCGCGATTTTGGGGGAATTAGAGCAAATAAAATATAACCAGATTGCA ATTTCCAAAGATTTACTAAGAATAAACAAAGATAATGAGTTATTATGGCAAGAGAATATG ATGGCCAGGGAAAGACATAGAACCCAACAGCAAGCCTTGGAAAAAATGTTCAGATTCTTG ACATCTATAGTCCCACACTTAGATCCCAAAATGATTATGGACGGGCTGGGAGATCCGAAA GTTAATAATGAAAAGCTAAACAGTGCGAATAACATTGGGTTAAATCGCGACAACACAGGC ACTATAGATGAACTAAAATCCAACGATTCTTTCATAAACGATGATCGTAATTCTTTCACC AATGCTACAACCAACGCCCGTAATAACATGAGTCCCAACAATGATGACAATAGTATTGAC ACCGCTAGCACTAATACCACCAACAGAAAGAAAAATATAGATGAAAACATCAAAAATAAC AACGACATAATTAATGACATTATATTTAATACCAACCTTGCCAACAATCTCAGCAATTAC AATTCCAACAATAATGCTGGCTCGCCAATAAGGCCCTATAAACAAAGATATCTTTTGAAA AATAGAGCCAATTCCTCGACATCGAGTGAGAATCCAAGCCTAACGCCCTTTGATATCGAA TCTAATAATGACCGCAAAATTTCAGAAATTCCTTTTGATGACGAAGAAGAAGAAGAAACG GATTTTAGGCCTTTTACCTCGCGAGATCCTAATAACCAAACGAGTGAAAACACTTTTGAT CCAAACAGATTTACGATGCTCTCTGATGATGATTTAAAAAAAGATTCTCATACCAATGAC AATAAACACAACGAAAGTGATCTTTTTTGGGACAACGTACATAGAAATATAGACGAACAA GATGCAAGACTCCAGAACTTGGAAAATATGGTTCACATACTTTCTCCTGGATATCCTAAT AAGTCGTTCAACAACAAAACTTCCTCGACAAACACTAATTCCAATATGGAAAGTGCTGTC AACGTTAATAGCCCTGGTTTCAACTTACAGGATTATTTAACTGGAGAGTCTAATTCCCCC AATTCTGTTCATTCTGTTCCCTCCAATGGCAGCGGCTCCACACCGTTGCCCATGCCAAAT GATAATGACACCGAGCACGCAAGTACAAGTGTCAATCAAGGCGAAAATGGAAGCGGATTA ACGCCCTTCCTCACGGTAGATGATCACACACTAAACGACAATAACACTAGTGAGGGAAGT ACAAGGGTGTCCCCCGATATAAAGTTCAGCGCCACTGAAAACACTAAAGTGAGTGATAAC CTGCCAAGCTTTAATGACCACAGTTATTCCACCCAGGCCGACACGGCGCCCGAGAACGCT AAGAAAAGATTTGTGGAGGAAATACCGGAACCGGCTATAGTCGAAATACAGGACCCGACA GAGTACAACGATCACCGCCTGCCCAAACGAGCTAAGAAATAGTACACAGGGCAAGGTCAT TAAATAGCGTATATAATCATTTAATATAGTATGTTCTCGAAGCTGATCGCGTAAGGCGCA GAGCGAACTAAAAAAAATACCGGCACCCATGCACCTCACACCGCCGCACGCGAGTGAGGT TGAACTGCACCCGGAAAATGCCAAGTAGATGAGTCGTGAAGAGTTCTCGTTATTCGAGCT AGTGAGAGCCTGAGAAGGGCTTGCCGAGTGAACTGGTGTCACATTGGCCGTTTTAACGCA AGTTGGCGTACTTATATTGACTGTTGGATGAAAGGGTAATCAAGAGAAACGGAAACGGCC TCCTCATCGTTAAGCTCATCAGTATTCATTTCTCCCCTTTCTGCTCCATCGCGTGCTCGA GACTATATTCTTCAGATTATCAAGCAGAAACAGAATTCGCATATTACATAACTTTCACAG GTTGAAGTATAAACCGCTACAGTACACAACCTCGGATAGAATATAGGGAAGAGGCCAATT CCGTGAAAACGATTTAATATTCTTTACAGTTACAAAAAGTATTACCTATTATCCTCTTTT CGGTGTCATTGACAAACCTCTTAGCGACAGAAACTCCCTAGC''</code>
*Gene Location ''Chromosome VII: 368,753-371,254''
*Gene Map 
[[File:Saccharomycescerevisiae HSF1.pdf]]
 
'''UniProt:'''
*Gene ID: ''P10961 (HSF_YEAST)''
*Protein Sequence 
<code>''MNNAANTGTTNESNVSDAPRIEPLPSLNDDDIEKILQPNDIFTTDRTDASTTSSTAIEDI
INPSLDPQSAASPVPSSSFFHDSRKPSTSTHLVRRGTPLGIYQTNLYGHNSRENTNPNST
LLSSKLLAHPPVPYGQNPDLLQHAVYRAQPSSGTTNAQPRQTTRRYQSHKSRPAFVNKLW
SMLNDDSNTKLIQWAEDGKSFIVTNREEFVHQILPKYFKHSNFASFVRQLNMYGWHKVQD
VKSGSIQSSSDDKWQFENENFIRGREDLLEKIIRQKGSSNNHNSPSGNGNPANGSNIPLD
NAAGSNNSNNNISSSNSFFNNGHLLQGKTLRLMNEANLGDKNDVTAILGELEQIKYNQIA
ISKDLLRINKDNELLWQENMMARERHRTQQQALEKMFRFLTSIVPHLDPKMIMDGLGDPK
VNNEKLNSANNIGLNRDNTGTIDELKSNDSFINDDRNSFTNATTNARNNMSPNNDDNSID
TASTNTTNRKKNIDENIKNNNDIINDIIFNTNLANNLSNYNSNNNAGSPIRPYKQRYLLK
NRANSSTSSENPSLTPFDIESNNDRKISEIPFDDEEEEETDFRPFTSRDPNNQTSENTFD
PNRFTMLSDDDLKKDSHTNDNKHNESDLFWDNVHRNIDEQDARLQNLENMVHILSPGYPN
KSFNNKTSSTNTNSNMESAVNVNSPGFNLQDYLTGESNSPNSVHSVPSNGSGSTPLPMPN
DNDTEHASTSVNQGENGSGLTPFLTVDDHTLNDNNTSEGSTRVSPDIKFSATENTKVSDN
LPSFNDHSYSTQADTAPENAKKRFVEEIPEPAIVEIQDPTEYNDHRLPKRAKK''</code>
*Similar Protein: ''N1P1W2'' and ID of Similar Protein: ''P10961''
*Protein Type/Name: ''Heat shock factor protein''
*Species: ''Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)''
 
'''SGD:'''
*Gene ID
**Standard Name ''HSF1''
**Systematic Name ''YGL073W''
**SGD ID ''S000003041''
*Regulation
**Regulators: ''6''
**Targets: ''478''
*Interaction
**Total Interactions: ''85 total interactions for 71 unique genes''
**Physical Interactions:
***''Affinity Capture-MS: 11''
***''Affinity Capture-RNA: 1''
***''Affinity Capture-Western: 4''
***''Biochemical Activity: 11''
***''Co-localization: 3''
***''Reconstituted Complex: 2''
***''Two-hybrid: 3''
**Genetic Interactions:
***''Dosage Rescue: 16''
***''Negative Genetic: 8''
***''Phenotypic Enhancement: 1''
***''Phenotypic Suppression: 5''
***''Synthetic Growth Defect: 2''
***''Synthetic Haploinsufficiency: 1''
***''Synthetic Lethality: 6''
***''Synthetic Rescue: 11''
*Gene Ontology
**Summary: ''Sequence-specific DNA binding transcription factor that induces expression of the Hsp90-family protein chaperones Hsc82p and Hsp82p during the cellular response to heat; also negatively regulates TOR signaling''
**Molecular Function:
***''Manually Curated: DNA binding transcription factor activity (IDA)''
***''High-Throughput: sequence-specific DNA binding (HDA)''
**Biological Process
***''Manually Curated: negative regulation of TOR signaling (IMP), positive regulation of transcription from RNA polymerase II promoter (IMP), regulation of establishment of protein localization to chromosome (IMP), regulation of transcription from RNA polymerase II promoter (IDA), response to heat (IMP)''
**Cellular Component:
***''Manually Curated: nucleus (IDA)''
***''High-Throughput: mitochondrion (HDA)''

JASPAR the Friendly Ghost

2017-12-05T07:26:59Z

Ebachour: /* Eddie's Executive Summary */ added break

==Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

Template:Ebachour

2017-12-05T07:26:12Z

Ebachour: Added this week to template

JASPAR the Friendly Ghost

2017-12-05T07:25:21Z

Ebachour: Adding my summary and team review

==Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]
# Screenshot of GRNsight Regulatory Network: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-11-21T05:47:23Z

Ebachour: /* Eddie's Reflection */ added signature

Ebachour Week 12

2017-11-21T03:32:04Z

Ebachour: /* Electronic Journal */ Finished

=Electronic Journal=
* Most of our work for this week was done in class.
* Creating branch:
** We waited for Blair and Zac to make the fork, and then John and Eddie A. to make their branch.
** Then I simply cloned the fork, switched to their branch, and made a new branch from there.
** The only issues at this step was when I tried to get the branch on Simon's laptop.
*** I didn't realize that I hadn't pushed my code after making the branch and therefore the branch didn't exist anywhere other than my laptop, noted for next time.
* Cloning and getting GRNsight working locally:
** Cloning was smooth.
** So was npm installing.
** So was npm starting.
** Went smooth for Simon as well.
* Writing the list of Milestones:
** Read through our list of tasks as Coders and then translated it all into our own summarized list:
** Sent the list to Quinn so that he could add it to our website.
* Added the executive summary and more to our shared journal Jaspar Page.
* Read through the Jaspar API documentation:
** Trying to get a better understanding before I actually start writing the code.

=Acknowledgements=
I worked with my homework partner in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:30, 20 November 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 15. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{Template:ebachour}}

Ebachour Week 12

2017-11-21T03:30:24Z

Ebachour: Added most of week 12

=Electronic Journal=
* Most of our work for this week was done in class.
* Creating branch:
** We waited for Blair and Zac to make the fork, and then John and Eddie A. to make their branch.
** Then I simply cloned the fork, switched to their branch, and made a new branch from there.
** The only issues at this step was when I tried to get the branch on Simon's laptop.
*** I didn't realize that I hadn't pushed my code after making the branch and therefore the branch didn't exist anywhere other than my laptop, noted for next time.
* Cloning and getting GRNsight working locally:
** Cloning was smooth.
** So was npm installing.
** So was npm starting.
** Went smooth for Simon as well.
* Writing the list of Milestones:
** Read through our list of tasks as Coders and then translated it all into our own summarized list:
** Sent the list to Quinn so that he could add it to our website.
* Added the executive summary and more to our shared journal Jaspar Page.

=Acknowledgements=
I worked with my homework partner in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:30, 20 November 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 15. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{Template:ebachour}}

Template:Ebachour

2017-11-21T03:17:09Z

Ebachour: Adding week 12

JASPAR the Friendly Ghost

2017-11-21T03:17:02Z

Ebachour: /* Eddie's Reflection */ added reflection

==Deliverables==
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/jaspar-api GitHub jaspar-api branch]
==Working Files==

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors and develop candidate gene reg network
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API DA:Model gene reg network
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code DA: Visualize results
|'''8'''
|'''9'''
|-
|'''10'''
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13'''
|'''14'''
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
Individual Journal Page: [[simonwro120 Week 11]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

*What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.
*What didn't work? Nothing specific prevented us from working efficiently.
*What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order t do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====

====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====

====Antonios's Reflection====

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-11-21T03:11:44Z

Ebachour: /* Eddie's Reflection */ added this

==Deliverables==
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/jaspar-api GitHub jaspar-api branch]
==Working Files==

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors and develop candidate gene reg network
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API DA:Model gene reg network
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code DA: Visualize results
|'''8'''
|'''9'''
|-
|'''10'''
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13'''
|'''14'''
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
Individual Journal Page: [[simonwro120 Week 11]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

*What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.
*What didn't work? Nothing specific prevented us from working efficiently.
*What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order t do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====

====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====

====Antonios's Reflection====

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-11-21T03:09:59Z

Ebachour: /* Eddie Bachoura's Executive Summary */ added break

==Deliverables==
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/jaspar-api GitHub jaspar-api branch]
==Working Files==

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors and develop candidate gene reg network
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API DA:Model gene reg network
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code DA: Visualize results
|'''8'''
|'''9'''
|-
|'''10'''
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13'''
|'''14'''
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
Individual Journal Page: [[simonwro120 Week 11]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

*What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.
*What didn't work? Nothing specific prevented us from working efficiently.
*What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order t do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====

====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====

====Eddie's Reflection====

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====

====Antonios's Reflection====

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-11-21T03:09:07Z

Ebachour: /* Eddie Bachoura's Executive Summary */ Added my executive summary

==Deliverables==
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/jaspar-api GitHub jaspar-api branch]
==Working Files==

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors and develop candidate gene reg network
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API DA:Model gene reg network
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code DA: Visualize results
|'''8'''
|'''9'''
|-
|'''10'''
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13'''
|'''14'''
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
Individual Journal Page: [[simonwro120 Week 11]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

*What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.
*What didn't work? Nothing specific prevented us from working efficiently.
*What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order t do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====

====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: *[[ebachour_Week_12| Edward Bachoura]]

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====

====Eddie's Reflection====

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====

====Antonios's Reflection====

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-11-21T03:04:16Z

Ebachour: /* Eddie Bachoura's Executive Summary */ small fix

==Deliverables==
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/jaspar-api GitHub jaspar-api branch]
==Working Files==

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors and develop candidate gene reg network
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API DA:Model gene reg network
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code DA: Visualize results
|'''8'''
|'''9'''
|-
|'''10'''
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13'''
|'''14'''
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
Individual Journal Page: [[simonwro120 Week 11]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

*What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.
*What didn't work? Nothing specific prevented us from working efficiently.
*What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order t do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====

====Eddie Bachoura's Executive Summary====
Listed above^^^

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====

====Eddie's Reflection====

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====

====Antonios's Reflection====

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

File:E and s presentation 2.pdf

2017-11-14T22:25:49Z

Ebachour: Ebachour uploaded a new version of File:E and s presentation 2.pdf

File:E and s presentation 2.pdf

2017-11-14T08:02:18Z

Ebachour: Ebachour uploaded a new version of File:E and s presentation 2.pdf

Ebachour Week 11

2017-11-14T07:51:24Z

Ebachour: /* Link to Presentation */ fixed link

=10 things I didn't know=
#Xcode
#Smalltalk
#Django
#Ui-router
#Yeoman
#Polymer
#Gulp
#The Bug by Ellen Ullman
#Research Kit
#NIH (“not invented here”)

Definitions covered below in outline.

=Outline and Electronic Journal=
*Xcode is the Apple IDE that you use to build software for Mac or iPhone.
**iOS SDK comes filled with dozens and dozens of APIs
***each API gives you access to some feature
****Location
****Playing sounds
****Rend text
****Collection information
***They don’t necessarily give you everything, but still they do a lot of the work
**The IDE does most of the work of giving you functions that you can use to write software, but it doesn’t necessarily give you everything.
***For example, they give you the time in milliseconds when playing a song, but you have to write the code that displays this time in minutes and seconds or even hours if that’s what you want for your program
**Software that is used to make software is usually free because it stimulates the development of even more software and therefore these developers want people to have access to it.
*Framework
**There are hundreds of frameworks to choose from
**Handles a lot of the tedious parts of writing software for you.
***Django has a command that makes a directory with some files and configurations inside, your project directory, which gives you access to libraries and services that add to and enhance the standard library
**Sometimes you can tell what framework was used to build a website just by looking at the finished product.
***Downsides
****Frameworks lock you into a way of thinking.
****Some people feel that the framework makes things too easy and that they become a crutch.
****You pay a price of speed and control for all the convenience they offer
**Most of the frameworks are free
*Debugging
**Debugging is programming. It’s running your code, finding out that there is some unexpected outcome, changing it, and then running again. It can be frustrating because bugs can be hard to find.
***Stupid like 4 + 20 vs. 4 + “20”
**Testing
***TDD = test driven development
***Tests are just code
****They check the functions in other code
****They run automatically, and you can find out if your day’s work broke things
*Version control
**Record every change made to the documents in your codebase
**Stores all of these records for you to have access to at any point
**Record who made every change
***Very transparent
**Totally free
**The best way to development collaboratively
***Open source
****Anybody can fork and do work on the project as much as they want without affecting any of the actual codebase, and then they can ask if their code can be added to the main codebase and the developers get to decide if it makes the cut
**Clone => Add => Commit => Push
***Gets code from Github, and brings it to you, and then you can push your code changes whenever you want with the next three commands
*Main message to show us how the modern world of development works and what tools are used in making software and websites
*This article was very clearly written and easy to read. It was important because it is able to provide a general understanding of development and stacks to anybody who reads it.
*Described IDE, SDK, Frameworks, Testing and Debugging, and Version Control in this paper. Explained them all in plain English which allows us all to understand everything.
*Every single one of these things mentioned above are pretty much crucial to the development of any software or website, just as we will be implementing most of them for our own project.

=Link to Presentation=
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Presentation]]

=Acknowledgements=
I worked with my homework partner [[User:Simonwro120 | Simon Wroblewski]] in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:37, 13 November 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 14. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14

{{Template:ebachour}}

File:E and s presentation 2.pdf

2017-11-14T07:50:43Z

Ebachour:

Ebachour Week 11

2017-11-14T07:40:42Z

Ebachour: Finished

=10 things I didn't know=
#Xcode
#Smalltalk
#Django
#Ui-router
#Yeoman
#Polymer
#Gulp
#The Bug by Ellen Ullman
#Research Kit
#NIH (“not invented here”)

Definitions covered below in outline.

=Outline and Electronic Journal=
*Xcode is the Apple IDE that you use to build software for Mac or iPhone.
**iOS SDK comes filled with dozens and dozens of APIs
***each API gives you access to some feature
****Location
****Playing sounds
****Rend text
****Collection information
***They don’t necessarily give you everything, but still they do a lot of the work
**The IDE does most of the work of giving you functions that you can use to write software, but it doesn’t necessarily give you everything.
***For example, they give you the time in milliseconds when playing a song, but you have to write the code that displays this time in minutes and seconds or even hours if that’s what you want for your program
**Software that is used to make software is usually free because it stimulates the development of even more software and therefore these developers want people to have access to it.
*Framework
**There are hundreds of frameworks to choose from
**Handles a lot of the tedious parts of writing software for you.
***Django has a command that makes a directory with some files and configurations inside, your project directory, which gives you access to libraries and services that add to and enhance the standard library
**Sometimes you can tell what framework was used to build a website just by looking at the finished product.
***Downsides
****Frameworks lock you into a way of thinking.
****Some people feel that the framework makes things too easy and that they become a crutch.
****You pay a price of speed and control for all the convenience they offer
**Most of the frameworks are free
*Debugging
**Debugging is programming. It’s running your code, finding out that there is some unexpected outcome, changing it, and then running again. It can be frustrating because bugs can be hard to find.
***Stupid like 4 + 20 vs. 4 + “20”
**Testing
***TDD = test driven development
***Tests are just code
****They check the functions in other code
****They run automatically, and you can find out if your day’s work broke things
*Version control
**Record every change made to the documents in your codebase
**Stores all of these records for you to have access to at any point
**Record who made every change
***Very transparent
**Totally free
**The best way to development collaboratively
***Open source
****Anybody can fork and do work on the project as much as they want without affecting any of the actual codebase, and then they can ask if their code can be added to the main codebase and the developers get to decide if it makes the cut
**Clone => Add => Commit => Push
***Gets code from Github, and brings it to you, and then you can push your code changes whenever you want with the next three commands
*Main message to show us how the modern world of development works and what tools are used in making software and websites
*This article was very clearly written and easy to read. It was important because it is able to provide a general understanding of development and stacks to anybody who reads it.
*Described IDE, SDK, Frameworks, Testing and Debugging, and Version Control in this paper. Explained them all in plain English which allows us all to understand everything.
*Every single one of these things mentioned above are pretty much crucial to the development of any software or website, just as we will be implementing most of them for our own project.

=Link to Presentation=
[[Media:e_and_s_presentation_2.pptx|Eddie and Simon Presentation]]

=Acknowledgements=
I worked with my homework partner [[User:Simonwro120 | Simon Wroblewski]] in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:37, 13 November 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 14. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14

{{Template:ebachour}}

Ebachour Week 11

2017-11-14T07:37:59Z

Ebachour: Starting assignment lol

=10 things I didn't know=

=Outline and Electronic Journal=
*Xcode is the Apple IDE that you use to build software for Mac or iPhone.
**iOS SDK comes filled with dozens and dozens of APIs
***each API gives you access to some feature
****Location
****Playing sounds
****Rend text
****Collection information
***They don’t necessarily give you everything, but still they do a lot of the work
**The IDE does most of the work of giving you functions that you can use to write software, but it doesn’t necessarily give you everything.
***For example, they give you the time in milliseconds when playing a song, but you have to write the code that displays this time in minutes and seconds or even hours if that’s what you want for your program
**Software that is used to make software is usually free because it stimulates the development of even more software and therefore these developers want people to have access to it.
*Framework
**There are hundreds of frameworks to choose from
**Handles a lot of the tedious parts of writing software for you.
***Django has a command that makes a directory with some files and configurations inside, your project directory, which gives you access to libraries and services that add to and enhance the standard library
**Sometimes you can tell what framework was used to build a website just by looking at the finished product.
***Downsides
****Frameworks lock you into a way of thinking.
****Some people feel that the framework makes things too easy and that they become a crutch.
****You pay a price of speed and control for all the convenience they offer
**Most of the frameworks are free
*Debugging
**Debugging is programming. It’s running your code, finding out that there is some unexpected outcome, changing it, and then running again. It can be frustrating because bugs can be hard to find.
***Stupid like 4 + 20 vs. 4 + “20”
**Testing
***TDD = test driven development
***Tests are just code
****They check the functions in other code
****They run automatically, and you can find out if your day’s work broke things
*Version control
**Record every change made to the documents in your codebase
**Stores all of these records for you to have access to at any point
**Record who made every change
***Very transparent
**Totally free
**The best way to development collaboratively
***Open source
****Anybody can fork and do work on the project as much as they want without affecting any of the actual codebase, and then they can ask if their code can be added to the main codebase and the developers get to decide if it makes the cut
**Clone => Add => Commit => Push
***Gets code from Github, and brings it to you, and then you can push your code changes whenever you want with the next three commands
*Main message to show us how the modern world of development works and what tools are used in making software and websites
*This article was very clearly written and easy to read. It was important because it is able to provide a general understanding of development and stacks to anybody who reads it.
*Described IDE, SDK, Frameworks, Testing and Debugging, and Version Control in this paper. Explained them all in plain English which allows us all to understand everything.
*Every single one of these things mentioned above are pretty much crucial to the development of any software or website, just as we will be implementing most of them for our own project.

=Acknowledgements=
I worked with my homework partner [[User:Simonwro120 | Simon Wroblewski]] in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:37, 13 November 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 14. Retrieved November 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14

{{Template:ebachour}}

Template:JASPAR the Friendly Ghost Links

2017-11-14T07:30:56Z

Ebachour: Adding to template: week 11

JASPAR the Friendly Ghost

2017-11-14T07:29:17Z

Ebachour: Adding my summary and team review

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]]

====Simon's Executive Summary====

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)
==Acknowledgements==

==References==
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11

==Links==

{{Template:JASPAR the Friendly Ghost Links}}

Template:Ebachour

2017-11-14T07:22:16Z

Ebachour: Adding this week

Ebachour Week 10

2017-11-07T07:50:48Z

Ebachour: Done with Week 10

=Electronic Journal=
==== Clustering and GO Term Enrichment with stem ====

# '''Prepare your microarray data file for loading into STEM.'''
#* Download your Excel workbook that you used for your [[Week 8]] assignment.
#* Insert a new worksheet into your Excel workbook, and name it "(STRAIN)_stem".
#* Select all of the data from your "(STRAIN)_ANOVA" worksheet and Paste special > paste values into your "(STRAIN)_stem" worksheet.
#** Your leftmost column should have the column header "Master_Index". Rename this column to "SPOT". Column B should be named "ID". Rename this column to "Gene Symbol". Delete the column named "Standard_Name".
#** Filter the data on the B-H corrected p value to be > 0.05 (that's '''greater than''' in this case).
#*** Once the data has been filtered, select all of the rows (except for your header row) and delete the rows by right-clicking and choosing "Delete Row" from the context menu. Undo the filter. This ensures that we will cluster only the genes with a "significant" change in expression and not the noise. '''''Record the number of genes left in your electronic notebook.'''''
#** Delete all of the data columns '''''EXCEPT''''' for the Average Log Fold change columns for each timepoint (for example, wt_AvgLogFC_t15, etc.).
#** Rename the data columns with just the time and units (for example, 15m, 30m, etc.).
#** Save your work. Then use ''Save As'' to save this spreadsheet as Text (Tab-delimited) (*.txt). Click OK to the warnings and close your file.
#*** Note that you should turn on the file extensions if you have not already done so.
# '''Now download and extract the STEM software.''' [http://www.cs.cmu.edu/~jernst/stem/ Click here to go to the STEM web site].
#* Click on the [http://www.andrew.cmu.edu/user/zivbj/stemreg.html download link], register, and download the <code>stem.zip</code> file to your Desktop.
#* Unzip the file. In Seaver 120, you can right click on the file icon and select the menu item ''7-zip > Extract Here''.
#* This will create a folder called <code>stem</code>. Inside the folder, double-click on the <code>stem.jar</code> to launch the STEM program.

# '''Running STEM'''
## In section 1 (Expression Data Info) of the the main STEM interface window, click on the ''Browse...'' button to navigate to and select your file.
##* Click on the radio button ''No normalization/add 0''.
##* Check the box next to ''Spot IDs included in the data file''.
## In section 2 (Gene Info) of the main STEM interface window, select ''Saccharomyces cerevisiae (SGD)'', from the drop-down menu for Gene Annotation Source. Select ''No cross references'', from the Cross Reference Source drop-down menu. Select ''No Gene Locations'' from the Gene Location Source drop-down menu.
## In section 3 (Options) of the main STEM interface window, make sure that the Clustering Method says "STEM Clustering Method" and do not change the defaults for Maximum Number of Model Profiles or Maximum Unit Change in Model Profiles between Time Points.
## In section 4 (Execute) click on the yellow Execute button to run STEM.
# '''Viewing and Saving STEM Results'''
## A new window will open called "All STEM Profiles (1)". Each box corresponds to a model expression profile. Colored profiles have a statistically significant number of genes assigned; they are arranged in order from most to least significant p value. Profiles with the same color belong to the same cluster of profiles. The number in each box is simply an ID number for the profile.
##* Click on the button that says "Interface Options...". At the bottom of the Interface Options window that appears below where it says "X-axis scale should be:", click on the radio button that says "Based on real time". Then close the Interface Options window.
##*Take a screenshot of this window (on a PC, simultaneously press the <code>Alt</code> and <code>PrintScreen</code> buttons to save the view in the active window to the clipboard) and paste it into a PowerPoint presentation to save your figures.
## Click on each of the SIGNIFICANT profiles (the colored ones) to open a window showing a more detailed plot containing all of the genes in that profile.
##* Take a screenshot of each of the individual profile windows and save the images in your PowerPoint presentation.
##* At the bottom of each profile window, there are two yellow buttons "Profile Gene Table" and "Profile GO Table". For each of the profiles, click on the "Profile Gene Table" button to see the list of genes belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_genelist.txt", where you replace the number symbol with the actual profile number.
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
##* For each of the significant profiles, click on the "Profile GO Table" to see the list of Gene Ontology terms belonging to the profile. In the window that appears, click on the "Save Table" button and save the file to your desktop. Make your filename descriptive of the contents, e.g. "wt_profile#_GOlist.txt", where you use "wt", "dGLN3", etc. to indicate the dataset and where you replace the number symbol with the actual profile number. At this point you have saved all of the primary data from the STEM software and it's time to interpret the results!
##** Upload these files to the wiki and link to them on your individual journal page. (Note that it will be easier to zip all the files together and upload them as one file).
# '''Analyzing and Interpreting STEM Results'''
## Select '''''one''''' of the profiles you saved in the previous step for further intepretation of the data. I suggest that you choose one that has a pattern of up- or down-regulated genes at the cold shock timepoints. '''''Each member of your group should choose a different profile.''''' Answer the following:
##* '''''Why did you select this profile? In other words, why was it interesting to you?'''''
##*: I picked it randomly, don't have enough of an understanding to make a choice with any other reason.
##* '''''How many genes belong to this profile?'''''
##*: 114
##* '''''How many genes were expected to belong to this profile?'''''
##: 49.1
##* '''''What is the p value for the enrichment of genes in this profile?''''' Bear in mind that we just finished computing p values to determine whether each individual gene had a significant change in gene expression at each time point. This p value determines whether the number of genes that show this particular expression profile across the time points is significantly more than expected.
##*: 7.1 E-16
##* Open the GO list file you saved for this profile in Excel. This list shows all of the Gene Ontology terms that are associated with genes that fit this profile. Select the third row and then choose from the menu Data > Filter > Autofilter. Filter on the "p-value" column to show only GO terms that have a p value of < 0.05. '''''How many GO terms are associated with this profile at p < 0.05?''''' The GO list also has a column called "Corrected p-value". This correction is needed because the software has performed thousands of significance tests. Filter on the "Corrected p-value" column to show only GO terms that have a corrected p value of < 0.05. '''''How many GO terms are associated with this profile with a corrected p value < 0.05?'''''
##*: 264 and 73
##* Select 6 Gene Ontology terms from your filtered list (either p < 0.05 or corrected p < 0.05).
##*: cellular response to stimulus, protein binding, organophosphate ester transport, protein localization to organelle, and proteasomal protein catabolic process.
##** Each member of the group will be reporting on his or her own cluster in your presentation next week. You should take care to choose terms that are the most significant, but that are also not too redundant. For example, "RNA metabolism" and "RNA biosynthesis" are redundant with each other because they mean almost the same thing.
##**'''''Look up the definitions for each of the terms at [http://geneontology.org http://geneontology.org]. In your final presentation, you will discuss the biological interpretation of these GO terms. In other words, why does the cell react to cold shock by changing the expression of genes associated with these GO terms? Also, what does this have to do with the transcription factor that was deleted from your strain?'''''
##** To easily look up the definitions, go to [http://geneontology.org http://geneontology.org].
##** Copy and paste the GO ID (e.g. GO:0044848) into the search field at center top of the page called "Search GO Data".
##** In the [http://amigo.geneontology.org/amigo/medial_search?q=GO%3A0044848 results] page, click on the button that says "Link to detailed information about <term>, in this case "biological phase"".
##** The definition will be on the next results page, e.g. [http://amigo.geneontology.org/amigo/term/GO:0044848 here].

'''''This is the stopping point for the Week 10 Assignment.''''' We will pick up the next steps in the analysis in subsequent weeks.
=Folder with PowerPoint and all files=
[[media:Ebachoura-week10.zip|Folder of Goodies]]
=Acknowledgements=
I worked with my homework partner [[User:Qlanners | Quinn Lanners]] in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the API part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:35, 6 November 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 10. Retrieved November 6, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10

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Ebachour Week 10

2017-11-07T07:35:50Z

Ebachour: Added Template for page

=Folder with PowerPoint and all files=
[[media:Ebachoura-week10.zip|Folder of Goodies]]
=Acknowledgements=
I worked with my homework partner [[User:Qlanners | Quinn Lanners]] in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the API part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:35, 6 November 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 10. Retrieved November 6, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10

{{Template:ebachour}}

File:Ebachoura-week10.zip

2017-11-07T07:33:58Z

Ebachour:

Class Journal Week 10

2017-11-07T00:54:51Z

Ebachour: Adding my response

=Class Journal Week 10=
==Hayden Hinsch's Responses==

{{hhinsch}}

==Mary Balducci's Responses==
#I would want for my teammates to be available if I have questions about the work, and also to feel like they can ask me questions. I would want us all to share equal amounts of the work, and to be able to get in touch with each other if we need help with something.
#I think communication makes teamwork go smoothly. If we are all able to tell each other what we're working on and how we're doing it, I think it helps everyone better understand the project being done. This also includes being responsive to questions and figuring out who is responsible for each aspect of the project together.
#I think teamwork does not go smoothly when members of the team are not responsive. I think it's harder when I'm not entirely sure what another person in my group is doing, or if I have a question and they are not available to answer it.

[[User:Mbalducc|Mbalducc]] ([[User talk:Mbalducc|talk]]) 07:44, 3 November 2017 (PDT)

==Zachary Van Ysseldyk's Responses==
#As far as characteristics for a teammate, I value those who do not procrastinate and plan out how the assignment will get done to avoid unnecessary stress. Stringing along the same thought, I think that communication is crucial so that every person on the team is on the same page. I would also value those who assume the same amount of work as everybody else so that we all get a fair and well deserved grade.
#Bleeding in from question 1, I think that solid communication and a laid out plan will help the project go smoothly. Knowing when things will get done and how long they will take will help for smooth project completion.
#On the other hand, poor communication will greatly negatively affect a project. People might be doing the same things, people might not understand what they are doing which leads to frustration and division among the team. Also if somebody does not put in a sufficient amount of effort, this will anger others as the person who didn't do the the work should not receive the same letter grade.
 
[[User:Zvanysse|Zvanysse]] ([[User talk:Zvanysse|talk]]) 13:36, 5 November 2017 (PST)
 
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==Dina Bashoura's Responses==
#I would like a partner who is well equipped in computer science, since I am lagging in that department. I also would like my partner to be good at communicating so that we can distinguish who should do what task and work together to make the overall project flow.
# Things like communication, trust, reliability, and good team chemistry make teamwork go smoothly.
#Things like lack of communication, doing sections not assigned to you or not assigning sections at all, not showing up to group meetings, and not being prepared when group meetings take place are things that make teamwork fail.
[[User:Dbashour|Dbashour]] ([[User talk:Dbashour|talk]]) 14:45, 6 November 2017 (PST)
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==Eddie Azinge's Responses==
# I don't find myself requiring very much from my teammates, just that the work that they hold themselves accountable for gets done at some point or another, and that inconsistencies in their work do not end up propogating upwards and affecting the status of the entire group, specifically because everyone has their own circumstances and priorities; as long as they deliver on their promises they're good in my book.
# Communication is key to teamwork; but trust and flexibility also play huge roles as well.
# Somewhat antithetical to the last question, a lack of trust and need to keep constant tabs on the members of the project often leads to rushed work, resentment, and dissidence within the team.
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 15:46, 6 November 2017 (PST)

==Edward Bachoura's Response==
# I am looking for teammates that are flexible with their schedules so that we can actually find time to meet. Also, looking for teammates that are accountable for themselves.
# I find it important that whenever you work on a team, there should be some fun involved with the assignment, no matter the topic. When everybody is happy, it is usually easier to do the work at hand.
# Teamwork doesn't go smoothly when someone is unaccountable and makes themselves become more a negative weight rather than a help on the team.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 16:54, 6 November 2017 (PST)

[[Category:Shared]]
[[Category:Journal Entry]]

Template:Ebachour

2017-11-02T22:11:59Z

Ebachour: Added week 10