LMU BioDB 2024 - User contributions [en]

Yeast Beasts

2024-05-03T02:29:30Z

Asandle1: /* Charlotte's Reflection Week 14/15: */ added andrew section

* This page will be the main place from which the Yeast Beasts team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''

[[Media:Yeast_Beasts_Presentation.pdf | Final version of presentation]]

[[Yeast Beasts Deliverables]]

==Week Reflections==
===Week 13===
====[[User:Hivanson|Hailey's]] Reflection [Quality Assurance]====
*I worked closely with Charlotte and Katie toward completing Milestones 2 and 3. We completed milestone 2 and are close to completing milestone 3.
*I thought it worked well to split up, with Natalija going with the coder/designers and me going with data analysis, ''but'' I would love to see where they are at on their progress so that we can join up for the upcoming milestone 4. I want to do this on or before next Tuesday, April 30th.
*It did not work to try to do tasks simultaneously with the data analysts. To fix this, we had one person with an open Excel sheet on their computer, another reading and checking off the steps, and another checking that all of the data and equations were being entered properly. This solution worked well for us and we will continue to have just one computer with Excel open on it, but switching roles between the person inputting data and the one checking off steps could be better for the future.

[[User:Hivanson|Hivanson]] ([[User talk:Hivanson|talk]]) 23:35, 17 April 2024 (PDT)

====Andrew's Reflection [Coder/Designer]====
To find my electronic notebook for this week please click on [[Asandle1 Week 13#Electronic Lab Notebook|Andrew Sandler's Week 13 Lab Notebook]]
'''Executive Summary'''

#Classified Significant P-values as 1 (P < 0.01) or '0'
#Found issues with data including missing gene descriptions.
#Initially tried to use Yeastmine to find the missing gene information but it was inefficient.
#Found additional blanks in the dataset and need to speak with Dr. Dahlquist about how to solve this issue.

'''What worked?'''
Everything "worked" but some surprises came up.

'''What didn't work?'''
Not that this didn't work but it provided a challenge, the issues with the #REF boxes, the blank boxes, the random text in some boxes, and the NaN coming up in some spots. I don't know how to deal with this and will need help from Dr. Dahlquist so I am not just guessing at a solution. I also need to figure out how to get a complete Gene ID list and then compare the whole ID list to the missing ID's. I also need that list for the ID's for the Access Database.

'''What will I do next to fix what didn't work?'''
I plan on speaking with Dean and Dr. Dahlquist in class tomorrow to fix these issues and then move onto working on the Access section of this assignment.

[[Category:Journal Entry]]
[[Category:Team Project]]

====Dean's Reflection [Coder/Designer]====
# This week, me and my partner completed milestones 1 and 2, and we are currently working on milestone 3, there are some complications in milestone 3, for a large part of it requires Microsoft Access, and there are also some issues in importing tables to excel. [[MSymond1]]
# Each team member should reflect on the team's progress:
## The things that worked well are cleaning up the data for the network table, which was done in class on Tuesday, the data table looks much more organized and the p values have all been successfully converted
## The other data tables are not pasting into excel as neatly as anticipated, I am also unaware of how to obtain the data from the yeastmine website.
## To fix these issues, I will ask Dr. Dahlquist for further advice in class on Thursday.
[[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 13:33, 18 April 2024 (PDT)

====Katie's Reflection====
#This week, Charlotte, Hailey, and I worked on completing Milestones 2 and 3. These milestones consisted of preparing the dataset from SGD for analysis, and then performing an ANOVA analysis like we had done in Week 9. A more detailed summary of the steps we followed is outlined on mine and Charlotte's individual page, linked below.
#* [[Data Analysts Week 13]]
#The data analysts, me and Charlotte, worked together with Hailey on progressing through Milestones 2 and 3 on the Data Analysis page. We contacted each other throughout the week to check in on what each person was doing. We then met in person to work together on performing the ANOVA analysis. This worked well, because when we couldn't meet we were still able to get some work done, and then once we got together we were able to ask any questions that we had. It was slightly difficult to progress through the steps in person because when attempting to work on the dataset at the same time, only one person could be actively making changes. I don't believe it is possible for this issue to be fixed, as we cannot have multiple people working at exactly the same time, because steps need to be followed in a specific order. In the future, we will continue to make sure that we split up the steps so that each person is doing an equal amount of work, and to be communicative about any questions that we have or can answer.

[[User:Kmill104|Kmill104]] ([[User talk:Kmill104|talk]]) 23:09, 17 April 2024 (PDT)

====Charlotte's Reflection:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 2 and Milestone 3 in person on April 17th, 2024. We messaged the Coder/Designers and got an update from them. I wrote out the steps taken on our [[Data Analysts Week 13]] page. It was helpful that we were able to meet in person to collaborate. However, it was hard to make changes to the data since we were working on one computer. We ended up splitting up the work well, but at first everyone trying to make edits at once was hard. Now we know a system that works for us as a group.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 14:00, 18 April 2024 (PDT)

===Week 14===
===Week 15===
====Dean's Reflection====
# This week and last week, the entire group and I completed milestones 3-6, as well as the rest of the deliverables for the final project.
# Each team member should reflect on the team's progress:
## The things that worked well are creating the database and getting it all well organized and working out any bugs or issues in the database. Running the queries in the database the way I did them also worked very well and was very quick once the issues in the database were resolved. The creation of the final project report also worked well since we also had presented on the project already.
## The things that did not work well were the collaboration on running the queries in the coders/designers since Andrew first tried doing it in a much more complicated way that required typing all of the syntax in the SQL mode and there was little to no communication between us on how these were done or what needs to be done in the future.
## To fix these issues, I made sure that for the rest of the project we all collaborated and communicated well for the final presentation and project.

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# Each team member should reflect on the team's progress:
## What worked?
## What didn't work?
## What will I do next to fix what didn't work?
# Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks.

====Charlotte's Reflection Week 14/15:====
[[User:Kmill104| Katherine Miller]] and I, being the data analysts, worked with Quality Assurance [[User:Hivanson| Hailey Ivanson]] to complete Milestone 3 and Milestone 4 in person for week 14. [[User:Kmill104| Katherine Miller]] [[User:Hivanson| Hailey Ivanson]] and I to complete Milestone 2 and Milestone 3 in person. We created our ANOVA sheet and calculated the Bonferroni and B&H values, obtaining our needed p-values, and we also performed a sanity check. We then created a CHP_STEM file to filter the correct BH values to p>0.05, getting rid of any div errors. We saved this as a text file and proceeded to work on our GO and Gene tables. We found 7 significant profiles within profile 41. We had issues creating the queries for Miestone 5, so [[User:Msymond1| Dean Symonds]] assisted us in creating the queries needed to run GRNmap. What worked since we had experience from previous assignments, creating our CHP_stem file, filtering p-values, and choosing our transcription factors did not raise too many questions. What we struggled with was creating the queries needed for Dr. Dahlquist to run the GRNmap. Without Dean's help, we could not have done this on our own. To fix what we had issues with, it would have been easier if all six of us could meet at the same time, although it is understandable due to varying schedules.

[[User:Ckapla12|Ckapla12]] ([[User talk:Ckapla12|talk]]) 19:21, 2 May 2024 (PDT)

===Andrew's Section===
1. What worked?

Everything, “worked” but we noticed we could save time by adding the gene name and systematic name both on the gene table.

2. What didn't work?

The class website did not work.

 3. What will I do next to fix what didn't work?

I don't have a fix but it meant that I took notes and did not have them save, so I lost some of my detailed notes on the methods for the past week. I am trying to determine what I would have saved them as.

Asandle1 Week 15

2024-05-03T00:48:39Z

Asandle1: updating info for questions

{{Template:Asandle1}}

== Electronic Lab Notebook ==
'''This Journal is combination between week 14 and 15.
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.
# Dean said there is an error in the Network table. He said he can't make something a primary key because of a null value. I told him thats an excel importing issue, and we need to fix it in excel. I told Dean I will deal with it because he is not understanding the issue.
# I connected all of the relationships for the primary keys. Meta data remains unconnected since it is a separate piece.

===April 25 Notes===
We are waiting for QA to finish Milestone 5 so we can do Milestone 6, In the meantime we are going to work on the presentation
Got the Gene list for profile 41 from the Data Analyst Team which are: Rpn4, Gcn4, Pdr1, Xbp1, Met28, Mga2, Spt23, Bas1, Yap1, Sok2, Msn2, Crz1, Rlm1, Fhl1, Pdr3, Cbf1, Rph1, Met31, Stp1, Msn4, Tec1, Rgm1, Stp2.

[https://docs.google.com/presentation/d/1DnYfkl9j5hy6EqTc1XT0tT7A_husJCJNNgsxhncsozY/edit?usp=sharing|presentation]

===Answers to Questions===
1. What worked?

Everything, “worked” but we noticed we could save time by adding the gene name and systematic name both on the gene table.

2. What didn't work?

The class website did not work.

 3. What will I do next to fix what didn't work?

I don't have a fix but it meant that I took notes and did not have them save, so I lost some of my detailed notes on the methods for the past week. I am trying to determine what I would have saved them as.

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 15

2024-05-03T00:43:13Z

Asandle1: /* Answers to Questions */ edited formatting

{{Template:Asandle1}}

== Electronic Lab Notebook ==
'''This Journal is combination between week 14 and 15.
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.
# Dean said there is an error in the Network table. He said he can't make something a primary key because of a null value. I told him thats an excel importing issue, and we need to fix it in excel. I told Dean I will deal with it because he is not understanding the issue.
# I connected all of the relationships for the primary keys. Meta data remains unconnected since it is a separate piece.

===April 25 Notes===
We are waiting for QA to finish Milestone 5 so we can do Milestone 6, In the meantime we are going to work on the presentation
Got the Gene list for profile 41 from the Data Analyst Team which are: Rpn4, Gcn4, Pdr1, Xbp1, Met28, Mga2, Spt23, Bas1, Yap1, Sok2, Msn2, Crz1, Rlm1, Fhl1, Pdr3, Cbf1, Rph1, Met31, Stp1, Msn4, Tec1, Rgm1, Stp2.

[https://docs.google.com/presentation/d/1DnYfkl9j5hy6EqTc1XT0tT7A_husJCJNNgsxhncsozY/edit?usp=sharing|presentation]

===Answers to Questions===
1. What worked?

Everything, “worked” but we noticed we could save time by adding the gene name and systematic name both on the gene table.

2. What didn't work?

Nothing didn’t “work” this week.

 3. What will I do next to fix what didn't work?

Nothing didn't work at this point.

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 15

2024-05-03T00:42:59Z

Asandle1: /* April 25 Notes */ answered questions

{{Template:Asandle1}}

== Electronic Lab Notebook ==
'''This Journal is combination between week 14 and 15.
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.
# Dean said there is an error in the Network table. He said he can't make something a primary key because of a null value. I told him thats an excel importing issue, and we need to fix it in excel. I told Dean I will deal with it because he is not understanding the issue.
# I connected all of the relationships for the primary keys. Meta data remains unconnected since it is a separate piece.

===April 25 Notes===
We are waiting for QA to finish Milestone 5 so we can do Milestone 6, In the meantime we are going to work on the presentation
Got the Gene list for profile 41 from the Data Analyst Team which are: Rpn4, Gcn4, Pdr1, Xbp1, Met28, Mga2, Spt23, Bas1, Yap1, Sok2, Msn2, Crz1, Rlm1, Fhl1, Pdr3, Cbf1, Rph1, Met31, Stp1, Msn4, Tec1, Rgm1, Stp2.

[https://docs.google.com/presentation/d/1DnYfkl9j5hy6EqTc1XT0tT7A_husJCJNNgsxhncsozY/edit?usp=sharing|presentation]

===Answers to Questions===
1. What worked?

Everything, “worked” but we noticed we could save time by adding the gene name and systematic name both on the gene table.

2. What didn't work?
Nothing didn’t “work” this week.

 3. What will I do next to fix what didn't work?
Nothing didn't work at this point.

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 15

2024-05-03T00:42:11Z

Asandle1: added answers to final questions

{{Template:Asandle1}}

== Electronic Lab Notebook ==
'''This Journal is combination between week 14 and 15.
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.
# Dean said there is an error in the Network table. He said he can't make something a primary key because of a null value. I told him thats an excel importing issue, and we need to fix it in excel. I told Dean I will deal with it because he is not understanding the issue.
# I connected all of the relationships for the primary keys. Meta data remains unconnected since it is a separate piece.

===April 25 Notes===
We are waiting for QA to finish Milestone 5 so we can do Milestone 6, In the meantime we are going to work on the presentation
Got the Gene list for profile 41 from the Data Analyst Team which are: Rpn4, Gcn4, Pdr1, Xbp1, Met28, Mga2, Spt23, Bas1, Yap1, Sok2, Msn2, Crz1, Rlm1, Fhl1, Pdr3, Cbf1, Rph1, Met31, Stp1, Msn4, Tec1, Rgm1, Stp2.

[https://docs.google.com/presentation/d/1DnYfkl9j5hy6EqTc1XT0tT7A_husJCJNNgsxhncsozY/edit?usp=sharing|presentation]

1. What worked?

Everything, “worked” but we noticed we could save time by adding the gene name and systematic name both on the gene table.

2. What didn't work?
Nothing didn’t “work” this week.
 3. What will I do next to fix what didn't work?
Nothing didn't work at this point.

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 15

2024-05-02T06:26:13Z

Asandle1: /* April 25 Notes */ filed

{{Template:Asandle1}}

== Electronic Lab Notebook ==
'''This Journal is combination between week 14 and 15.
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.
# Dean said there is an error in the Network table. He said he can't make something a primary key because of a null value. I told him thats an excel importing issue, and we need to fix it in excel. I told Dean I will deal with it because he is not understanding the issue.
# I connected all of the relationships for the primary keys. Meta data remains unconnected since it is a separate piece.

===April 25 Notes===
We are waiting for QA to finish Milestone 5 so we can do Milestone 6, In the meantime we are going to work on the presentation
Got the Gene list for profile 41 from the Data Analyst Team which are: Rpn4, Gcn4, Pdr1, Xbp1, Met28, Mga2, Spt23, Bas1, Yap1, Sok2, Msn2, Crz1, Rlm1, Fhl1, Pdr3, Cbf1, Rph1, Met31, Stp1, Msn4, Tec1, Rgm1, Stp2.

[[File:Yeast_Beasts_Presentation.pdf]]

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 15

2024-05-02T06:25:42Z

Asandle1: /* April 25 Notes */ Yeast Beasts presentation

{{Template:Asandle1}}

== Electronic Lab Notebook ==
'''This Journal is combination between week 14 and 15.
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.
# Dean said there is an error in the Network table. He said he can't make something a primary key because of a null value. I told him thats an excel importing issue, and we need to fix it in excel. I told Dean I will deal with it because he is not understanding the issue.
# I connected all of the relationships for the primary keys. Meta data remains unconnected since it is a separate piece.

===April 25 Notes===
We are waiting for QA to finish Milestone 5 so we can do Milestone 6, In the meantime we are going to work on the presentation
Got the Gene list for profile 41 from the Data Analyst Team which are: Rpn4, Gcn4, Pdr1, Xbp1, Met28, Mga2, Spt23, Bas1, Yap1, Sok2, Msn2, Crz1, Rlm1, Fhl1, Pdr3, Cbf1, Rph1, Met31, Stp1, Msn4, Tec1, Rgm1, Stp2.

[[Media:Yeast_Beasts_Presentation.pdf]]

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

File:Yeast Beasts Presentation.pdf

2024-05-02T06:24:50Z

Asandle1: Rough Draft

== Summary ==
Rough Draft

Week 15

2024-05-02T06:20:52Z

Asandle1: /* Team Journal Assignment */ saving media

'''This journal entry is due on Friday, May 3, at 12:00pm (noon) PDT.'''

== Overview ==

* The purpose of this week is to complete the [[Final Project Deliverables]].

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 10 points.
* Your team journal entry for this week is worth a total of 3 points.
* Note that each pair of Coder/Designers, QA's, and Data Analysts can create a shared individual page with contributions by both members.
* Details about the grading for the [[Final Project Deliverables]] can be found on that page.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 15" or "''guild name'' Week 15" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your personal template that you created for the [[Week 1 | Week 1 Assignment]] on your individual journal entry page. Your template should provide the following set of navigation links:
** Link to your user page.
** Links to the weekly Assignment pages.
** Links to your weekly Individual Journal entry pages.
** Links to the weekly Class Journal pages.
** The category "Journal Entry".
* '''''Note that this week, we will add a new category, "Team Project".''' Please do not add these to your individual templates because we want these categories to be precisely used for the Team Project.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual/partner progress in your '''''electronic laboratory notebook'''''.

=== Electronic Lab Notebook ===

Record your progress toward your team's [[Final_Project_Deliverables | deliverables]] for this week in an '''''electronic lab notebook'''''.

== Team Journal Assignment ==

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# Each team member should reflect on the team's progress:
## What worked?
## What didn't work?
## What will I do next to fix what didn't work?

[[Media:Yeast_Beasts_Presentation.zip]]

[[Category:Assignment]]
[[Category:Team Project]]

Week 15

2024-05-02T06:20:34Z

Asandle1: Testing file

'''This journal entry is due on Friday, May 3, at 12:00pm (noon) PDT.'''

== Overview ==

* The purpose of this week is to complete the [[Final Project Deliverables]].

=== Grading for this assignment ===

* Your individual journal entry for this week is worth a total of 10 points.
* Your team journal entry for this week is worth a total of 3 points.
* Note that each pair of Coder/Designers, QA's, and Data Analysts can create a shared individual page with contributions by both members.
* Details about the grading for the [[Final Project Deliverables]] can be found on that page.

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 15" or "''guild name'' Week 15" (i.e., this is the text to place between the square brackets when you link to this page).
* Invoke your personal template that you created for the [[Week 1 | Week 1 Assignment]] on your individual journal entry page. Your template should provide the following set of navigation links:
** Link to your user page.
** Links to the weekly Assignment pages.
** Links to your weekly Individual Journal entry pages.
** Links to the weekly Class Journal pages.
** The category "Journal Entry".
* '''''Note that this week, we will add a new category, "Team Project".''' Please do not add these to your individual templates because we want these categories to be precisely used for the Team Project.''
* Include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.
* For your assignment this week document your individual/partner progress in your '''''electronic laboratory notebook'''''.

=== Electronic Lab Notebook ===

Record your progress toward your team's [[Final_Project_Deliverables | deliverables]] for this week in an '''''electronic lab notebook'''''.

== Team Journal Assignment ==

# Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
# Each team member should reflect on the team's progress:
## What worked?
## What didn't work?
## What will I do next to fix what didn't work?

[[File:Yeast_Beasts_Presentation.zip]]

[[Category:Assignment]]
[[Category:Team Project]]

File:Yeast Beasts Presentation.zip

2024-05-02T06:19:31Z

Asandle1:

Asandle1 Week 15

2024-04-25T21:55:42Z

Asandle1: /* April 25 Notes */ added genes

{{Template:Asandle1}}

== Electronic Lab Notebook ==
'''This Journal is combination between week 14 and 15.
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.
# Dean said there is an error in the Network table. He said he can't make something a primary key because of a null value. I told him thats an excel importing issue, and we need to fix it in excel. I told Dean I will deal with it because he is not understanding the issue.
# I connected all of the relationships for the primary keys. Meta data remains unconnected since it is a separate piece.

===April 25 Notes===
We are waiting for QA to finish Milestone 5 so we can do Milestone 6, In the meantime we are going to work on the presentation
Got the Gene list for profile 41 from the Data Analyst Team which are: Rpn4, Gcn4, Pdr1, Xbp1, Met28, Mga2, Spt23, Bas1, Yap1, Sok2, Msn2, Crz1, Rlm1, Fhl1, Pdr3, Cbf1, Rph1, Met31, Stp1, Msn4, Tec1, Rgm1, Stp2.

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 15

2024-04-25T21:04:37Z

Asandle1: /* April 25 Notes */ presentation note

{{Template:Asandle1}}

== Electronic Lab Notebook ==
'''This Journal is combination between week 14 and 15.
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.
# Dean said there is an error in the Network table. He said he can't make something a primary key because of a null value. I told him thats an excel importing issue, and we need to fix it in excel. I told Dean I will deal with it because he is not understanding the issue.
# I connected all of the relationships for the primary keys. Meta data remains unconnected since it is a separate piece.

===April 25 Notes===
We are waiting for QA to finish Milestone 5 so we can do Milestone 6, In the meantime we are going to work on the presentation

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 15

2024-04-25T20:59:08Z

Asandle1: week 15 created with week 14, also added a small notes section for April 25th

{{Template:Asandle1}}

== Electronic Lab Notebook ==
'''This Journal is combination between week 14 and 15.
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.
# Dean said there is an error in the Network table. He said he can't make something a primary key because of a null value. I told him thats an excel importing issue, and we need to fix it in excel. I told Dean I will deal with it because he is not understanding the issue.
# I connected all of the relationships for the primary keys. Meta data remains unconnected since it is a separate piece.

===April 25 Notes===

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Template:Asandle1

2024-04-25T20:57:43Z

Asandle1: /* Individual */ week 15 added

To User Page: [[User: Asandle1]]
To Template: [[Template:Asandle1]]

====Assignment Pages====

[[week 1]]

[[week 2]]

[[week 3]]

[[week 4]]

[[week 5]]

[[week 6]]

[[week 7]]

[[week 8]]

[[week 9]]

[[week 10]]

[[week 11]]

[[week 12]]

[[week 13]]

[[week 14]]

[[week 15]]

====Journals====

=====Individual=====
[[User:Asandle1]]

[[Asandle1 Week 2]]

[[SIR2 Week 3]]

[[Monarch Initiative Week 4]]

[[Asandle1 Week 5]]

[[Asandle1 Week 6]]

[[Asandle1 Week 8]]

[[Asandle1 Week 9]]

[[Asandle1 Week 10]]

[[Asandle1 Week 12]]

[[Asandle1 Week 13]]

[[Asandle1 Week 14]]

[[Asandle1 Week 15]]

====Class Journals====
[[Class Journal Week 1]]

[[Class Journal Week 2]]

[[Class Journal Week 3]]

[[Class Journal Week 4]]

[[Class Journal Week 5]]

[[Class Journal Week 6]]

[[Class Journal Week 8]]

[[Class Journal Week 9]]

[[Class Journal Week 10]]

[[Class Journal Week 12]]

[[Category: Journal Entry]]

[[Category: Shared]]

Asandle1 Week 14

2024-04-23T21:49:07Z

Asandle1: /* April 23 Notes */ notes added

{{Template:Asandle1}}

== Electronic Lab Notebook ==
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.
# Dean said there is an error in the Network table. He said he can't make something a primary key because of a null value. I told him thats an excel importing issue, and we need to fix it in excel. I told Dean I will deal with it because he is not understanding the issue.
# I connected all of the relationships for the primary keys. Meta data remains unconnected since it is a separate piece.

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 14

2024-04-23T21:31:29Z

Asandle1: /* April 23 Notes */ notes

{{Template:Asandle1}}

== Electronic Lab Notebook ==
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.
# Dean said there is an error in the Network table. He said he can't make something a primary key because of a null value. I told him thats an excel importing issue, and we need to fix it in excel. I told Dean I will deal with it because he is not understanding the issue.

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 14

2024-04-23T21:28:34Z

Asandle1: /* Acknowlegements */ notes

{{Template:Asandle1}}

== Electronic Lab Notebook ==
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.

==References & Acknowledgements==
===Acknowlegements===
* Dean and I communicated about the project via text, at one point I didn't hear from him so I called him and he promptly got back to me.
* Dr. Dahlquist helped us solve some issues with the data in the production_rates and degradation_rates tables. She also provided assistance with the expression table.

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 14

2024-04-23T21:26:29Z

Asandle1: /* April 23 Notes */ notes updated

{{Template:Asandle1}}

== Electronic Lab Notebook ==
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine
# Dean is working on the Expression_Table right now while I was fixing these. He encountered some issues for the Data team to solve.

==References & Acknowledgements==
===Acknowlegements===

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 14

2024-04-23T21:25:30Z

Asandle1: /* April 23 Notes */ notes updated

{{Template:Asandle1}}

== Electronic Lab Notebook ==
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues
# Fixed the issues and everything worked fine

==References & Acknowledgements==
===Acknowlegements===

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 14

2024-04-23T21:19:41Z

Asandle1: /* April 23 Notes */ note

{{Template:Asandle1}}

== Electronic Lab Notebook ==
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.
# I tried importing and had no issues

==References & Acknowledgements==
===Acknowlegements===

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 14

2024-04-23T21:16:03Z

Asandle1: /* April 23 Notes */ notes

{{Template:Asandle1}}

== Electronic Lab Notebook ==
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.
# Dr. Dahlquist tried reimporting and it works, so I am going to import both Degradation_Rates and Production_Rates again.

==References & Acknowledgements==
===Acknowlegements===

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 14

2024-04-23T21:12:46Z

Asandle1: /* April 23 Notes */ added notes

{{Template:Asandle1}}

== Electronic Lab Notebook ==
To get to the Team Journal Page please click here: [[Yeast Beasts]]
To get to the Previous Journal click here: [[Asandle1 Week 13]]

===In Class Thursday April 18th Notes===

*Dean immediately told me he needed help getting the text for the degradation imported
*I told him I knew how to fix it and he just needed to import the text to excel instead of copy pasting. Dr. Dahlquist helped him with that.
* we solved the issue of the #REF and Blanks, we didn't end up needing those two columns so we just deleted them
* Dean shared into the box up to the additional steps he took.
* Everything is into the file and we are having the other group look over what we did.
* We are now thinking about what to put down for metadata, I asked what we need for metadata and Dr. Dahlquist is explaining to us what metadata is and what to put in for it.
* Added a sheet and named it Metadata
* Added a Primary Key, Description, Data Source, Date Accessed, Data Updated Date, and Publication (Pubmed ID) or DOI Column
* Entered the info under each of these sections, and shared a screenshot with Dean to make sure we don't do the same work twice
----

===April 21 Notes===
* Trying to get in touch with to see where he left off so I know where to progress for next steps

===April 22 Notes===
* Dean looks to have created 4 of the tables but I need to speak with him in person to make corrections
* Created the metadata table
* Added detailed descriptions for table items
* Access File is on Box in each iteration, uploaded most recent version to box.

===April 23 Notes===
#Issue with Degradation rates and production rates on access going to 0's and 1's.
# I told Dean to ignore this issue and I will Deal with it while he deals with the expression table.

==References & Acknowledgements==
===Acknowlegements===

===References===
#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Used week 13 as an outline
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 14

2024-04-23T21:10:58Z

Asandle1: /* Electronic Lab Notebook */ added issue

Asandle1 Week 14

2024-04-23T21:07:56Z

Asandle1: /* References & Acknowledgements */ divided acknowledgements and references

Asandle1 Week 14

2024-04-23T02:21:02Z

Asandle1: /* April 22 Notes */ notes

Asandle1 Week 14

2024-04-23T01:48:15Z

Asandle1: /* April 22 Notes */ additional note

Asandle1 Week 14

2024-04-23T01:25:36Z

Asandle1: /* April 22 Notes */ added journal notes

Asandle1 Week 14

2024-04-22T23:01:59Z

Asandle1: /* Electronic Lab Notebook */ updates

Asandle1 Week 14

2024-04-18T22:01:28Z

Asandle1: /* In Class Thursday April 18th Notes */

Asandle1 Week 14

2024-04-18T21:44:04Z

Asandle1: /* In Class Thursday April 18th Notes */ more info steps for metadata

Asandle1 Week 14

2024-04-18T21:33:03Z

Asandle1: /* In Class Thursday April 18th Notes */ added sheet

Asandle1 Week 14

2024-04-18T21:31:15Z

Asandle1: /* In Class Thursday April 18th Notes */ added meta data info

Asandle1 Week 14

2024-04-18T21:25:28Z

Asandle1: /* In Class Thursday April 18th Notes */ added what we did

Asandle1 Week 14

2024-04-18T21:11:39Z

Asandle1: added basic outline from previous week 13

Template:Asandle1

2024-04-18T21:09:02Z

Asandle1: /* Individual */ added week 14

To User Page: [[User: Asandle1]]
To Template: [[Template:Asandle1]]

====Assignment Pages====

[[week 1]]

[[week 2]]

[[week 3]]

[[week 4]]

[[week 5]]

[[week 6]]

[[week 7]]

[[week 8]]

[[week 9]]

[[week 10]]

[[week 11]]

[[week 12]]

[[week 13]]

[[week 14]]

[[week 15]]

====Journals====

=====Individual=====
[[User:Asandle1]]

[[Asandle1 Week 2]]

[[SIR2 Week 3]]

[[Monarch Initiative Week 4]]

[[Asandle1 Week 5]]

[[Asandle1 Week 6]]

[[Asandle1 Week 8]]

[[Asandle1 Week 9]]

[[Asandle1 Week 10]]

[[Asandle1 Week 12]]

[[Asandle1 Week 13]]

[[Asandle1 Week 14]]

====Class Journals====
[[Class Journal Week 1]]

[[Class Journal Week 2]]

[[Class Journal Week 3]]

[[Class Journal Week 4]]

[[Class Journal Week 5]]

[[Class Journal Week 6]]

[[Class Journal Week 8]]

[[Class Journal Week 9]]

[[Class Journal Week 10]]

[[Class Journal Week 12]]

[[Category: Journal Entry]]

[[Category: Shared]]

Yeast Beasts

2024-04-18T05:25:14Z

Asandle1: /* Andrew's Reflection [Coder/Designer] */ changed from * to # for numbering

Yeast Beasts

2024-04-18T05:24:44Z

Asandle1: /* Andrew's Reflection [Coder/Designer] */ Summary added

Yeast Beasts

2024-04-18T05:19:19Z

Asandle1: /* Andrew's Reflection [Coder/Designer] */ saving progress, executive summary changed to be after the link to week 13

Yeast Beasts

2024-04-18T05:18:09Z

Asandle1: /* Andrew's Reflection [Coder/Designer] */ Added reflection section

Asandle1 Week 13

2024-04-18T05:10:38Z

Asandle1: /* References & Acknowledgements */ Signed and sealed

{{Template:Asandle1}}

== Electronic Lab Notebook ==
===Biological Databases P-val by Gene Initial Notes===
Harbison Paper

To get to the Team Journal Page please click here: [[Yeast Beasts]]
====Things I notice====
* The document is called Pval by Gene which makes me think that we are looking at the Pvalues in the genes which tracks considering what the paper is based on.
* The document has 6,231 rows which aligns with the gene numbers from the paper
* The document has 206 columns, 203 are values. This makes me think the columns are for each transcriptional regulator.
* There are some value boxes that just say NaN. Not sure how to deal with these
* We have the gene names in column 1
* We have the gene tags that humans can actually read in column 2
* We have plain english descriptions of what everything is in column 3

====Thought Process:====
''' Layout Assumptions:''' (Maybe incorrect)
*Primary Key should be Gene ID Column for the Data

'''Questions:'''
* Data preprocessing?
**Can we worry about the NaN entries once everything has been added to Access or do we need to figure out how to remove those without removing every entry?
** How do we want to import by?
*We want to be able to view by Gene or by environmental difference, does this mean making an access entry for the Genes and for the different experimental conditions?
*How do we make sure the database for the Harbison paper also works with all the others? I think this probably has to do with the primary key which then means we can really only organize across the Gene ID’s because that is what will be common across other experiments.
*Is there anything I am missing?

===In Class Tuesday April 16th Notes===

Added a Folder to the BIOL367_Spring2024 Box Folder and Labeled it Dean and Andrew Database File Folder

If there is a significant P value we make it a 1 anything else we give a 0. We will do =IF(pval<0.01,1,0)

Made a copy of YPD and called it YPD edits so I have the original saved in case of any errors.

I then did =if(YPD!D3 < 0.001,1,0) in my new copy document referring to the same cell in the original document.

I dragged my selection across the top line of P-values and then double clicked to expand down the entire data selection.

I then filtered the data in column D and selected only the check box for 1's. It came back with 6 results which was the same number of results that Dr. Dahlquist found.

Then I cleared the filter.

I removed the top row that had numbers that I didn't have any context for.

Next I removed the _YPD at the end of the row that was now the new top row. I replaced it with nothing, using the find and replace feature and selected replace all.

Then I filtered again to double check all my data and formulas still existed and worked correctly and it did.

[[File:Pvalbygene_forpaper_abbrAndrewDay1.xls]]
----
===After Class===
Take a look at this image:
[[File:Andrew's_Ref_Discovery.png| You can see that the shorthand name and the description are missing|600px]]
You can see that the shorthand name and the description are missing in line 37. This happens in other places as well.

For now, I am going to sort by blanks and ones that have Ref in them so I can find what needs fixing

Now I noticed after filtering another issue, which the image below shows. (Blanks and then some random information that I am unsure about.)

[[File:AnotherIssueInDataAndrew.png|300px]]

I tried to go to Yeastmine with the list of identifiers for the missing symbols but realized this would be a really slow process and there is probably a better way. Also wasn't sure which to select. Here is what I saw.

[[File:YeastmineIdentifiersFinalProjectAndrewSandler.png|500px]]

==References & Acknowledgements==

* Dr. Dahlquist helped Dean and I with the excel file steps, specifically relating to setting up the =if equation to change the significant P-values to 1 and the non-significant values to 0. This was in class on tuesday. She also responded to some questions I had asked her over email that can be found at the top of this journal.

* I spoke with Dean and uploaded my excel file since he was having difficulties. I also spoke to him Wednesday April 17th at around 9 P.M. over text.

#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer
#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]])

[[Category: Team Project]]

Asandle1 Week 13

2024-04-18T05:09:55Z

Asandle1: /* References & Acknowledgements */ added final reference

{{Template:Asandle1}}

== Electronic Lab Notebook ==
===Biological Databases P-val by Gene Initial Notes===
Harbison Paper

To get to the Team Journal Page please click here: [[Yeast Beasts]]
====Things I notice====
* The document is called Pval by Gene which makes me think that we are looking at the Pvalues in the genes which tracks considering what the paper is based on.
* The document has 6,231 rows which aligns with the gene numbers from the paper
* The document has 206 columns, 203 are values. This makes me think the columns are for each transcriptional regulator.
* There are some value boxes that just say NaN. Not sure how to deal with these
* We have the gene names in column 1
* We have the gene tags that humans can actually read in column 2
* We have plain english descriptions of what everything is in column 3

====Thought Process:====
''' Layout Assumptions:''' (Maybe incorrect)
*Primary Key should be Gene ID Column for the Data

'''Questions:'''
* Data preprocessing?
**Can we worry about the NaN entries once everything has been added to Access or do we need to figure out how to remove those without removing every entry?
** How do we want to import by?
*We want to be able to view by Gene or by environmental difference, does this mean making an access entry for the Genes and for the different experimental conditions?
*How do we make sure the database for the Harbison paper also works with all the others? I think this probably has to do with the primary key which then means we can really only organize across the Gene ID’s because that is what will be common across other experiments.
*Is there anything I am missing?

===In Class Tuesday April 16th Notes===

Added a Folder to the BIOL367_Spring2024 Box Folder and Labeled it Dean and Andrew Database File Folder

If there is a significant P value we make it a 1 anything else we give a 0. We will do =IF(pval<0.01,1,0)

Made a copy of YPD and called it YPD edits so I have the original saved in case of any errors.

I then did =if(YPD!D3 < 0.001,1,0) in my new copy document referring to the same cell in the original document.

I dragged my selection across the top line of P-values and then double clicked to expand down the entire data selection.

I then filtered the data in column D and selected only the check box for 1's. It came back with 6 results which was the same number of results that Dr. Dahlquist found.

Then I cleared the filter.

I removed the top row that had numbers that I didn't have any context for.

Next I removed the _YPD at the end of the row that was now the new top row. I replaced it with nothing, using the find and replace feature and selected replace all.

Then I filtered again to double check all my data and formulas still existed and worked correctly and it did.

[[File:Pvalbygene_forpaper_abbrAndrewDay1.xls]]
----
===After Class===
Take a look at this image:
[[File:Andrew's_Ref_Discovery.png| You can see that the shorthand name and the description are missing|600px]]
You can see that the shorthand name and the description are missing in line 37. This happens in other places as well.

For now, I am going to sort by blanks and ones that have Ref in them so I can find what needs fixing

Now I noticed after filtering another issue, which the image below shows. (Blanks and then some random information that I am unsure about.)

[[File:AnotherIssueInDataAndrew.png|300px]]

I tried to go to Yeastmine with the list of identifiers for the missing symbols but realized this would be a really slow process and there is probably a better way. Also wasn't sure which to select. Here is what I saw.

[[File:YeastmineIdentifiersFinalProjectAndrewSandler.png|500px]]

==References & Acknowledgements==

* Dr. Dahlquist helped Dean and I with the excel file steps, specifically relating to setting up the =if equation to change the significant P-values to 1 and the non-significant values to 0. This was in class on tuesday. She also responded to some questions I had asked her over email that can be found at the top of this journal.

* I spoke with Dean and uploaded my excel file since he was having difficulties. I also spoke to him Wednesday April 17th at around 9 P.M. over text.

#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer

#Community Central Fandom. (2024). Forum:How do I link to a heading on another page?. Retrieved April 17, 2024, from https://community.fandom.com/wiki/Forum:How_do_I_link_to_a_heading_on_another_page%3F

[[Category: Team Project]]

Yeast Beasts

2024-04-18T05:07:31Z

Asandle1: testing naming

Yeast Beasts

2024-04-18T05:07:04Z

Asandle1: testing link

Asandle1 Week 13

2024-04-18T05:06:33Z

Asandle1: /* Biological Databases P-val by Gene Initial Notes */ added link

Asandle1 Week 13

2024-04-18T05:04:29Z

Asandle1: testing a header link

{{Template:Asandle1}}

== Electronic Lab Notebook ==
===Biological Databases P-val by Gene Initial Notes===
Harbison Paper

To get to the Team Journal Page please click here: [[Yeast Beasts#Andrew's Reflection [Coder/Designer]]]
====Things I notice====
* The document is called Pval by Gene which makes me think that we are looking at the Pvalues in the genes which tracks considering what the paper is based on.
* The document has 6,231 rows which aligns with the gene numbers from the paper
* The document has 206 columns, 203 are values. This makes me think the columns are for each transcriptional regulator.
* There are some value boxes that just say NaN. Not sure how to deal with these
* We have the gene names in column 1
* We have the gene tags that humans can actually read in column 2
* We have plain english descriptions of what everything is in column 3

====Thought Process:====
''' Layout Assumptions:''' (Maybe incorrect)
*Primary Key should be Gene ID Column for the Data

'''Questions:'''
* Data preprocessing?
**Can we worry about the NaN entries once everything has been added to Access or do we need to figure out how to remove those without removing every entry?
** How do we want to import by?
*We want to be able to view by Gene or by environmental difference, does this mean making an access entry for the Genes and for the different experimental conditions?
*How do we make sure the database for the Harbison paper also works with all the others? I think this probably has to do with the primary key which then means we can really only organize across the Gene ID’s because that is what will be common across other experiments.
*Is there anything I am missing?

===In Class Tuesday April 16th Notes===

Added a Folder to the BIOL367_Spring2024 Box Folder and Labeled it Dean and Andrew Database File Folder

If there is a significant P value we make it a 1 anything else we give a 0. We will do =IF(pval<0.01,1,0)

Made a copy of YPD and called it YPD edits so I have the original saved in case of any errors.

I then did =if(YPD!D3 < 0.001,1,0) in my new copy document referring to the same cell in the original document.

I dragged my selection across the top line of P-values and then double clicked to expand down the entire data selection.

I then filtered the data in column D and selected only the check box for 1's. It came back with 6 results which was the same number of results that Dr. Dahlquist found.

Then I cleared the filter.

I removed the top row that had numbers that I didn't have any context for.

Next I removed the _YPD at the end of the row that was now the new top row. I replaced it with nothing, using the find and replace feature and selected replace all.

Then I filtered again to double check all my data and formulas still existed and worked correctly and it did.

[[File:Pvalbygene_forpaper_abbrAndrewDay1.xls]]
----
===After Class===
Take a look at this image:
[[File:Andrew's_Ref_Discovery.png| You can see that the shorthand name and the description are missing|600px]]
You can see that the shorthand name and the description are missing in line 37. This happens in other places as well.

For now, I am going to sort by blanks and ones that have Ref in them so I can find what needs fixing

Now I noticed after filtering another issue, which the image below shows. (Blanks and then some random information that I am unsure about.)

[[File:AnotherIssueInDataAndrew.png|300px]]

I tried to go to Yeastmine with the list of identifiers for the missing symbols but realized this would be a really slow process and there is probably a better way. Also wasn't sure which to select. Here is what I saw.

[[File:YeastmineIdentifiersFinalProjectAndrewSandler.png|500px]]

==References & Acknowledgements==

* Dr. Dahlquist helped Dean and I with the excel file steps, specifically relating to setting up the =if equation to change the significant P-values to 1 and the non-significant values to 0. This was in class on tuesday. She also responded to some questions I had asked her over email that can be found at the top of this journal.

* I spoke with Dean and uploaded my excel file since he was having difficulties. I also spoke to him Wednesday April 17th at around 9 P.M. over text.

#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer

[[Category: Team Project]]

Yeast Beasts

2024-04-18T05:02:18Z

Asandle1: /* Andrew's Reflection [Coder/Designer] */ added link to week 13

Asandle1 Week 13

2024-04-18T04:59:52Z

Asandle1: /* After Class */ fixed formatting

{{Template:Asandle1}}

== Electronic Lab Notebook ==
===Biological Databases P-val by Gene Initial Notes===
Harbison Paper

====Things I notice====
* The document is called Pval by Gene which makes me think that we are looking at the Pvalues in the genes which tracks considering what the paper is based on.
* The document has 6,231 rows which aligns with the gene numbers from the paper
* The document has 206 columns, 203 are values. This makes me think the columns are for each transcriptional regulator.
* There are some value boxes that just say NaN. Not sure how to deal with these
* We have the gene names in column 1
* We have the gene tags that humans can actually read in column 2
* We have plain english descriptions of what everything is in column 3

====Thought Process:====
''' Layout Assumptions:''' (Maybe incorrect)
*Primary Key should be Gene ID Column for the Data

'''Questions:'''
* Data preprocessing?
**Can we worry about the NaN entries once everything has been added to Access or do we need to figure out how to remove those without removing every entry?
** How do we want to import by?
*We want to be able to view by Gene or by environmental difference, does this mean making an access entry for the Genes and for the different experimental conditions?
*How do we make sure the database for the Harbison paper also works with all the others? I think this probably has to do with the primary key which then means we can really only organize across the Gene ID’s because that is what will be common across other experiments.
*Is there anything I am missing?

===In Class Tuesday April 16th Notes===

Added a Folder to the BIOL367_Spring2024 Box Folder and Labeled it Dean and Andrew Database File Folder

If there is a significant P value we make it a 1 anything else we give a 0. We will do =IF(pval<0.01,1,0)

Made a copy of YPD and called it YPD edits so I have the original saved in case of any errors.

I then did =if(YPD!D3 < 0.001,1,0) in my new copy document referring to the same cell in the original document.

I dragged my selection across the top line of P-values and then double clicked to expand down the entire data selection.

I then filtered the data in column D and selected only the check box for 1's. It came back with 6 results which was the same number of results that Dr. Dahlquist found.

Then I cleared the filter.

I removed the top row that had numbers that I didn't have any context for.

Next I removed the _YPD at the end of the row that was now the new top row. I replaced it with nothing, using the find and replace feature and selected replace all.

Then I filtered again to double check all my data and formulas still existed and worked correctly and it did.

[[File:Pvalbygene_forpaper_abbrAndrewDay1.xls]]
----
===After Class===
Take a look at this image:

[[File:Andrew's_Ref_Discovery.png| You can see that the shorthand name and the description are missing|600px]]

You can see that the shorthand name and the description are missing in line 37. This happens in other places as well.

For now, I am going to sort by blanks and ones that have Ref in them so I can find what needs fixing

Now I noticed after filtering another issue, which the image below shows. (Blanks and then some random information that I am unsure about.)

[[File:AnotherIssueInDataAndrew.png|300px]]

I tried to go to Yeastmine with the list of identifiers for the missing symbols but realized this would be a really slow process and there is probably a better way. Also wasn't sure which to select. Here is what I saw.

[[File:YeastmineIdentifiersFinalProjectAndrewSandler.png|500px]]

==References & Acknowledgements==

* Dr. Dahlquist helped Dean and I with the excel file steps, specifically relating to setting up the =if equation to change the significant P-values to 1 and the non-significant values to 0. This was in class on tuesday. She also responded to some questions I had asked her over email that can be found at the top of this journal.

* I spoke with Dean and uploaded my excel file since he was having difficulties. I also spoke to him Wednesday April 17th at around 9 P.M. over text.

* Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]]) 21:59, 17 April 2024 (PDT)

#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer

[[Category: Team Project]]

Asandle1 Week 13

2024-04-18T04:59:11Z

Asandle1: /* References & Acknowledgements */ signed page

{{Template:Asandle1}}

== Electronic Lab Notebook ==
===Biological Databases P-val by Gene Initial Notes===
Harbison Paper

====Things I notice====
* The document is called Pval by Gene which makes me think that we are looking at the Pvalues in the genes which tracks considering what the paper is based on.
* The document has 6,231 rows which aligns with the gene numbers from the paper
* The document has 206 columns, 203 are values. This makes me think the columns are for each transcriptional regulator.
* There are some value boxes that just say NaN. Not sure how to deal with these
* We have the gene names in column 1
* We have the gene tags that humans can actually read in column 2
* We have plain english descriptions of what everything is in column 3

====Thought Process:====
''' Layout Assumptions:''' (Maybe incorrect)
*Primary Key should be Gene ID Column for the Data

'''Questions:'''
* Data preprocessing?
**Can we worry about the NaN entries once everything has been added to Access or do we need to figure out how to remove those without removing every entry?
** How do we want to import by?
*We want to be able to view by Gene or by environmental difference, does this mean making an access entry for the Genes and for the different experimental conditions?
*How do we make sure the database for the Harbison paper also works with all the others? I think this probably has to do with the primary key which then means we can really only organize across the Gene ID’s because that is what will be common across other experiments.
*Is there anything I am missing?

===In Class Tuesday April 16th Notes===

Added a Folder to the BIOL367_Spring2024 Box Folder and Labeled it Dean and Andrew Database File Folder

If there is a significant P value we make it a 1 anything else we give a 0. We will do =IF(pval<0.01,1,0)

Made a copy of YPD and called it YPD edits so I have the original saved in case of any errors.

I then did =if(YPD!D3 < 0.001,1,0) in my new copy document referring to the same cell in the original document.

I dragged my selection across the top line of P-values and then double clicked to expand down the entire data selection.

I then filtered the data in column D and selected only the check box for 1's. It came back with 6 results which was the same number of results that Dr. Dahlquist found.

Then I cleared the filter.

I removed the top row that had numbers that I didn't have any context for.

Next I removed the _YPD at the end of the row that was now the new top row. I replaced it with nothing, using the find and replace feature and selected replace all.

Then I filtered again to double check all my data and formulas still existed and worked correctly and it did.

[[File:Pvalbygene_forpaper_abbrAndrewDay1.xls]]
----
===After Class===
Take a look at this image:
[[File:Andrew's_Ref_Discovery.png| You can see that the shorthand name and the description are missing|600px]]
You can see that the shorthand name and the description are missing in line 37. This happens in other places as well.

For now, I am going to sort by blanks and ones that have Ref in them so I can find what needs fixing

Now I noticed after filtering another issue, which the image below shows. (Blanks and then some random information that I am unsure about.)

[[File:AnotherIssueInDataAndrew.png|300px]]

I tried to go to Yeastmine with the list of identifiers for the missing symbols but realized this would be a really slow process and there is probably a better way. Also wasn't sure which to select. Here is what I saw.

[[File:YeastmineIdentifiersFinalProjectAndrewSandler.png|500px]]

==References & Acknowledgements==

* Dr. Dahlquist helped Dean and I with the excel file steps, specifically relating to setting up the =if equation to change the significant P-values to 1 and the non-significant values to 0. This was in class on tuesday. She also responded to some questions I had asked her over email that can be found at the top of this journal.

* I spoke with Dean and uploaded my excel file since he was having difficulties. I also spoke to him Wednesday April 17th at around 9 P.M. over text.

* Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Asandle1|Asandle1]] ([[User talk:Asandle1|talk]]) 21:59, 17 April 2024 (PDT)

#LMU BioDB 2024. (2024). Coder/Designer. Retrieved April 17, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Coder/Designer

[[Category: Team Project]]

Yeast Beasts

2024-04-18T04:55:48Z

Asandle1: /* Week 13 */ Fixed formatting for headers added coder designer to name