https://xmlpipedb2024.lmucs.io/biodb/fall2019/api.php?action=feedcontributions&feedformat=atom&user=NtesfaioLMU BioDB 2019 - User contributions [en]2026-04-04T20:02:05ZUser contributionsMediaWiki 1.32.1https://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7739Sulfiknights Deliverables2019-12-12T22:43:24Z<p>Ntesfaio: /* Naomi Tesfaiohannes's Reflection */ added to reflection</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Checklist:==<br />
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''INCOMPLETE'''<br />
#Group Report (.doc, .docx or .pdf file) '''INCOMPLETE'''<br />
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''INCOMPLETE'''<br />
#Group PowerPoint presentation (given on Tuesday, December 10, .ppt, .pptx or .pdf file) '''COMPLETE'''<br />
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx) '''COMPLETE'''<br />
#PowerPoint of ANOVA table, screenshots of stem results (.pptx), screenshot of black and white GRNsight input network and colored GRNsight output networks '''COMPLETE'''<br />
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) '''COMPLETE'''<br />
#YEASTRACT "rank by TF" results (.xlsx) '''COMPLETE'''<br />
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''COMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''COMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''COMPLETE'''<br />
#ReadMe for the database that describes the design of the database, references the sources of the data, and has a database schema diagram (.doc, .docx, .pdf) '''COMPLETE'''<br />
#Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, .txt) '''COMPLETE'''<br />
#Electronic notebook corresponding to these the microarray results files (Week 12/13 and Week 15) to support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results. '''INCOMPLETE'''<br />
<br />
==Group Report==<br />
==Individual Statements of Work, Assessments, Reflections==<br />
==Group Powerpoint Presentation==<br />
<br />
[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
<br />
==Excel Spreadsheet with ANOVA Results/STEM Formatting==<br />
[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
<br />
==PowerPoint of ANOVA Table...==<br />
[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
<br />
[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]]<br />
<br />
[[Image:Profil923_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored_GRNsight_923.PNG|500px]]<br />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Image:Profile4048_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored GRNsight 4048.PNG|500px]]<br />
<br />
==Gene List and GO List files==<br />
[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]<br />
<br />
[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
<br />
==YEASTRACT "Rank by TF" Results==<br />
[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
<br />
[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
<br />
==GRNmap input workbook==<br />
[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet: Profiles 40 and 48]]<br />
<br />
==GRNmap output workbook and output plots==<br />
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048_output.zip|GRNmap Output Files: Profiles 40 and 48]]<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==ReadMe==<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
'''Profiles 9 and 23:'''<br />
<br />
[[Image:Productionrates_923_querydesign.PNG|350]]<br />
[[Image:Degradationrates_923_querydesign.PNG|350]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|350]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|350]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG]]<br />
<br />
==Electronic notebook corresponding to the microarray results files==<br />
'''Electronic notebook for Data Analysts:'''<br />
<br />
[[Sulfiknights DA Week 12/13]]<br />
<br />
[[Sulfiknights DA Week 14]]<br />
<br />
'''Electronic notebook for Quality Assurance'''<br />
<br />
[[Ntesfaio Week 12/13]]<br />
<br />
[[Ntesfaio Week 15]]<br />
<br />
'''Electronic notebook for Designer'''<br />
<br />
==Merge completed databases into a single database==<br />
[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ]]<br />
<br />
[[Image:Access_Database_Schema_Screenshot.PNG|1000px|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
==Final Reflection==<br />
===Marcus Avila's Final Reflection===<br />
==== Individual Assessment and Reflection ====<br />
===== Statement of Work =====<br />
<br />
* Describe exactly what you did on the project.<br />
** For the project I worked with Ivy to decide how to organize the Thorsen data to run an ANOVA. After doing the ANOVA and running STEM, I then downloaded the [[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip| Gene Lists]] for Profiles 40 & 48 and combined them to input into "Rank by TF" on YEASTRACT. Next, I selected the 15 most significant transcription factors to include on the network. After inputting the 15 transcription factors into the Generate Regulation Matrix I downloaded and transposed the [[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 network excel sheet]]. I then used GRNsight to create the weighted and unweighted network maps.<br />
** I then created the production rate sheet, degradation rate sheet, expression data sheet, network sheet, network weights sheet, optimization parameters, and the threshold b sheet using the [https://github.com/kdahlquist/DahlquistLab/raw/master/data/Spring2019/15-genes_28-edges_sample_Sigmoid_estimation_2019.xlsx sample workbook] provided. Finally, I input the GRNmap input workbook from the [[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet Profiles 40 and 48]] into MATLAB for analysis.<br />
<br />
===== Assessment of Project =====<br />
<br />
# Give an objective assessment of the success of your project workflow and teamwork.<br />
#* The team did a good job making sure things were done in a timely manner and we also had very few problems meeting up outside of class time to work on the project which made the workflow much more efficient.<br />
# What worked and what didn't work?<br />
#* Communication via text messages and scheduling meet up times worked very well. It seemed like the work load distribution was not completely equal, but this is not something we could change as a group. <br />
# What would you do differently if you could do it all over again?<br />
#* I would ensure that each job had defined tasks or were assigned to help other members in their tasks.<br />
# Evaluate your team’s portion of the Final Project and Group Report in the following areas:<br />
#* Content: What is the quality of the work? <br />
#** The quality of the work was good, but might have some issues because some steps were unclear and did not always parallel the steps done in the example data analysis assignment.<br />
#* Organization: Comment on the organization of the project and of your group's wiki pages.<br />
#** Our wiki page was very organized because each section included a header and files were broken up into categories/steps.<br />
#* Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
#** Yes, the Microsoft Access database was successfully made after analyzing the publish microarray data.<br />
<br />
===== Reflection on the Process =====<br />
<br />
* What did you learn?<br />
# With your head (biological or computer science principles)<br />
#* I learned about how microarray experiments can be used to study gene expression changes in response to stress.<br />
# With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
#* I learned that meeting up is much more effective than working individually or texting when analyzing and interpreting data, as well as when working on editing presentations.<br />
# With your hands (technical skills)?<br />
#* I learned how to input microarray data into MS Access, how to use GRNsight, YEASTRACT, and MATLAB.<br />
* What lesson will you take away from this project that you will still use a year from now?<br />
# I will take away the lesson that my attitude plays a major role in whether each person is equally invested in a group assignment or not.<br />
<br />
===Naomi Tesfaiohannes's Final Reflection===<br />
<br />
'''Statement of Work'''<br />
<br />
Describe exactly what you did on the project.<br />
<br />
For this project I served as the project manager and the quality assurance guild. As project manager I communicated with Dr. Dahlquist of the steps that were made and need to continue to be made for the project. I also checked in with my team members of their progress with their roles. As QA I worked along with Joey on the datasheets to hand off to the Data Analysts. I also contributed to presenting and putting together the final presentation.<br />
<br />
'''Provide references or links to artifacts of your work, such as:'''<br />
<br />
[[Sulfiknights]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
'''Give an objective assessment of the success of your project workflow and teamwork.'''<br />
<br />
What worked and what didn't work?<br />
<br />
What worked was meeting outside of class and keeping in touch with progress by using the group chat<br />
What didn't work was sometimes not being able to answer each other's questions. Leaving us all confused. <br />
<br />
What would you do differently if you could do it all over again?<br />
<br />
Ask more questions about analyzing new data instead of trying to figure it out on my own. <br />
<br />
'''Evaluate your team’s portion of the Final Project and Group Report in the following areas:'''<br />
<br />
Content: What is the quality of the work?<br />
<br />
Our work is a reflection of the collaborative effort from all of the team members in trying to understand the new data we reanalyzed. <br />
<br />
Organization: Comment on the organization of the project and of your group's wiki pages.<br />
<br />
Our group stayed organized by splitting up what sections we would work on. That way we could come together at the end of the slides to review what still needs to be understood. <br />
<br />
Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
Yes, but at our own pace. The objectives were completed by going through the deliverables for each members. <br />
<br />
Reflection on the Process<br />
<br />
What did you learn?<br />
<br />
With your head (biological or computer science principles)<br />
<br />
Connecting the affects of arsenic to budding yeast<br />
<br />
With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
<br />
Teamwork and collaborating with others by contributing my own section of work with theirs to form an overall analysis of the data. <br />
<br />
With your hands (technical skills)?<br />
<br />
Formatting the database column titles <br />
<br />
What lesson will you take away from this project that you will still use a year from now?<br />
<br />
It's important to ask questions when struggling with something new, for example a database format you are not familiar with. It's not a bad thing to ask questions, and it doesn't mean you are unaware of what is happening. Questions help with understanding making it easier for the student to present on the material.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:02, 9 December 2019 (PST)</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7738Sulfiknights Deliverables2019-12-12T22:43:02Z<p>Ntesfaio: /* Naomi Tesfaiohannes's Reflection */ added to reflection</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Checklist:==<br />
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''INCOMPLETE'''<br />
#Group Report (.doc, .docx or .pdf file) '''INCOMPLETE'''<br />
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''INCOMPLETE'''<br />
#Group PowerPoint presentation (given on Tuesday, December 10, .ppt, .pptx or .pdf file) '''COMPLETE'''<br />
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx) '''COMPLETE'''<br />
#PowerPoint of ANOVA table, screenshots of stem results (.pptx), screenshot of black and white GRNsight input network and colored GRNsight output networks '''COMPLETE'''<br />
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) '''COMPLETE'''<br />
#YEASTRACT "rank by TF" results (.xlsx) '''COMPLETE'''<br />
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''COMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''COMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''COMPLETE'''<br />
#ReadMe for the database that describes the design of the database, references the sources of the data, and has a database schema diagram (.doc, .docx, .pdf) '''COMPLETE'''<br />
#Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, .txt) '''COMPLETE'''<br />
#Electronic notebook corresponding to these the microarray results files (Week 12/13 and Week 15) to support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results. '''INCOMPLETE'''<br />
<br />
==Group Report==<br />
==Individual Statements of Work, Assessments, Reflections==<br />
==Group Powerpoint Presentation==<br />
<br />
[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
<br />
==Excel Spreadsheet with ANOVA Results/STEM Formatting==<br />
[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
<br />
==PowerPoint of ANOVA Table...==<br />
[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
<br />
[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]]<br />
<br />
[[Image:Profil923_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored_GRNsight_923.PNG|500px]]<br />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Image:Profile4048_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored GRNsight 4048.PNG|500px]]<br />
<br />
==Gene List and GO List files==<br />
[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]<br />
<br />
[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
<br />
==YEASTRACT "Rank by TF" Results==<br />
[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
<br />
[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
<br />
==GRNmap input workbook==<br />
[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet: Profiles 40 and 48]]<br />
<br />
==GRNmap output workbook and output plots==<br />
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048_output.zip|GRNmap Output Files: Profiles 40 and 48]]<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==ReadMe==<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
'''Profiles 9 and 23:'''<br />
<br />
[[Image:Productionrates_923_querydesign.PNG|350]]<br />
[[Image:Degradationrates_923_querydesign.PNG|350]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|350]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|350]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG]]<br />
<br />
==Electronic notebook corresponding to the microarray results files==<br />
'''Electronic notebook for Data Analysts:'''<br />
<br />
[[Sulfiknights DA Week 12/13]]<br />
<br />
[[Sulfiknights DA Week 14]]<br />
<br />
'''Electronic notebook for Quality Assurance'''<br />
<br />
[[Ntesfaio Week 12/13]]<br />
<br />
[[Ntesfaio Week 15]]<br />
<br />
'''Electronic notebook for Designer'''<br />
<br />
==Merge completed databases into a single database==<br />
[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ]]<br />
<br />
[[Image:Access_Database_Schema_Screenshot.PNG|1000px|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
==Final Reflection==<br />
===Marcus Avila's Final Reflection===<br />
==== Individual Assessment and Reflection ====<br />
===== Statement of Work =====<br />
<br />
* Describe exactly what you did on the project.<br />
** For the project I worked with Ivy to decide how to organize the Thorsen data to run an ANOVA. After doing the ANOVA and running STEM, I then downloaded the [[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip| Gene Lists]] for Profiles 40 & 48 and combined them to input into "Rank by TF" on YEASTRACT. Next, I selected the 15 most significant transcription factors to include on the network. After inputting the 15 transcription factors into the Generate Regulation Matrix I downloaded and transposed the [[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 network excel sheet]]. I then used GRNsight to create the weighted and unweighted network maps.<br />
** I then created the production rate sheet, degradation rate sheet, expression data sheet, network sheet, network weights sheet, optimization parameters, and the threshold b sheet using the [https://github.com/kdahlquist/DahlquistLab/raw/master/data/Spring2019/15-genes_28-edges_sample_Sigmoid_estimation_2019.xlsx sample workbook] provided. Finally, I input the GRNmap input workbook from the [[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet Profiles 40 and 48]] into MATLAB for analysis.<br />
<br />
===== Assessment of Project =====<br />
<br />
# Give an objective assessment of the success of your project workflow and teamwork.<br />
#* The team did a good job making sure things were done in a timely manner and we also had very few problems meeting up outside of class time to work on the project which made the workflow much more efficient.<br />
# What worked and what didn't work?<br />
#* Communication via text messages and scheduling meet up times worked very well. It seemed like the work load distribution was not completely equal, but this is not something we could change as a group. <br />
# What would you do differently if you could do it all over again?<br />
#* I would ensure that each job had defined tasks or were assigned to help other members in their tasks.<br />
# Evaluate your team’s portion of the Final Project and Group Report in the following areas:<br />
#* Content: What is the quality of the work? <br />
#** The quality of the work was good, but might have some issues because some steps were unclear and did not always parallel the steps done in the example data analysis assignment.<br />
#* Organization: Comment on the organization of the project and of your group's wiki pages.<br />
#** Our wiki page was very organized because each section included a header and files were broken up into categories/steps.<br />
#* Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
#** Yes, the Microsoft Access database was successfully made after analyzing the publish microarray data.<br />
<br />
===== Reflection on the Process =====<br />
<br />
* What did you learn?<br />
# With your head (biological or computer science principles)<br />
#* I learned about how microarray experiments can be used to study gene expression changes in response to stress.<br />
# With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
#* I learned that meeting up is much more effective than working individually or texting when analyzing and interpreting data, as well as when working on editing presentations.<br />
# With your hands (technical skills)?<br />
#* I learned how to input microarray data into MS Access, how to use GRNsight, YEASTRACT, and MATLAB.<br />
* What lesson will you take away from this project that you will still use a year from now?<br />
# I will take away the lesson that my attitude plays a major role in whether each person is equally invested in a group assignment or not.<br />
<br />
===Naomi Tesfaiohannes's Reflection===<br />
<br />
'''Statement of Work'''<br />
<br />
Describe exactly what you did on the project.<br />
<br />
For this project I served as the project manager and the quality assurance guild. As project manager I communicated with Dr. Dahlquist of the steps that were made and need to continue to be made for the project. I also checked in with my team members of their progress with their roles. As QA I worked along with Joey on the datasheets to hand off to the Data Analysts. I also contributed to presenting and putting together the final presentation.<br />
<br />
'''Provide references or links to artifacts of your work, such as:'''<br />
<br />
[[Sulfiknights]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
'''Give an objective assessment of the success of your project workflow and teamwork.'''<br />
<br />
What worked and what didn't work?<br />
<br />
What worked was meeting outside of class and keeping in touch with progress by using the group chat<br />
What didn't work was sometimes not being able to answer each other's questions. Leaving us all confused. <br />
<br />
What would you do differently if you could do it all over again?<br />
<br />
Ask more questions about analyzing new data instead of trying to figure it out on my own. <br />
<br />
'''Evaluate your team’s portion of the Final Project and Group Report in the following areas:'''<br />
<br />
Content: What is the quality of the work?<br />
<br />
Our work is a reflection of the collaborative effort from all of the team members in trying to understand the new data we reanalyzed. <br />
<br />
Organization: Comment on the organization of the project and of your group's wiki pages.<br />
<br />
Our group stayed organized by splitting up what sections we would work on. That way we could come together at the end of the slides to review what still needs to be understood. <br />
<br />
Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
Yes, but at our own pace. The objectives were completed by going through the deliverables for each members. <br />
<br />
Reflection on the Process<br />
<br />
What did you learn?<br />
<br />
With your head (biological or computer science principles)<br />
<br />
Connecting the affects of arsenic to budding yeast<br />
<br />
With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
<br />
Teamwork and collaborating with others by contributing my own section of work with theirs to form an overall analysis of the data. <br />
<br />
With your hands (technical skills)?<br />
<br />
Formatting the database column titles <br />
<br />
What lesson will you take away from this project that you will still use a year from now?<br />
<br />
It's important to ask questions when struggling with something new, for example a database format you are not familiar with. It's not a bad thing to ask questions, and it doesn't mean you are unaware of what is happening. Questions help with understanding making it easier for the student to present on the material.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:02, 9 December 2019 (PST)</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Final_Individual_Reflection&diff=7737Ntesfaio Final Individual Reflection2019-12-12T22:40:47Z<p>Ntesfaio: added to questions</p>
<hr />
<div>Naomi Tesfaiohannes<br />
<br />
'''Statement of Work'''<br />
<br />
Describe exactly what you did on the project.<br />
<br />
For this project I served as the project manager and the quality assurance guild. As project manager I communicated with Dr. Dahlquist of the steps that were made and need to continue to be made for the project. I also checked in with my team members of their progress with their roles. As QA I worked along with Joey on the datasheets to hand off to the Data Analysts. I also contributed to presenting and putting together the final presentation. <br />
<br />
'''Provide references or links to artifacts of your work, such as:'''<br />
<br />
[[Sulfiknights Deliverables]]<br />
<br />
[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
<br />
'''Assessment of Project'''<br />
<br />
'''Give an objective assessment of the success of your project workflow and teamwork.'''<br />
<br />
It took a lot of responsibility to complete this assignment since much of the work was a collaborative effort with each member needing to do their part. The major objective was to communicate with one another as we went through the project. <br />
<br />
'''What worked and what didn't work?'''<br />
<br />
Meeting outside of class helped. What didn't work was the confusion with how many networks to have since we only had 4 profiles or the changes in column headers due to miscommunication with the other groups. <br />
<br />
'''What would you do differently if you could do it all over again?'''<br />
<br />
Ask more questions instead of staying confused with trying to figure it out on my own. <br />
<br />
'''Evaluate your team’s portion of the Final Project and Group Report in the following areas:'''<br />
<br />
'''Content: What is the quality of the work?'''<br />
<br />
My group and I met consistently and communicated well to get the presentation done in an organized manner. The quality of our work was effective because of our timeliness. <br />
<br />
'''Organization: Comment on the organization of the project and of your group's wiki pages.'''<br />
<br />
We organized the wiki by going through what was being completed at the time. That way, we avoided any confusions with the work that needed to be completed. <br />
<br />
'''Completeness: Did your team achieve all of the project objectives? Why or why not?'''<br />
<br />
Yes, we completed the project objectives well and focused our time mainly on the things that mattered most such as the presentation and group report. This was done by splitting the work evenly among all of us. <br />
<br />
'''Reflection on the Process'''<br />
<br />
'''What did you learn?'''<br />
<br />
I've never taken a computer science-ish class. So I learned a whole new world of data analysis and how to write a wikipedia page. <br />
<br />
'''With your head (biological or computer science principles)'''<br />
<br />
New coding tricks that I can use in the future, whether that be with Excel, Microsoft ACCESS, etc. <br />
<br />
'''With your heart (personal qualities and teamwork qualities that make things work or not work)?'''<br />
<br />
Getting work done with a group of friends while still being productive. We had some good laughs during the project and got to lift each other up throughout the late nights of coding. I think I enjoyed that part the most.<br />
<br />
'''With your hands (technical skills)?'''<br />
<br />
Typing away. I have never taken a class that involved computers everyday so this was interesting. <br />
<br />
'''What lesson will you take away from this project that you will still use a year from now?'''<br />
<br />
Work smarter not harder. Be sure to speak up when needing help. Always communicate with those around you. Ask questions because someone else might have the same question but is too scared to ask. Be open to working with new people, whether that be every day or even every week. The transitions we had in this class allowed me to interact with different people and work on my communication with others. That will be helpful in the workforce when I have to work with new people as well. <br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 14:40, 12 December 2019 (PST)</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Template:Ntesfaio&diff=7736Template:Ntesfaio2019-12-12T22:25:45Z<p>Ntesfaio: added individual reflection section</p>
<hr />
<div>[[Main Page|Bio DB Home page]]<br />
<br />
[[Template:Ntesfaio]]<br />
<br />
'''[[Week 1]]'''<br />
<br />
[[User:Ntesfaio]]<br />
<br />
[[:Class Journal Week 1]]<br />
<br />
'''[[Week 2]]'''<br />
<br />
[[Ntesfaio Week 2]]<br />
<br />
[[Class Journal Week 2]]<br />
<br />
[[Category: Journal Entry]]<br />
<br />
'''[[Week 3]]'''<br />
<br />
[[RAD53 / YPL153C Week 3]]<br />
<br />
[[Class Journal Week 3]]<br />
<br />
<br />
'''[[Week 4]]'''<br />
<br />
[[Ntesfaio Week 4]]<br />
<br />
[[Class Journal Week 4]]<br />
<br />
'''[[Week 5]]'''<br />
<br />
[[DrugCentral Week 5]]<br />
<br />
[[Class Journal Week 5]]<br />
<br />
'''[[Week 6]]'''<br />
<br />
[[Ntesfaio Week 6]]<br />
<br />
[[Class Journal Week 6]]<br />
<br />
'''[[Week 7]]'''<br />
<br />
[[Ntesfaio Week 7]]<br />
<br />
[[Class Journal Week 7]]<br />
<br />
'''[[Week 8]]'''<br />
<br />
[[Ntesfaio Week 8]]<br />
<br />
[[Class Journal Week 8]]<br />
<br />
'''[[Week 9]]'''<br />
<br />
[[Ntesfaio Week 9]]<br />
<br />
[[Class Journal Week 9]]<br />
<br />
'''[[Week 10]]'''<br />
<br />
[[Ntesfaio Week 10]]<br />
<br />
'''[[Week 11]]'''<br />
<br />
[[Ntesfaio Week 11]]<br />
<br />
[[Sulfiknights]]<br />
<br />
'''[[Week 12/13]]'''<br />
<br />
[[Ntesfaio Week 12/13]]<br />
<br />
[[Sulfiknights]]<br />
<br />
[[Sulfiknights Deliverables]]<br />
<br />
[[Ntesfaio Week 15]]<br />
<br />
[[Ntesfaio Final Individual Reflection]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7717Sulfiknights Deliverables2019-12-10T19:59:40Z<p>Ntesfaio: /* Checklist: */ added completion</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Checklist:==<br />
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''INCOMPLETE'''<br />
#Group Report (.doc, .docx or .pdf file) '''INCOMPLETE'''<br />
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''INCOMPLETE'''<br />
#Group PowerPoint presentation (given on Tuesday, December 10, .ppt, .pptx or .pdf file) '''COMPLETE'''<br />
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx) '''COMPLETE'''<br />
#PowerPoint of ANOVA table, screenshots of stem results (.pptx), screenshot of black and white GRNsight input network and colored GRNsight output networks '''COMPLETE'''<br />
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) '''COMPLETE'''<br />
#YEASTRACT "rank by TF" results (.xlsx) '''COMPLETE'''<br />
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''COMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''COMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''COMPLETE'''<br />
#ReadMe for the database that describes the design of the database, references the sources of the data, and has a database schema diagram (.doc, .docx, .pdf) '''COMPLETE'''<br />
#Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, .txt) '''COMPLETE'''<br />
#Electronic notebook corresponding to these the microarray results files (Week 12/13 and Week 15) to support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results. '''INCOMPLETE'''<br />
<br />
==Group Report==<br />
==Individual Statements of Work, Assessments, Reflections==<br />
==Group Powerpoint Presentation==<br />
<br />
[[Media:Sulfiknights Final Presentation.pptx| Sulfiknights Final Presentation]]<br />
<br />
==Excel Spreadsheet with ANOVA Results/STEM Formatting==<br />
[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
<br />
==PowerPoint of ANOVA Table...==<br />
[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
<br />
[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]]<br />
<br />
[[Image:Profil923_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored_GRNsight_923.PNG|500px]]<br />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Image:Profile4048_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored GRNsight 4048.PNG|500px]]<br />
<br />
==Gene List and GO List files==<br />
[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]<br />
<br />
[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
<br />
==YEASTRACT "Rank by TF" Results==<br />
[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
<br />
[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
<br />
==GRNmap input workbook==<br />
[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet: Profiles 40 and 48]]<br />
<br />
==GRNmap output workbook and output plots==<br />
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048_output.zip|GRNmap Output Files: Profiles 40 and 48]]<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==ReadMe==<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
'''Profiles 9 and 23:'''<br />
<br />
[[Image:Productionrates_923_querydesign.PNG|350]]<br />
[[Image:Degradationrates_923_querydesign.PNG|350]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|350]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|350]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG]]<br />
<br />
==Electronic notebook corresponding to the microarray results files==<br />
'''Electronic notebook for Data Analysts:'''<br />
<br />
[[Sulfiknights DA Week 12/13]]<br />
<br />
[[Sulfiknights DA Week 14]]<br />
<br />
'''Electronic notebook for Quality Assurance'''<br />
<br />
[[Ntesfaio Week 12/13]]<br />
<br />
[[Ntesfaio Week 15]]<br />
<br />
'''Electronic notebook for Designer'''<br />
<br />
==Merge completed databases into a single database==<br />
[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
==Final Reflection==<br />
===Marcus Avila's Final Reflection===<br />
==== Individual Assessment and Reflection ====<br />
===== Statement of Work =====<br />
<br />
* Describe exactly what you did on the project.<br />
** For the project I worked with Ivy to decide how to organize the Thorsen data to run an ANOVA. After doing the ANOVA and running STEM, I then downloaded the gene lists for Profiles #40 & #48 and combined them to "Rank by TF" on YEASTRACT. Next, I chose the 15 most significant transcription factors to include on the network.<br />
* Provide references or links to artifacts of your work, such as:<br />
** Wiki pages<br />
** Other files or documents<br />
** Code or scripts<br />
<br />
===== Assessment of Project =====<br />
<br />
* Give an objective assessment of the success of your project workflow and teamwork. <br />
* What worked and what didn't work? <br />
* What would you do differently if you could do it all over again?<br />
* Evaluate your team’s portion of the Final Project and Group Report in the following areas:<br />
*# Content: What is the quality of the work? <br />
*# Organization: Comment on the organization of the project and of your group's wiki pages.<br />
*# Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
===== Reflection on the Process =====<br />
<br />
* What did you learn?<br />
** With your head (biological or computer science principles)<br />
** With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
** With your hands (technical skills)?<br />
* What lesson will you take away from this project that you will still use a year from now?<br />
<br />
===Naomi Tesfaiohannes's Reflection===<br />
<br />
'''Statement of Work'''<br />
<br />
Describe exactly what you did on the project.<br />
<br />
My role as a QA was to work with DeLisa and Joey on the ACCESS datasheet so that the data analysts (Marcus and Ivy) had the information necessary to do GRNmap. <br />
<br />
'''Provide references or links to artifacts of your work, such as:'''<br />
<br />
[[Sulfiknights]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
'''Give an objective assessment of the success of your project workflow and teamwork.'''<br />
<br />
What worked and what didn't work?<br />
<br />
What worked was meeting outside of class and keeping in touch with progress by using the group chat<br />
What didn't work was sometimes not being able to answer each other's questions. Leaving us all confused. <br />
<br />
What would you do differently if you could do it all over again?<br />
<br />
Ask more questions about analyzing new data instead of trying to figure it out on my own. <br />
<br />
'''Evaluate your team’s portion of the Final Project and Group Report in the following areas:'''<br />
<br />
Content: What is the quality of the work?<br />
<br />
Our work is a reflection of the collaborative effort from all of the team members in trying to understand the new data we reanalyzed. <br />
<br />
Organization: Comment on the organization of the project and of your group's wiki pages.<br />
<br />
Our group stayed organized by splitting up what sections we would work on. That way we could come together at the end of the slides to review what still needs to be understood. <br />
<br />
Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
Yes, but at our own pace. The objectives were completed by going through the deliverables for each members. <br />
<br />
Reflection on the Process<br />
<br />
What did you learn?<br />
<br />
With your head (biological or computer science principles)<br />
<br />
Connecting the affects of arsenic to budding yeast<br />
<br />
With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
<br />
Teamwork and collaborating with others by contributing my own section of work with theirs to form an overall analysis of the data. <br />
<br />
With your hands (technical skills)?<br />
<br />
Formatting the database column titles <br />
<br />
What lesson will you take away from this project that you will still use a year from now?<br />
<br />
It's important to ask questions when struggling with something new, for example a database format you are not familiar with. It's not a bad thing to ask questions, and it doesn't mean you are unaware of what is happening. Questions help with understanding making it easier for the student to present on the material.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:02, 9 December 2019 (PST)</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_15&diff=7713Ntesfaio Week 152019-12-10T19:45:42Z<p>Ntesfaio: /* Milestones */ added final presentation</p>
<hr />
<div>Electronic Notebook<br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment was to finalize the deliverables. The deliverables ended with the making of a presentation of the re-analysis of the paper we read with a comparison of what we found. We also worked on a group report that summarizes the information.<br />
<br />
==Milestones==<br />
<br />
I completed the ACCESS datasheet along with Joey and DeLisa to hand off to our data analysts. From there the data was used to form a GRNmap.<br />
<br />
[[Media:Sulfiknights Final Presentation.pptx| Sulfiknights Final Presentation]]<br />
<br />
==Conclusion==<br />
<br />
This week's assignment was completed with the formation of the presentation that will be shared with the class.<br />
<br />
==References==<br />
<br />
Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006<br />
<br />
[[Sulfiknights Deliverables]]<br />
<br />
==Acknowledgments==<br />
<br />
I would like to acknowledge my teammates (The sulfiknights) as well as the other two groups for their contributions to this project. I would also like to acknowledge Dr. Dahlquist for her assistance in following the steps for this assignment <br />
<br />
"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:07, 9 December 2019 (PST)</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7712Sulfiknights Deliverables2019-12-10T19:44:11Z<p>Ntesfaio: /* Group Powerpoint Presentation */ added presentation</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Checklist:==<br />
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''INCOMPLETE'''<br />
#Group Report (.doc, .docx or .pdf file) '''INCOMPLETE'''<br />
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''INCOMPLETE'''<br />
#Group PowerPoint presentation (given on Tuesday, December 10, .ppt, .pptx or .pdf file) '''INCOMPLETE'''<br />
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx) '''COMPLETE'''<br />
#PowerPoint of ANOVA table, screenshots of stem results (.pptx), screenshot of black and white GRNsight input network and colored GRNsight output networks '''COMPLETE'''<br />
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) '''COMPLETE'''<br />
#YEASTRACT "rank by TF" results (.xlsx) '''COMPLETE'''<br />
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''COMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''COMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''COMPLETE'''<br />
#ReadMe for the database that describes the design of the database, references the sources of the data, and has a database schema diagram (.doc, .docx, .pdf) '''INCOMPLETE'''<br />
#Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, .txt) '''COMPLETE'''<br />
#Electronic notebook corresponding to these the microarray results files (Week 12/13 and Week 15) to support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results. '''INCOMPLETE'''<br />
<br />
==Group Report==<br />
==Individual Statements of Work, Assessments, Reflections==<br />
==Group Powerpoint Presentation==<br />
<br />
[[Media:Sulfiknights Final Presentation.pptx| Sulfiknights Final Presentation]]<br />
<br />
==Excel Spreadsheet with ANOVA Results/STEM Formatting==<br />
[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
<br />
==PowerPoint of ANOVA Table...==<br />
[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
<br />
[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]]<br />
<br />
[[Image:Profil923_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored_GRNsight_923.PNG|500px]]<br />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Image:Profile4048_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored GRNsight 4048.PNG|500px]]<br />
<br />
==Gene List and GO List files==<br />
[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]<br />
<br />
[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
<br />
==YEASTRACT "Rank by TF" Results==<br />
[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
<br />
[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
<br />
==GRNmap input workbook==<br />
[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet: Profiles 40 and 48]]<br />
<br />
==GRNmap output workbook and output plots==<br />
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048_output.zip|GRNmap Output Files: Profiles 40 and 48]]<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==ReadMe==<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
'''Profiles 9 and 23:'''<br />
<br />
[[Image:Productionrates_923_querydesign.PNG|350]]<br />
[[Image:Degradationrates_923_querydesign.PNG|350]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|350]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|350]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG]]<br />
<br />
==Electronic notebook corresponding to the microarray results files==<br />
'''Electronic notebook for Data Analysts:'''<br />
<br />
[[Sulfiknights DA Week 12/13]]<br />
<br />
[[Sulfiknights DA Week 14]]<br />
<br />
'''Electronic notebook for Quality Assurance'''<br />
<br />
[[Ntesfaio Week 12/13]]<br />
<br />
[[Ntesfaio Week 15]]<br />
<br />
'''Electronic notebook for Designer'''<br />
<br />
==Merge completed databases into a single database==<br />
[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
==Final Reflection==<br />
===Marcus Avila's Final Reflection===<br />
==== Individual Assessment and Reflection ====<br />
===== Statement of Work =====<br />
<br />
* Describe exactly what you did on the project.<br />
** For the project I worked with Ivy to decide how to organize the Thorsen data to run an ANOVA. After doing the ANOVA and running STEM, I then downloaded the gene lists for Profiles #40 & #48 and combined them to "Rank by TF" on YEASTRACT. Next, I chose the 15 most significant transcription factors to include on the network.<br />
* Provide references or links to artifacts of your work, such as:<br />
** Wiki pages<br />
** Other files or documents<br />
** Code or scripts<br />
<br />
===== Assessment of Project =====<br />
<br />
* Give an objective assessment of the success of your project workflow and teamwork. <br />
* What worked and what didn't work? <br />
* What would you do differently if you could do it all over again?<br />
* Evaluate your team’s portion of the Final Project and Group Report in the following areas:<br />
*# Content: What is the quality of the work? <br />
*# Organization: Comment on the organization of the project and of your group's wiki pages.<br />
*# Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
===== Reflection on the Process =====<br />
<br />
* What did you learn?<br />
** With your head (biological or computer science principles)<br />
** With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
** With your hands (technical skills)?<br />
* What lesson will you take away from this project that you will still use a year from now?<br />
<br />
===Naomi Tesfaiohannes's Reflection===<br />
<br />
'''Statement of Work'''<br />
<br />
Describe exactly what you did on the project.<br />
<br />
My role as a QA was to work with DeLisa and Joey on the ACCESS datasheet so that the data analysts (Marcus and Ivy) had the information necessary to do GRNmap. <br />
<br />
'''Provide references or links to artifacts of your work, such as:'''<br />
<br />
[[Sulfiknights]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
'''Give an objective assessment of the success of your project workflow and teamwork.'''<br />
<br />
What worked and what didn't work?<br />
<br />
What worked was meeting outside of class and keeping in touch with progress by using the group chat<br />
What didn't work was sometimes not being able to answer each other's questions. Leaving us all confused. <br />
<br />
What would you do differently if you could do it all over again?<br />
<br />
Ask more questions about analyzing new data instead of trying to figure it out on my own. <br />
<br />
'''Evaluate your team’s portion of the Final Project and Group Report in the following areas:'''<br />
<br />
Content: What is the quality of the work?<br />
<br />
Our work is a reflection of the collaborative effort from all of the team members in trying to understand the new data we reanalyzed. <br />
<br />
Organization: Comment on the organization of the project and of your group's wiki pages.<br />
<br />
Our group stayed organized by splitting up what sections we would work on. That way we could come together at the end of the slides to review what still needs to be understood. <br />
<br />
Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
Yes, but at our own pace. The objectives were completed by going through the deliverables for each members. <br />
<br />
Reflection on the Process<br />
<br />
What did you learn?<br />
<br />
With your head (biological or computer science principles)<br />
<br />
Connecting the affects of arsenic to budding yeast<br />
<br />
With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
<br />
Teamwork and collaborating with others by contributing my own section of work with theirs to form an overall analysis of the data. <br />
<br />
With your hands (technical skills)?<br />
<br />
Formatting the database column titles <br />
<br />
What lesson will you take away from this project that you will still use a year from now?<br />
<br />
It's important to ask questions when struggling with something new, for example a database format you are not familiar with. It's not a bad thing to ask questions, and it doesn't mean you are unaware of what is happening. Questions help with understanding making it easier for the student to present on the material.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:02, 9 December 2019 (PST)</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Sulfiknights_Final_Presentation.pptx&diff=7711File:Sulfiknights Final Presentation.pptx2019-12-10T19:43:34Z<p>Ntesfaio: added presentation</p>
<hr />
<div>== Summary ==<br />
added presentation</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7706Sulfiknights Deliverables2019-12-10T04:10:33Z<p>Ntesfaio: /* Electronic notebook corresponding to the microarray results files */ added to week 15</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Checklist:==<br />
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''INCOMPLETE'''<br />
#Group Report (.doc, .docx or .pdf file) '''INCOMPLETE'''<br />
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''INCOMPLETE'''<br />
#Group PowerPoint presentation (given on Tuesday, December 10, .ppt, .pptx or .pdf file) '''INCOMPLETE'''<br />
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx) '''COMPLETE'''<br />
#PowerPoint of ANOVA table, screenshots of stem results (.pptx), screenshot of black and white GRNsight input network and colored GRNsight output networks '''COMPLETE'''<br />
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) '''COMPLETE'''<br />
#YEASTRACT "rank by TF" results (.xlsx) '''COMPLETE'''<br />
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''COMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''COMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''COMPLETE'''<br />
#ReadMe for the database that describes the design of the database, references the sources of the data, and has a database schema diagram (.doc, .docx, .pdf) '''INCOMPLETE'''<br />
#Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, .txt) '''COMPLETE'''<br />
#Electronic notebook corresponding to these the microarray results files (Week 12/13 and Week 15) to support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results. '''INCOMPLETE'''<br />
<br />
==Group Report==<br />
==Individual Statements of Work, Assessments, Reflections==<br />
==Group Powerpoint Presentation==<br />
==Excel Spreadsheet with ANOVA Results/STEM Formatting==<br />
[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
<br />
==PowerPoint of ANOVA Table...==<br />
[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
<br />
[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]]<br />
<br />
[[Image:Profil923_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored_GRNsight_923.PNG|500px]]<br />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Image:Profile4048_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored GRNsight 4048.PNG|500px]]<br />
<br />
==Gene List and GO List files==<br />
[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]<br />
<br />
[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
<br />
==YEASTRACT "Rank by TF" Results==<br />
[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
<br />
[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
<br />
==GRNmap input workbook==<br />
[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet: Profiles 40 and 48]]<br />
<br />
==GRNmap output workbook and output plots==<br />
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048_output.zip|GRNmap Output Files: Profiles 40 and 48]]<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==ReadMe==<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
'''Profiles 9 and 23:'''<br />
<br />
[[Image:Productionrates_923_querydesign.PNG|350]]<br />
[[Image:Degradationrates_923_querydesign.PNG|350]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|350]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|350]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG]]<br />
<br />
==Electronic notebook corresponding to the microarray results files==<br />
'''Electronic notebook for Data Analysts:'''<br />
<br />
[[Sulfiknights DA Week 12/13]]<br />
<br />
[[Sulfiknights DA Week 14]]<br />
<br />
'''Electronic notebook for Quality Assurance'''<br />
<br />
[[Ntesfaio Week 12/13]]<br />
<br />
[[Ntesfaio Week 15]]<br />
<br />
'''Electronic notebook for Designer'''<br />
<br />
==Merge completed databases into a single database==<br />
[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
==Final Reflection==<br />
===Marcus Avila's Final Reflection===<br />
==== Individual Assessment and Reflection ====<br />
===== Statement of Work =====<br />
<br />
* Describe exactly what you did on the project.<br />
** For the project I worked with Ivy to decide how to organize the Thorsen data to run an ANOVA. After doing the ANOVA and running STEM, I then downloaded the gene lists for Profiles #40 & #48 and combined them to "Rank by TF" on YEASTRACT. Next, I chose the 15 most significant transcription factors to include on the network.<br />
* Provide references or links to artifacts of your work, such as:<br />
** Wiki pages<br />
** Other files or documents<br />
** Code or scripts<br />
<br />
===== Assessment of Project =====<br />
<br />
* Give an objective assessment of the success of your project workflow and teamwork. <br />
* What worked and what didn't work? <br />
* What would you do differently if you could do it all over again?<br />
* Evaluate your team’s portion of the Final Project and Group Report in the following areas:<br />
*# Content: What is the quality of the work? <br />
*# Organization: Comment on the organization of the project and of your group's wiki pages.<br />
*# Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
===== Reflection on the Process =====<br />
<br />
* What did you learn?<br />
** With your head (biological or computer science principles)<br />
** With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
** With your hands (technical skills)?<br />
* What lesson will you take away from this project that you will still use a year from now?<br />
<br />
===Naomi Tesfaiohannes's Reflection===<br />
<br />
'''Statement of Work'''<br />
<br />
Describe exactly what you did on the project.<br />
<br />
My role as a QA was to work with DeLisa and Joey on the ACCESS datasheet so that the data analysts (Marcus and Ivy) had the information necessary to do GRNmap. <br />
<br />
'''Provide references or links to artifacts of your work, such as:'''<br />
<br />
[[Sulfiknights]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
'''Give an objective assessment of the success of your project workflow and teamwork.'''<br />
<br />
What worked and what didn't work?<br />
<br />
What worked was meeting outside of class and keeping in touch with progress by using the group chat<br />
What didn't work was sometimes not being able to answer each other's questions. Leaving us all confused. <br />
<br />
What would you do differently if you could do it all over again?<br />
<br />
Ask more questions about analyzing new data instead of trying to figure it out on my own. <br />
<br />
'''Evaluate your team’s portion of the Final Project and Group Report in the following areas:'''<br />
<br />
Content: What is the quality of the work?<br />
<br />
Our work is a reflection of the collaborative effort from all of the team members in trying to understand the new data we reanalyzed. <br />
<br />
Organization: Comment on the organization of the project and of your group's wiki pages.<br />
<br />
Our group stayed organized by splitting up what sections we would work on. That way we could come together at the end of the slides to review what still needs to be understood. <br />
<br />
Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
Yes, but at our own pace. The objectives were completed by going through the deliverables for each members. <br />
<br />
Reflection on the Process<br />
<br />
What did you learn?<br />
<br />
With your head (biological or computer science principles)<br />
<br />
Connecting the affects of arsenic to budding yeast<br />
<br />
With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
<br />
Teamwork and collaborating with others by contributing my own section of work with theirs to form an overall analysis of the data. <br />
<br />
With your hands (technical skills)?<br />
<br />
Formatting the database column titles <br />
<br />
What lesson will you take away from this project that you will still use a year from now?<br />
<br />
It's important to ask questions when struggling with something new, for example a database format you are not familiar with. It's not a bad thing to ask questions, and it doesn't mean you are unaware of what is happening. Questions help with understanding making it easier for the student to present on the material.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:02, 9 December 2019 (PST)</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_15&diff=7704Ntesfaio Week 152019-12-10T04:09:12Z<p>Ntesfaio: /* References */ added two references</p>
<hr />
<div>Electronic Notebook<br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment was to finalize the deliverables. The deliverables ended with the making of a presentation of the re-analysis of the paper we read with a comparison of what we found. We also worked on a group report that summarizes the information.<br />
<br />
==Milestones==<br />
<br />
I completed the ACCESS datasheet along with Joey and DeLisa to hand off to our data analysts. From there the data was used to form a GRNmap.<br />
<br />
==Conclusion==<br />
<br />
This week's assignment was completed with the formation of the presentation that will be shared with the class.<br />
<br />
==References==<br />
<br />
Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006<br />
<br />
[[Sulfiknights Deliverables]]<br />
<br />
==Acknowledgments==<br />
<br />
I would like to acknowledge my teammates (The sulfiknights) as well as the other two groups for their contributions to this project. I would also like to acknowledge Dr. Dahlquist for her assistance in following the steps for this assignment <br />
<br />
"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:07, 9 December 2019 (PST)</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_15&diff=7703Ntesfaio Week 152019-12-10T04:07:53Z<p>Ntesfaio: /* Acknowledgements */ added to acknowledgement</p>
<hr />
<div>Electronic Notebook<br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment was to finalize the deliverables. The deliverables ended with the making of a presentation of the re-analysis of the paper we read with a comparison of what we found. We also worked on a group report that summarizes the information.<br />
<br />
==Milestones==<br />
<br />
I completed the ACCESS datasheet along with Joey and DeLisa to hand off to our data analysts. From there the data was used to form a GRNmap.<br />
<br />
==Conclusion==<br />
<br />
This week's assignment was completed with the formation of the presentation that will be shared with the class.<br />
<br />
==References==<br />
<br />
==Acknowledgments==<br />
<br />
I would like to acknowledge my teammates (The sulfiknights) as well as the other two groups for their contributions to this project. I would also like to acknowledge Dr. Dahlquist for her assistance in following the steps for this assignment <br />
<br />
"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:07, 9 December 2019 (PST)</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_15&diff=7700Ntesfaio Week 152019-12-10T04:06:18Z<p>Ntesfaio: /* Conclusion */ added to conclusion</p>
<hr />
<div>Electronic Notebook<br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment was to finalize the deliverables. The deliverables ended with the making of a presentation of the re-analysis of the paper we read with a comparison of what we found. We also worked on a group report that summarizes the information.<br />
<br />
==Milestones==<br />
<br />
I completed the ACCESS datasheet along with Joey and DeLisa to hand off to our data analysts. From there the data was used to form a GRNmap.<br />
<br />
==Conclusion==<br />
<br />
This week's assignment was completed with the formation of the presentation that will be shared with the class.<br />
<br />
==References==<br />
<br />
==Acknowledgements==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_15&diff=7699Ntesfaio Week 152019-12-10T04:05:44Z<p>Ntesfaio: /* Milestones */ added to milestone</p>
<hr />
<div>Electronic Notebook<br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment was to finalize the deliverables. The deliverables ended with the making of a presentation of the re-analysis of the paper we read with a comparison of what we found. We also worked on a group report that summarizes the information.<br />
<br />
==Milestones==<br />
<br />
I completed the ACCESS datasheet along with Joey and DeLisa to hand off to our data analysts. From there the data was used to form a GRNmap.<br />
<br />
==Conclusion==<br />
<br />
==References==<br />
<br />
==Acknowledgements==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_15&diff=7698Ntesfaio Week 152019-12-10T04:04:53Z<p>Ntesfaio: /* Purpose */ added to purpose</p>
<hr />
<div>Electronic Notebook<br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment was to finalize the deliverables. The deliverables ended with the making of a presentation of the re-analysis of the paper we read with a comparison of what we found. We also worked on a group report that summarizes the information.<br />
<br />
==Milestones==<br />
<br />
==Conclusion==<br />
<br />
==References==<br />
<br />
==Acknowledgements==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_15&diff=7697Ntesfaio Week 152019-12-10T04:02:01Z<p>Ntesfaio: added sections for electronic notebook</p>
<hr />
<div>Electronic Notebook<br />
<br />
==Purpose==<br />
<br />
==Milestones==<br />
<br />
==Conclusion==<br />
<br />
==References==<br />
<br />
==Acknowledgements==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Template:Ntesfaio&diff=7696Template:Ntesfaio2019-12-10T04:00:27Z<p>Ntesfaio: added a week 15 section</p>
<hr />
<div>[[Main Page|Bio DB Home page]]<br />
<br />
[[Template:Ntesfaio]]<br />
<br />
'''[[Week 1]]'''<br />
<br />
[[User:Ntesfaio]]<br />
<br />
[[:Class Journal Week 1]]<br />
<br />
'''[[Week 2]]'''<br />
<br />
[[Ntesfaio Week 2]]<br />
<br />
[[Class Journal Week 2]]<br />
<br />
[[Category: Journal Entry]]<br />
<br />
'''[[Week 3]]'''<br />
<br />
[[RAD53 / YPL153C Week 3]]<br />
<br />
[[Class Journal Week 3]]<br />
<br />
<br />
'''[[Week 4]]'''<br />
<br />
[[Ntesfaio Week 4]]<br />
<br />
[[Class Journal Week 4]]<br />
<br />
'''[[Week 5]]'''<br />
<br />
[[DrugCentral Week 5]]<br />
<br />
[[Class Journal Week 5]]<br />
<br />
'''[[Week 6]]'''<br />
<br />
[[Ntesfaio Week 6]]<br />
<br />
[[Class Journal Week 6]]<br />
<br />
'''[[Week 7]]'''<br />
<br />
[[Ntesfaio Week 7]]<br />
<br />
[[Class Journal Week 7]]<br />
<br />
'''[[Week 8]]'''<br />
<br />
[[Ntesfaio Week 8]]<br />
<br />
[[Class Journal Week 8]]<br />
<br />
'''[[Week 9]]'''<br />
<br />
[[Ntesfaio Week 9]]<br />
<br />
[[Class Journal Week 9]]<br />
<br />
'''[[Week 10]]'''<br />
<br />
[[Ntesfaio Week 10]]<br />
<br />
'''[[Week 11]]'''<br />
<br />
[[Ntesfaio Week 11]]<br />
<br />
[[Sulfiknights]]<br />
<br />
'''[[Week 12/13]]'''<br />
<br />
[[Ntesfaio Week 12/13]]<br />
<br />
[[Sulfiknights]]<br />
<br />
[[Sulfiknights Deliverables]]<br />
<br />
[[Ntesfaio Week 15]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7695Sulfiknights Deliverables2019-12-10T03:56:07Z<p>Ntesfaio: /* Electronic notebook corresponding to the microarray results files */ added my week 12/13 DA</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Checklist:==<br />
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''INCOMPLETE'''<br />
#Group Report (.doc, .docx or .pdf file) '''INCOMPLETE'''<br />
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''INCOMPLETE'''<br />
#Group PowerPoint presentation (given on Tuesday, December 10, .ppt, .pptx or .pdf file) '''INCOMPLETE'''<br />
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx) '''COMPLETE'''<br />
#PowerPoint of ANOVA table, screenshots of stem results (.pptx), screenshot of black and white GRNsight input network and colored GRNsight output networks '''COMPLETE'''<br />
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) '''COMPLETE'''<br />
#YEASTRACT "rank by TF" results (.xlsx) '''COMPLETE'''<br />
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''COMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''COMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''COMPLETE'''<br />
#ReadMe for the database that describes the design of the database, references the sources of the data, and has a database schema diagram (.doc, .docx, .pdf) '''INCOMPLETE'''<br />
#Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, .txt) '''COMPLETE'''<br />
#Electronic notebook corresponding to these the microarray results files (Week 12/13 and Week 15) to support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results. '''INCOMPLETE'''<br />
<br />
==Group Report==<br />
==Individual Statements of Work, Assessments, Reflections==<br />
==Group Powerpoint Presentation==<br />
==Excel Spreadsheet with ANOVA Results/STEM Formatting==<br />
[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
<br />
==PowerPoint of ANOVA Table...==<br />
[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
<br />
[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]]<br />
<br />
[[Image:Profil923_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored_GRNsight_923.PNG|500px]]<br />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Image:Profile4048_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored GRNsight 4048.PNG|500px]]<br />
<br />
==Gene List and GO List files==<br />
[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]<br />
<br />
[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
<br />
==YEASTRACT "Rank by TF" Results==<br />
[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
<br />
[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
<br />
==GRNmap input workbook==<br />
[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet: Profiles 40 and 48]]<br />
<br />
==GRNmap output workbook and output plots==<br />
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048_output.zip|GRNmap Output Files: Profiles 40 and 48]]<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==ReadMe==<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
'''Profiles 9 and 23:'''<br />
<br />
[[Image:Productionrates_923_querydesign.PNG|350]]<br />
[[Image:Degradationrates_923_querydesign.PNG|350]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|350]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|350]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG]]<br />
<br />
==Electronic notebook corresponding to the microarray results files==<br />
'''Electronic notebook for Data Analysts:'''<br />
<br />
[[Sulfiknights DA Week 12/13]]<br />
<br />
[[Sulfiknights DA Week 14]]<br />
<br />
'''Electronic notebook for Quality Assurance'''<br />
<br />
[[Ntesfaio Week 12/13]]<br />
<br />
<br />
'''Electronic notebook for Designer'''<br />
<br />
==Merge completed databases into a single database==<br />
[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
==Final Reflection==<br />
===Marcus Avila's Final Reflection===<br />
==== Individual Assessment and Reflection ====<br />
===== Statement of Work =====<br />
<br />
* Describe exactly what you did on the project.<br />
** For the project I worked with Ivy to decide how to organize the Thorsen data to run an ANOVA. After doing the ANOVA and running STEM, I then downloaded the gene lists for Profiles #40 & #48 and combined them to "Rank by TF" on YEASTRACT. Next, I chose the 15 most significant transcription factors to include on the network.<br />
* Provide references or links to artifacts of your work, such as:<br />
** Wiki pages<br />
** Other files or documents<br />
** Code or scripts<br />
<br />
===== Assessment of Project =====<br />
<br />
* Give an objective assessment of the success of your project workflow and teamwork. <br />
* What worked and what didn't work? <br />
* What would you do differently if you could do it all over again?<br />
* Evaluate your team’s portion of the Final Project and Group Report in the following areas:<br />
*# Content: What is the quality of the work? <br />
*# Organization: Comment on the organization of the project and of your group's wiki pages.<br />
*# Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
===== Reflection on the Process =====<br />
<br />
* What did you learn?<br />
** With your head (biological or computer science principles)<br />
** With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
** With your hands (technical skills)?<br />
* What lesson will you take away from this project that you will still use a year from now?<br />
<br />
===Naomi Tesfaiohannes's Reflection===<br />
<br />
'''Statement of Work'''<br />
<br />
Describe exactly what you did on the project.<br />
<br />
My role as a QA was to work with DeLisa and Joey on the ACCESS datasheet so that the data analysts (Marcus and Ivy) had the information necessary to do GRNmap. <br />
<br />
'''Provide references or links to artifacts of your work, such as:'''<br />
<br />
[[Sulfiknights]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
'''Give an objective assessment of the success of your project workflow and teamwork.'''<br />
<br />
What worked and what didn't work?<br />
<br />
What worked was meeting outside of class and keeping in touch with progress by using the group chat<br />
What didn't work was sometimes not being able to answer each other's questions. Leaving us all confused. <br />
<br />
What would you do differently if you could do it all over again?<br />
<br />
Ask more questions about analyzing new data instead of trying to figure it out on my own. <br />
<br />
'''Evaluate your team’s portion of the Final Project and Group Report in the following areas:'''<br />
<br />
Content: What is the quality of the work?<br />
<br />
Our work is a reflection of the collaborative effort from all of the team members in trying to understand the new data we reanalyzed. <br />
<br />
Organization: Comment on the organization of the project and of your group's wiki pages.<br />
<br />
Our group stayed organized by splitting up what sections we would work on. That way we could come together at the end of the slides to review what still needs to be understood. <br />
<br />
Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
Yes, but at our own pace. The objectives were completed by going through the deliverables for each members. <br />
<br />
Reflection on the Process<br />
<br />
What did you learn?<br />
<br />
With your head (biological or computer science principles)<br />
<br />
Connecting the affects of arsenic to budding yeast<br />
<br />
With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
<br />
Teamwork and collaborating with others by contributing my own section of work with theirs to form an overall analysis of the data. <br />
<br />
With your hands (technical skills)?<br />
<br />
Formatting the database column titles <br />
<br />
What lesson will you take away from this project that you will still use a year from now?<br />
<br />
It's important to ask questions when struggling with something new, for example a database format you are not familiar with. It's not a bad thing to ask questions, and it doesn't mean you are unaware of what is happening. Questions help with understanding making it easier for the student to present on the material.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:02, 9 December 2019 (PST)</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Template:Ntesfaio&diff=7693Template:Ntesfaio2019-12-10T02:05:26Z<p>Ntesfaio: added deliverables page</p>
<hr />
<div>[[Main Page|Bio DB Home page]]<br />
<br />
[[Template:Ntesfaio]]<br />
<br />
'''[[Week 1]]'''<br />
<br />
[[User:Ntesfaio]]<br />
<br />
[[:Class Journal Week 1]]<br />
<br />
'''[[Week 2]]'''<br />
<br />
[[Ntesfaio Week 2]]<br />
<br />
[[Class Journal Week 2]]<br />
<br />
[[Category: Journal Entry]]<br />
<br />
'''[[Week 3]]'''<br />
<br />
[[RAD53 / YPL153C Week 3]]<br />
<br />
[[Class Journal Week 3]]<br />
<br />
<br />
'''[[Week 4]]'''<br />
<br />
[[Ntesfaio Week 4]]<br />
<br />
[[Class Journal Week 4]]<br />
<br />
'''[[Week 5]]'''<br />
<br />
[[DrugCentral Week 5]]<br />
<br />
[[Class Journal Week 5]]<br />
<br />
'''[[Week 6]]'''<br />
<br />
[[Ntesfaio Week 6]]<br />
<br />
[[Class Journal Week 6]]<br />
<br />
'''[[Week 7]]'''<br />
<br />
[[Ntesfaio Week 7]]<br />
<br />
[[Class Journal Week 7]]<br />
<br />
'''[[Week 8]]'''<br />
<br />
[[Ntesfaio Week 8]]<br />
<br />
[[Class Journal Week 8]]<br />
<br />
'''[[Week 9]]'''<br />
<br />
[[Ntesfaio Week 9]]<br />
<br />
[[Class Journal Week 9]]<br />
<br />
'''[[Week 10]]'''<br />
<br />
[[Ntesfaio Week 10]]<br />
<br />
'''[[Week 11]]'''<br />
<br />
[[Ntesfaio Week 11]]<br />
<br />
[[Sulfiknights]]<br />
<br />
'''[[Week 12/13]]'''<br />
<br />
[[Ntesfaio Week 12/13]]<br />
<br />
[[Sulfiknights]]<br />
<br />
[[Sulfiknights Deliverables]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7692Sulfiknights Deliverables2019-12-10T02:02:42Z<p>Ntesfaio: /* Naomi Tesfaiohannes's Reflection */ added to reflection</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Checklist:==<br />
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''INCOMPLETE'''<br />
#Group Report (.doc, .docx or .pdf file) '''INCOMPLETE'''<br />
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''INCOMPLETE'''<br />
#Group PowerPoint presentation (given on Tuesday, December 10, .ppt, .pptx or .pdf file) '''INCOMPLETE'''<br />
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx) '''COMPLETE'''<br />
#PowerPoint of ANOVA table, screenshots of stem results (.pptx), screenshot of black and white GRNsight input network and colored GRNsight output networks '''COMPLETE'''<br />
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) '''COMPLETE'''<br />
#YEASTRACT "rank by TF" results (.xlsx) '''COMPLETE'''<br />
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''COMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''COMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''COMPLETE'''<br />
#ReadMe for the database that describes the design of the database, references the sources of the data, and has a database schema diagram (.doc, .docx, .pdf) '''INCOMPLETE'''<br />
#Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, .txt) '''COMPLETE'''<br />
#Electronic notebook corresponding to these the microarray results files (Week 12/13 and Week 15) to support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results. '''INCOMPLETE'''<br />
<br />
==Group Report==<br />
==Individual Statements of Work, Assessments, Reflections==<br />
==Group Powerpoint Presentation==<br />
==Excel Spreadsheet with ANOVA Results/STEM Formatting==<br />
[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
<br />
==PowerPoint of ANOVA Table...==<br />
[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
<br />
[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]]<br />
<br />
[[Image:Profil923_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored_GRNsight_923.PNG|500px]]<br />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Image:Profile4048_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored GRNsight 4048.PNG|500px]]<br />
<br />
==Gene List and GO List files==<br />
[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]<br />
<br />
[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
<br />
==YEASTRACT "Rank by TF" Results==<br />
[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
<br />
[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
<br />
==GRNmap input workbook==<br />
[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet: Profiles 40 and 48]]<br />
<br />
==GRNmap output workbook and output plots==<br />
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048_output.zip|GRNmap Output Files: Profiles 40 and 48]]<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==ReadMe==<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
'''Profiles 9 and 23:'''<br />
<br />
[[Image:Productionrates_923_querydesign.PNG|350]]<br />
[[Image:Degradationrates_923_querydesign.PNG|350]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|350]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|350]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG]]<br />
<br />
==Electronic notebook corresponding to the microarray results files==<br />
'''Electronic notebook for Data Analysts:'''<br />
<br />
[[Sulfiknights DA Week 12/13]]<br />
<br />
[[Sulfiknights DA Week 14]]<br />
<br />
'''Electronic notebook for Quality Assurance'''<br />
<br />
'''Electronic notebook for Designer'''<br />
<br />
==Merge completed databases into a single database==<br />
[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
==Final Reflection==<br />
===Marcus Avila's Final Reflection===<br />
==== Individual Assessment and Reflection ====<br />
===== Statement of Work =====<br />
<br />
* Describe exactly what you did on the project.<br />
** For the project I worked with Ivy to decide how to organize the Thorsen data to run an ANOVA. After running the ANOVA we went on to <br />
* Provide references or links to artifacts of your work, such as:<br />
** Wiki pages<br />
** Other files or documents<br />
** Code or scripts<br />
<br />
===== Assessment of Project =====<br />
<br />
* Give an objective assessment of the success of your project workflow and teamwork. <br />
* What worked and what didn't work? <br />
* What would you do differently if you could do it all over again?<br />
* Evaluate your team’s portion of the Final Project and Group Report in the following areas:<br />
*# Content: What is the quality of the work? <br />
*# Organization: Comment on the organization of the project and of your group's wiki pages.<br />
*# Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
===== Reflection on the Process =====<br />
<br />
* What did you learn?<br />
** With your head (biological or computer science principles)<br />
** With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
** With your hands (technical skills)?<br />
* What lesson will you take away from this project that you will still use a year from now?<br />
<br />
===Naomi Tesfaiohannes's Reflection===<br />
<br />
'''Statement of Work'''<br />
<br />
Describe exactly what you did on the project.<br />
<br />
My role as a QA was to work with DeLisa and Joey on the ACCESS datasheet so that the data analysts (Marcus and Ivy) had the information necessary to do GRNmap. <br />
<br />
'''Provide references or links to artifacts of your work, such as:'''<br />
<br />
[[Sulfiknights]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
'''Give an objective assessment of the success of your project workflow and teamwork.'''<br />
<br />
What worked and what didn't work?<br />
<br />
What worked was meeting outside of class and keeping in touch with progress by using the group chat<br />
What didn't work was sometimes not being able to answer each other's questions. Leaving us all confused. <br />
<br />
What would you do differently if you could do it all over again?<br />
<br />
Ask more questions about analyzing new data instead of trying to figure it out on my own. <br />
<br />
'''Evaluate your team’s portion of the Final Project and Group Report in the following areas:'''<br />
<br />
Content: What is the quality of the work?<br />
<br />
Our work is a reflection of the collaborative effort from all of the team members in trying to understand the new data we reanalyzed. <br />
<br />
Organization: Comment on the organization of the project and of your group's wiki pages.<br />
<br />
Our group stayed organized by splitting up what sections we would work on. That way we could come together at the end of the slides to review what still needs to be understood. <br />
<br />
Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
<br />
Yes, but at our own pace. The objectives were completed by going through the deliverables for each members. <br />
<br />
Reflection on the Process<br />
<br />
What did you learn?<br />
<br />
With your head (biological or computer science principles)<br />
<br />
Connecting the affects of arsenic to budding yeast<br />
<br />
With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
<br />
Teamwork and collaborating with others by contributing my own section of work with theirs to form an overall analysis of the data. <br />
<br />
With your hands (technical skills)?<br />
<br />
Formatting the database column titles <br />
<br />
What lesson will you take away from this project that you will still use a year from now?<br />
<br />
It's important to ask questions when struggling with something new, for example a database format you are not familiar with. It's not a bad thing to ask questions, and it doesn't mean you are unaware of what is happening. Questions help with understanding making it easier for the student to present on the material.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:02, 9 December 2019 (PST)</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7690Sulfiknights Deliverables2019-12-10T01:32:44Z<p>Ntesfaio: /* Final Reflection */ added reflection</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Checklist:==<br />
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''INCOMPLETE'''<br />
#Group Report (.doc, .docx or .pdf file) '''INCOMPLETE'''<br />
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''INCOMPLETE'''<br />
#Group PowerPoint presentation (given on Tuesday, December 10, .ppt, .pptx or .pdf file) '''INCOMPLETE'''<br />
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx) '''COMPLETE'''<br />
#PowerPoint of ANOVA table, screenshots of stem results (.pptx), screenshot of black and white GRNsight input network and colored GRNsight output networks '''COMPLETE'''<br />
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) '''COMPLETE'''<br />
#YEASTRACT "rank by TF" results (.xlsx) '''COMPLETE'''<br />
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''COMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''COMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''COMPLETE'''<br />
#ReadMe for the database that describes the design of the database, references the sources of the data, and has a database schema diagram (.doc, .docx, .pdf) '''INCOMPLETE'''<br />
#Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, .txt) '''COMPLETE'''<br />
#Electronic notebook corresponding to these the microarray results files (Week 12/13 and Week 15) to support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results. '''INCOMPLETE'''<br />
<br />
==Group Report==<br />
==Individual Statements of Work, Assessments, Reflections==<br />
==Group Powerpoint Presentation==<br />
==Excel Spreadsheet with ANOVA Results/STEM Formatting==<br />
[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
<br />
==PowerPoint of ANOVA Table...==<br />
[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
<br />
[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]]<br />
<br />
[[Image:Profil923_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored_GRNsight_923.PNG|500px]]<br />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Image:Profile4048_GRNsight_matrix.PNG|500px]]<br />
[[Image:Colored GRNsight 4048.PNG|500px]]<br />
<br />
==Gene List and GO List files==<br />
[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]]<br />
<br />
[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
<br />
==YEASTRACT "Rank by TF" Results==<br />
[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
<br />
[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
<br />
==GRNmap input workbook==<br />
[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048 input worksheet.xlsx|GRNmap Input Worksheet: Profiles 40 and 48]]<br />
<br />
==GRNmap output workbook and output plots==<br />
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap4048_output.zip|GRNmap Output Files: Profiles 40 and 48]]<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==ReadMe==<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
'''Profiles 9 and 23:'''<br />
<br />
[[Image:Productionrates_923_querydesign.PNG|350]]<br />
[[Image:Degradationrates_923_querydesign.PNG|350]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|350]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|350]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG]]<br />
<br />
==Electronic notebook corresponding to the microarray results files==<br />
'''Electronic notebook for Data Analysts:'''<br />
<br />
[[Sulfiknights DA Week 12/13]]<br />
<br />
[[Sulfiknights DA Week 14]]<br />
<br />
'''Electronic notebook for Quality Assurance'''<br />
<br />
'''Electronic notebook for Designer'''<br />
<br />
==Merge completed databases into a single database==<br />
[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ]]<br />
<br />
[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
<br />
==Final Reflection==<br />
===Marcus Avila's Final Reflection===<br />
<br />
===Naomi Tesfaiohannes's Reflection===</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7348Ntesfaio Week 12/132019-11-26T05:21:22Z<p>Ntesfaio: /* References */ added article reference</p>
<hr />
<div>==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks.<br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment is to continue building on the team's wiki page and to progress through the milestones for each of the categories.<br />
<br />
==Methods==<br />
<br />
* Downloaded the information from the article link<br />
<br />
* Put the information into one excel worksheet<br />
<br />
* Ran an ANOVA <br />
<br />
==Conclusion==<br />
<br />
This week's assignment led to more work being done to complete the milestones. By running the ANOVA we are now ready to go onto STEM. <br />
<br />
==Acknowledgments==<br />
<br />
My homework partners this week were User:Jnimmers (Quality Assurance), User:Imacarae (Data Analysis), User:Mavila9 (Data Analysis), and User:Dmadere (Designer). We continued working on our Team page and the milestones following the downloading of the excel spreadsheet values.<br />
<br />
LMU BioDB 2019. (2019). Week 12/13. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13 <br />
<br />
'''"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."''' [[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 10:53, 25 November 2019 (PST)<br />
<br />
==References==<br />
<br />
Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006<br />
<br />
https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13<br />
<br />
https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Sulfiknights<br />
<br />
File:NtesfaioThorsen 2007 PMID 17327492 (1).zip<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights&diff=7347Sulfiknights2019-11-26T05:20:03Z<p>Ntesfaio: /* Naomi Tesfaiohannes */ added to what worked</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
Create a schedule by Tuesday, November 26 that has goals for each member of the Sulfiknights team. Though this may not be completely followed day-by-day it is still helpful to have a outline of checkpoints that should be met for completing this assignment. <br />
<br />
Check in with the members of the team to assist in making sure the assignment is complete.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:44, 21 November 2019 (PST)<br />
<br />
===Quality Assurance===<br />
<br />
As on Thursday, November 21st the Quality Assurance guilds were an intermediate for our designer (DeLisa) and our Data Analysts (Marcus and Ivy). <br />
<br />
Our goal before Tuesday, November 26 is to assist the Data Analysts in running an ANOVA and running stem. As for Quality Assurance we have completed Milestone 4 and are moving onto Milestone 5 as of Thursday, November 21st.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:40, 23 November 2019 (PST)<br />
<br />
===Data Analysis===<br />
<br />
<br />
===Coder/Designer===<br />
<br />
<br />
==Team Journal Assignments==<br />
===Week 12/13===<br />
====Naomi Tesfaiohannes====<br />
<br />
Each team member should reflect on the team's progress:<br />
<br />
What worked?<br />
<br />
Working together in class and taking advantage of asking questions while going through the assignment <br />
<br />
What didn't work?<br />
<br />
Not working on a shared document or excel workbook because progress could be made on one and not seen by the other partner. Also the metasheet was difficult to put together because of the inconsistent datapoints between the groups. <br />
<br />
What will I do next to fix what didn't work?<br />
<br />
Continue communicating with my team on how we want to progress through with the assignment<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 21:20, 25 November 2019 (PST)<br />
<br />
====Ivy Macaraeg====<br />
#What worked?<br />
#*We figured out what we needed to be working on, and that helped get us going even more than before. <br />
#What didn't work?<br />
#*We had some trouble organizing the data in a way that would be clear but compatible with future programs.<br />
#What will I do next to fix what didn't work?<br />
#*I think sticking to the directions and making sure that we are thorough will help us.<br />
====John Nimmers-Minor====<br />
Each team member should reflect on the team's progress:<br />
<br />
What worked?<br />
<br />
A. Splitting up the work and knowing exactly what each role was in charge of helped tremendously this week.<br />
<br />
What didn't work?<br />
<br />
A. Having two people work on the exact same task didn't help because one of those two individuals could have potentially been working on a separate piece of the project.<br />
<br />
What will I do next to fix what didn't work?<br />
<br />
A. Communication throughout the project group will make sure that two people are not doing the same thing at the same time unnecesarily. This will allow us to complete more tasks in a shorter amount of time.<br />
<br />
===Week 11===<br />
====Naomi Tesfaiohannes====<br />
Each team member should reflect on the team's progress:<br />
<br />
*What worked?<br />
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure. <br />
<br />
*What didn't work?<br />
My time management due to other coursework<br />
<br />
*What will I do next to fix what didn't work?<br />
Have a better control of what work I put in each day for this assignment<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)<br />
====Joey Nimmers-Minor====<br />
*What worked?<br />
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.<br />
*What didn't work?<br />
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week<br />
*What will I do next to fix what didn't work?<br />
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.<br />
<br />
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)<br />
====Marcus Avila====<br />
# What worked?<br />
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.<br />
# What didn't work?<br />
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.<br />
# What will I do next to fix what didn't work?<br />
#* Next time I will allocate more time to the assignment.<br />
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)<br />
====DeLisa Madere====<br />
<br />
'''What Worked?'''<br />
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.<br />
<br />
'''What didn't work?'''<br />
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.<br />
<br />
'''What will I do next to fix what didn't work?'''<br />
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.<br />
====Ivy Macaraeg====<br />
*What worked?<br />
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out. <br />
*What didn't work?<br />
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it. <br />
*What will I do next to fix what didn't work?<br />
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.<br />
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)<br />
<br />
==Annotated Bibliography Sources==<br />
===DeLisa Madere===<br />
<br />
1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938<br />
<br />
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x<br />
===Naomi Tesfaiohannes===<br />
<br />
1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013<br />
<br />
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003<br />
===Ivy Macaraeg===<br />
<br />
1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712<br />
<br />
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5<br />
===Marcus Avila===<br />
<br />
1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98<br />
<br />
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0<br />
===John Nimmers-Minor===<br />
<br />
1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005<br />
<br />
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x<br />
<br />
==Data/Files==<br />
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]<br />
*Other files can be found on our [[Sulfiknights Deliverables|deliverables page]]<br />
<br />
==References==<br />
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006<br />
<br />
<br />
<br />
[[Category:Group Projects]]<br />
[[Category:Sulfiknights]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7346Ntesfaio Week 12/132019-11-26T05:16:20Z<p>Ntesfaio: added to conclusion added to acknowledgments</p>
<hr />
<div>==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks.<br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment is to continue building on the team's wiki page and to progress through the milestones for each of the categories.<br />
<br />
==Methods==<br />
<br />
* Downloaded the information from the article link<br />
<br />
* Put the information into one excel worksheet<br />
<br />
* Ran an ANOVA <br />
<br />
==Conclusion==<br />
<br />
This week's assignment led to more work being done to complete the milestones. By running the ANOVA we are now ready to go onto STEM. <br />
<br />
==Acknowledgments==<br />
<br />
My homework partners this week were User:Jnimmers (Quality Assurance), User:Imacarae (Data Analysis), User:Mavila9 (Data Analysis), and User:Dmadere (Designer). We continued working on our Team page and the milestones following the downloading of the excel spreadsheet values.<br />
<br />
LMU BioDB 2019. (2019). Week 12/13. Retrieved November 25, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13 <br />
<br />
'''"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."''' [[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 10:53, 25 November 2019 (PST)<br />
<br />
==References==<br />
<br />
https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13<br />
<br />
https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Sulfiknights<br />
<br />
File:NtesfaioThorsen 2007 PMID 17327492 (1).zip<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:NtesfaioThorsen_2007_PMID_17327492_(1).zip&diff=7345File:NtesfaioThorsen 2007 PMID 17327492 (1).zip2019-11-26T05:14:59Z<p>Ntesfaio: added a zip file</p>
<hr />
<div>== Summary ==<br />
added a zip file</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7257Ntesfaio Week 12/132019-11-25T18:53:00Z<p>Ntesfaio: /* Acknowledgments */ added signature</p>
<hr />
<div>==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks.<br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment is to continue building on the team's wiki page and to progress through the milestones for each of the categories.<br />
<br />
==Acknowledgments==<br />
<br />
My homework partners this week were User:Jnimmers (Quality Assurance), User:Imacarae (Data Analysis), User:Mavila9 (Data Analysis), and User:Dmadere (Designer). We continued working on our Team page and the milestones following the downloading of the excel spreadsheet values.<br />
<br />
'''"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."''' [[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 10:53, 25 November 2019 (PST)<br />
<br />
==References==<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7256Ntesfaio Week 12/132019-11-25T18:52:40Z<p>Ntesfaio: added to acknowledgement</p>
<hr />
<div>==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks.<br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment is to continue building on the team's wiki page and to progress through the milestones for each of the categories.<br />
<br />
==Acknowledgments==<br />
<br />
My homework partners this week were User:Jnimmers (Quality Assurance), User:Imacarae (Data Analysis), User:Mavila9 (Data Analysis), and User:Dmadere (Designer). We continued working on our Team page and the milestones following the downloading of the excel spreadsheet values.<br />
<br />
'''"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."'''<br />
<br />
==References==<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7255Ntesfaio Week 12/132019-11-25T18:46:09Z<p>Ntesfaio: /* Acknowledgments */ added to acknowledgements</p>
<hr />
<div>==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks.<br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment is to continue building on the team's wiki page and to progress through the milestones for each of the categories.<br />
<br />
==Acknowledgments==<br />
<br />
My homework partners this week were User:Jnimmers (Quality Assurance), User:Imacarae (Data Analysis), User:Mavila9 (Data Analysis), and User:Dmadere (Designer). We continued working on our Team page and the milestones following the downloading of the excel spreadsheet values.<br />
<br />
==References==<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7254Ntesfaio Week 12/132019-11-25T18:35:43Z<p>Ntesfaio: rearranged page</p>
<hr />
<div>==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks.<br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment is to continue building on the team's wiki page and to progress through the milestones for each of the categories.<br />
<br />
==Acknowledgments==<br />
<br />
==References==<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7253Ntesfaio Week 12/132019-11-25T18:33:42Z<p>Ntesfaio: /* Purpose */ added to purpose</p>
<hr />
<div>==Electronic Lab Notebook==<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks.<br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
==Purpose==<br />
<br />
The purpose of this week's assignment is to continue building on the team's wiki page and to progress through the milestones for each of the categories.<br />
<br />
==Methods and Results==<br />
<br />
==Data==<br />
<br />
==Conclusion==<br />
<br />
===Week 12/13 Milestones===<br />
<br />
<br />
<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7252Ntesfaio Week 12/132019-11-25T16:22:44Z<p>Ntesfaio: /* Project Manager */ added to first #</p>
<hr />
<div>==Electronic Lab Notebook==<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks.<br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
==Purpose==<br />
<br />
==Methods and Results==<br />
<br />
==Data==<br />
<br />
==Conclusion==<br />
<br />
===Week 12/13 Milestones===<br />
<br />
<br />
<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7251Ntesfaio Week 12/132019-11-25T16:22:12Z<p>Ntesfaio: added to electronic lab notebook section</p>
<hr />
<div>==Electronic Lab Notebook==<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks. <br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
==Purpose==<br />
<br />
==Methods and Results==<br />
<br />
==Data==<br />
<br />
==Conclusion==<br />
<br />
===Week 12/13 Milestones===<br />
<br />
<br />
<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7250Ntesfaio Week 12/132019-11-25T16:21:22Z<p>Ntesfaio: added the sections to individuals wiki page</p>
<hr />
<div>==Electronic Lab Notebook==<br />
<br />
==Purpose==<br />
<br />
==Methods and Results==<br />
<br />
==Data==<br />
<br />
==Conclusion==<br />
<br />
===Week 12/13 Milestones===<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks. <br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights&diff=7247Sulfiknights2019-11-24T02:40:50Z<p>Ntesfaio: /* Quality Assurance */ added to sulfiknights</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
Create a schedule by Tuesday, November 26 that has goals for each member of the Sulfiknights team. Though this may not be completely followed day-by-day it is still helpful to have a outline of checkpoints that should be met for completing this assignment. <br />
<br />
Check in with the members of the team to assist in making sure the assignment is complete.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:44, 21 November 2019 (PST)<br />
<br />
===Quality Assurance===<br />
<br />
As on Thursday, November 21st the Quality Assurance guilds were an intermediate for our designer (DeLisa) and our Data Analysts (Marcus and Ivy). <br />
<br />
Our goal before Tuesday, November 26 is to assist the Data Analysts in running an ANOVA and running stem. As for Quality Assurance we have completed Milestone 4 and are moving onto Milestone 5 as of Thursday, November 21st.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:40, 23 November 2019 (PST)<br />
<br />
===Data Analysis===<br />
<br />
<br />
===Coder/Designer===<br />
<br />
<br />
==Data/Files==<br />
<br />
'''[[Sulfiknights Deliverables]]'''<br />
<br />
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]<br />
<br />
==Team Journal Assignment Week 12/13==<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
Each team member should reflect on the team's progress:<br />
<br />
What worked?<br />
<br />
What didn't work?<br />
<br />
What will I do next to fix what didn't work?<br />
<br />
==Team Feedback Week 11==<br />
<br />
===Naomi Tesfaiohannes===<br />
Each team member should reflect on the team's progress:<br />
<br />
*What worked?<br />
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure. <br />
<br />
*What didn't work?<br />
My time management due to other coursework<br />
<br />
*What will I do next to fix what didn't work?<br />
Have a better control of what work I put in each day for this assignment<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Joey Nimmers-Minor===<br />
*What worked?<br />
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.<br />
*What didn't work?<br />
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week<br />
*What will I do next to fix what didn't work?<br />
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.<br />
<br />
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Marcus Avila===<br />
# What worked?<br />
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.<br />
# What didn't work?<br />
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.<br />
# What will I do next to fix what didn't work?<br />
#* Next time I will allocate more time to the assignment.<br />
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)<br />
<br />
===DeLisa Madere===<br />
<br />
'''What Worked?'''<br />
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.<br />
<br />
'''What didn't work?'''<br />
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.<br />
<br />
'''What will I do next to fix what didn't work?'''<br />
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.<br />
<br />
===Ivy Macaraeg===<br />
*What worked?<br />
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out. <br />
*What didn't work?<br />
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it. <br />
*What will I do next to fix what didn't work?<br />
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.<br />
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)<br />
<br />
==Annotated Bibliography Sources==<br />
<br />
===DeLisa Madere===<br />
<br />
1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938<br />
<br />
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013<br />
<br />
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003<br />
<br />
===Ivy Macaraeg===<br />
<br />
1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712<br />
<br />
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5<br />
<br />
===Marcus Avila===<br />
<br />
1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98<br />
<br />
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0<br />
<br />
===John Nimmers-Minor===<br />
<br />
1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005<br />
<br />
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x<br />
<br />
==References==<br />
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006<br />
<br />
<br />
<br />
[[Category:Group Projects]]<br />
[[Category:Sulfiknights]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7246Ntesfaio Week 12/132019-11-24T02:39:54Z<p>Ntesfaio: /* Week 12/13 Milestones */ added to milestones</p>
<hr />
<div>==Electronic Lab Notebook==<br />
<br />
===Week 12/13 Milestones===<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks. <br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7245Ntesfaio Week 12/132019-11-24T02:39:32Z<p>Ntesfaio: /* Week 12/13 Milestones */ added signature and position tdescription for week 12/13</p>
<hr />
<div>==Electronic Lab Notebook==<br />
<br />
==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
# This week, my role as project manager was to oversee the progress of the team's work. I also worked with communicating with the other project managers to have a consistent meta spreadsheet of all our information. My role will continue by working with all members of the team with check ins and forming the schedule needed to complete all the tasks. <br />
<br />
===Quality Assurance===<br />
<br />
# This week, my role as a quality assurance guild was to work alongside the data analysts in going through the excel spreadsheet. While doing this, I worked with the designer on contributing to the class meta spreadsheet so that our information was consistent with the two groups. <br />
<br />
<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 18:39, 23 November 2019 (PST)<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights&diff=7244Sulfiknights2019-11-22T04:48:31Z<p>Ntesfaio: /* Quality Assurance */ added to sulfiknights</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
Create a schedule by Tuesday, November 26 that has goals for each member of the Sulfiknights team. Though this may not be completely followed day-by-day it is still helpful to have a outline of checkpoints that should be met for completing this assignment. <br />
<br />
Check in with the members of the team to assist in making sure the assignment is complete.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:44, 21 November 2019 (PST)<br />
<br />
===Quality Assurance===<br />
<br />
As on Thursday, November 21st the Quality Assurance guilds (Myself and Joey) were an intermediate for our designer (DeLisa) and our Data Analysts (Marcus and Ivy). <br />
<br />
Our goal before Tuesday, November 26 is to assist the Data Analysts in running an ANOVA and running stem. As for Quality Assurance we have completed Milestone 4 and are moving onto Milestone 5 as of Thursday, November 21st.<br />
<br />
===Data Analysis===<br />
<br />
<br />
===Coder/Designer===<br />
<br />
<br />
==Data/Files==<br />
<br />
'''[[Sulfiknights Deliverables]]'''<br />
<br />
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]<br />
<br />
==Team Journal Assignment Week 12/13==<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
Each team member should reflect on the team's progress:<br />
<br />
What worked?<br />
<br />
What didn't work?<br />
<br />
What will I do next to fix what didn't work?<br />
<br />
==Team Feedback Week 11==<br />
<br />
===Naomi Tesfaiohannes===<br />
Each team member should reflect on the team's progress:<br />
<br />
*What worked?<br />
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure. <br />
<br />
*What didn't work?<br />
My time management due to other coursework<br />
<br />
*What will I do next to fix what didn't work?<br />
Have a better control of what work I put in each day for this assignment<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Joey Nimmers-Minor===<br />
*What worked?<br />
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.<br />
*What didn't work?<br />
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week<br />
*What will I do next to fix what didn't work?<br />
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.<br />
<br />
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Marcus Avila===<br />
# What worked?<br />
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.<br />
# What didn't work?<br />
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.<br />
# What will I do next to fix what didn't work?<br />
#* Next time I will allocate more time to the assignment.<br />
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)<br />
<br />
===DeLisa Madere===<br />
<br />
'''What Worked?'''<br />
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.<br />
<br />
'''What didn't work?'''<br />
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.<br />
<br />
'''What will I do next to fix what didn't work?'''<br />
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.<br />
<br />
===Ivy Macaraeg===<br />
*What worked?<br />
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out. <br />
*What didn't work?<br />
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it. <br />
*What will I do next to fix what didn't work?<br />
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.<br />
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)<br />
<br />
==Annotated Bibliography Sources==<br />
<br />
===DeLisa Madere===<br />
<br />
1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938<br />
<br />
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013<br />
<br />
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003<br />
<br />
===Ivy Macaraeg===<br />
<br />
1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712<br />
<br />
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5<br />
<br />
===Marcus Avila===<br />
<br />
1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98<br />
<br />
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0<br />
<br />
===John Nimmers-Minor===<br />
<br />
1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005<br />
<br />
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x<br />
<br />
==References==<br />
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006<br />
<br />
<br />
<br />
[[Category:Group Projects]]<br />
[[Category:Sulfiknights]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights&diff=7243Sulfiknights2019-11-22T04:44:25Z<p>Ntesfaio: /* Project Manager */ added signature</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
Create a schedule by Tuesday, November 26 that has goals for each member of the Sulfiknights team. Though this may not be completely followed day-by-day it is still helpful to have a outline of checkpoints that should be met for completing this assignment. <br />
<br />
Check in with the members of the team to assist in making sure the assignment is complete.<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 20:44, 21 November 2019 (PST)<br />
<br />
===Quality Assurance===<br />
<br />
<br />
===Data Analysis===<br />
<br />
<br />
===Coder/Designer===<br />
<br />
<br />
==Data/Files==<br />
<br />
'''[[Sulfiknights Deliverables]]'''<br />
<br />
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]<br />
<br />
==Team Journal Assignment Week 12/13==<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
Each team member should reflect on the team's progress:<br />
<br />
What worked?<br />
<br />
What didn't work?<br />
<br />
What will I do next to fix what didn't work?<br />
<br />
==Team Feedback Week 11==<br />
<br />
===Naomi Tesfaiohannes===<br />
Each team member should reflect on the team's progress:<br />
<br />
*What worked?<br />
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure. <br />
<br />
*What didn't work?<br />
My time management due to other coursework<br />
<br />
*What will I do next to fix what didn't work?<br />
Have a better control of what work I put in each day for this assignment<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Joey Nimmers-Minor===<br />
*What worked?<br />
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.<br />
*What didn't work?<br />
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week<br />
*What will I do next to fix what didn't work?<br />
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.<br />
<br />
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Marcus Avila===<br />
# What worked?<br />
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.<br />
# What didn't work?<br />
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.<br />
# What will I do next to fix what didn't work?<br />
#* Next time I will allocate more time to the assignment.<br />
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)<br />
<br />
===DeLisa Madere===<br />
<br />
'''What Worked?'''<br />
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.<br />
<br />
'''What didn't work?'''<br />
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.<br />
<br />
'''What will I do next to fix what didn't work?'''<br />
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.<br />
<br />
===Ivy Macaraeg===<br />
*What worked?<br />
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out. <br />
*What didn't work?<br />
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it. <br />
*What will I do next to fix what didn't work?<br />
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.<br />
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)<br />
<br />
==Annotated Bibliography Sources==<br />
<br />
===DeLisa Madere===<br />
<br />
1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938<br />
<br />
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013<br />
<br />
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003<br />
<br />
===Ivy Macaraeg===<br />
<br />
1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712<br />
<br />
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5<br />
<br />
===Marcus Avila===<br />
<br />
1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98<br />
<br />
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0<br />
<br />
===John Nimmers-Minor===<br />
<br />
1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005<br />
<br />
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x<br />
<br />
==References==<br />
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006<br />
<br />
<br />
<br />
[[Category:Group Projects]]<br />
[[Category:Sulfiknights]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights&diff=7242Sulfiknights2019-11-22T04:44:03Z<p>Ntesfaio: /* Project Manager */ added to milestone checks</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
Create a schedule by Tuesday, November 26 that has goals for each member of the Sulfiknights team. Though this may not be completely followed day-by-day it is still helpful to have a outline of checkpoints that should be met for completing this assignment. <br />
<br />
Check in with the members of the team to assist in making sure the assignment is complete.<br />
<br />
===Quality Assurance===<br />
<br />
<br />
===Data Analysis===<br />
<br />
<br />
===Coder/Designer===<br />
<br />
<br />
==Data/Files==<br />
<br />
'''[[Sulfiknights Deliverables]]'''<br />
<br />
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]<br />
<br />
==Team Journal Assignment Week 12/13==<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
Each team member should reflect on the team's progress:<br />
<br />
What worked?<br />
<br />
What didn't work?<br />
<br />
What will I do next to fix what didn't work?<br />
<br />
==Team Feedback Week 11==<br />
<br />
===Naomi Tesfaiohannes===<br />
Each team member should reflect on the team's progress:<br />
<br />
*What worked?<br />
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure. <br />
<br />
*What didn't work?<br />
My time management due to other coursework<br />
<br />
*What will I do next to fix what didn't work?<br />
Have a better control of what work I put in each day for this assignment<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Joey Nimmers-Minor===<br />
*What worked?<br />
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.<br />
*What didn't work?<br />
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week<br />
*What will I do next to fix what didn't work?<br />
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.<br />
<br />
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Marcus Avila===<br />
# What worked?<br />
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.<br />
# What didn't work?<br />
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.<br />
# What will I do next to fix what didn't work?<br />
#* Next time I will allocate more time to the assignment.<br />
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)<br />
<br />
===DeLisa Madere===<br />
<br />
'''What Worked?'''<br />
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.<br />
<br />
'''What didn't work?'''<br />
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.<br />
<br />
'''What will I do next to fix what didn't work?'''<br />
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.<br />
<br />
===Ivy Macaraeg===<br />
*What worked?<br />
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out. <br />
*What didn't work?<br />
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it. <br />
*What will I do next to fix what didn't work?<br />
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.<br />
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)<br />
<br />
==Annotated Bibliography Sources==<br />
<br />
===DeLisa Madere===<br />
<br />
1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938<br />
<br />
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013<br />
<br />
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003<br />
<br />
===Ivy Macaraeg===<br />
<br />
1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712<br />
<br />
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5<br />
<br />
===Marcus Avila===<br />
<br />
1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98<br />
<br />
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0<br />
<br />
===John Nimmers-Minor===<br />
<br />
1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005<br />
<br />
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x<br />
<br />
==References==<br />
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006<br />
<br />
<br />
<br />
[[Category:Group Projects]]<br />
[[Category:Sulfiknights]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights&diff=7241Sulfiknights2019-11-22T04:41:09Z<p>Ntesfaio: added week 12/13</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
<br />
===Quality Assurance===<br />
<br />
<br />
===Data Analysis===<br />
<br />
<br />
===Coder/Designer===<br />
<br />
<br />
==Data/Files==<br />
<br />
'''[[Sulfiknights Deliverables]]'''<br />
<br />
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]<br />
<br />
==Team Journal Assignment Week 12/13==<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
Each team member should reflect on the team's progress:<br />
<br />
What worked?<br />
<br />
What didn't work?<br />
<br />
What will I do next to fix what didn't work?<br />
<br />
==Team Feedback Week 11==<br />
<br />
===Naomi Tesfaiohannes===<br />
Each team member should reflect on the team's progress:<br />
<br />
*What worked?<br />
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure. <br />
<br />
*What didn't work?<br />
My time management due to other coursework<br />
<br />
*What will I do next to fix what didn't work?<br />
Have a better control of what work I put in each day for this assignment<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Joey Nimmers-Minor===<br />
*What worked?<br />
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.<br />
*What didn't work?<br />
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week<br />
*What will I do next to fix what didn't work?<br />
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.<br />
<br />
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Marcus Avila===<br />
# What worked?<br />
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.<br />
# What didn't work?<br />
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.<br />
# What will I do next to fix what didn't work?<br />
#* Next time I will allocate more time to the assignment.<br />
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)<br />
<br />
===DeLisa Madere===<br />
<br />
'''What Worked?'''<br />
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.<br />
<br />
'''What didn't work?'''<br />
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.<br />
<br />
'''What will I do next to fix what didn't work?'''<br />
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.<br />
<br />
===Ivy Macaraeg===<br />
*What worked?<br />
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out. <br />
*What didn't work?<br />
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it. <br />
*What will I do next to fix what didn't work?<br />
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.<br />
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)<br />
<br />
==Annotated Bibliography Sources==<br />
<br />
===DeLisa Madere===<br />
<br />
1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938<br />
<br />
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013<br />
<br />
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003<br />
<br />
===Ivy Macaraeg===<br />
<br />
1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712<br />
<br />
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5<br />
<br />
===Marcus Avila===<br />
<br />
1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98<br />
<br />
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0<br />
<br />
===John Nimmers-Minor===<br />
<br />
1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005<br />
<br />
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x<br />
<br />
==References==<br />
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: https://doi.org/10.1152/physiolgenomics.00236.2006<br />
<br />
<br />
<br />
[[Category:Group Projects]]<br />
[[Category:Sulfiknights]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Template:Ntesfaio&diff=7240Template:Ntesfaio2019-11-22T04:40:04Z<p>Ntesfaio: added sulfiknights</p>
<hr />
<div>[[Main Page|Bio DB Home page]]<br />
<br />
[[Template:Ntesfaio]]<br />
<br />
'''[[Week 1]]'''<br />
<br />
[[User:Ntesfaio]]<br />
<br />
[[:Class Journal Week 1]]<br />
<br />
'''[[Week 2]]'''<br />
<br />
[[Ntesfaio Week 2]]<br />
<br />
[[Class Journal Week 2]]<br />
<br />
[[Category: Journal Entry]]<br />
<br />
'''[[Week 3]]'''<br />
<br />
[[RAD53 / YPL153C Week 3]]<br />
<br />
[[Class Journal Week 3]]<br />
<br />
<br />
'''[[Week 4]]'''<br />
<br />
[[Ntesfaio Week 4]]<br />
<br />
[[Class Journal Week 4]]<br />
<br />
'''[[Week 5]]'''<br />
<br />
[[DrugCentral Week 5]]<br />
<br />
[[Class Journal Week 5]]<br />
<br />
'''[[Week 6]]'''<br />
<br />
[[Ntesfaio Week 6]]<br />
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[[Class Journal Week 6]]<br />
<br />
'''[[Week 7]]'''<br />
<br />
[[Ntesfaio Week 7]]<br />
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[[Class Journal Week 7]]<br />
<br />
'''[[Week 8]]'''<br />
<br />
[[Ntesfaio Week 8]]<br />
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[[Class Journal Week 8]]<br />
<br />
'''[[Week 9]]'''<br />
<br />
[[Ntesfaio Week 9]]<br />
<br />
[[Class Journal Week 9]]<br />
<br />
'''[[Week 10]]'''<br />
<br />
[[Ntesfaio Week 10]]<br />
<br />
'''[[Week 11]]'''<br />
<br />
[[Ntesfaio Week 11]]<br />
<br />
[[Sulfiknights]]<br />
<br />
'''[[Week 12/13]]'''<br />
<br />
[[Ntesfaio Week 12/13]]<br />
<br />
[[Sulfiknights]]<br />
<br />
'''[[Week 14]]'''<br />
<br />
'''[[Week 15]]'''</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7191Ntesfaio Week 12/132019-11-21T22:55:56Z<p>Ntesfaio: added sections</p>
<hr />
<div>==Electronic Lab Notebook==<br />
<br />
==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
<br />
===Quality Assurance===<br />
<br />
<br />
===Data Analysis===<br />
<br />
<br />
===Coder/Designer===<br />
<br />
<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights&diff=7189Sulfiknights2019-11-21T22:55:05Z<p>Ntesfaio: added sections</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Week 12/13 Milestones==<br />
<br />
===Project Manager===<br />
<br />
<br />
===Quality Assurance===<br />
<br />
<br />
===Data Analysis===<br />
<br />
<br />
===Coder/Designer===<br />
<br />
<br />
==Data/Files==<br />
'''[[Sulfiknights Deliverables]]'''<br />
<br />
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]<br />
<br />
==Team Feedback==<br />
===Naomi Tesfaiohannes===<br />
Each team member should reflect on the team's progress:<br />
<br />
*What worked?<br />
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure. <br />
<br />
*What didn't work?<br />
My time management due to other coursework<br />
<br />
*What will I do next to fix what didn't work?<br />
Have a better control of what work I put in each day for this assignment<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Joey Nimmers-Minor===<br />
*What worked?<br />
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.<br />
*What didn't work?<br />
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week<br />
*What will I do next to fix what didn't work?<br />
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.<br />
<br />
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Marcus Avila===<br />
# What worked?<br />
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.<br />
# What didn't work?<br />
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.<br />
# What will I do next to fix what didn't work?<br />
#* Next time I will allocate more time to the assignment.<br />
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)<br />
<br />
===DeLisa Madere===<br />
<br />
'''What Worked?'''<br />
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.<br />
<br />
'''What didn't work?'''<br />
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.<br />
<br />
'''What will I do next to fix what didn't work?'''<br />
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.<br />
<br />
===Ivy Macaraeg===<br />
*What worked?<br />
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out. <br />
*What didn't work?<br />
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it. <br />
*What will I do next to fix what didn't work?<br />
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.<br />
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)<br />
<br />
==Annotated Bibliography Sources==<br />
<br />
===DeLisa Madere===<br />
<br />
1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938<br />
<br />
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013<br />
<br />
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003<br />
<br />
===Ivy Macaraeg===<br />
<br />
1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712<br />
<br />
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5<br />
<br />
===Marcus Avila===<br />
<br />
1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98<br />
<br />
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0<br />
<br />
===John Nimmers-Minor===<br />
<br />
1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005<br />
<br />
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x<br />
<br />
==References==<br />
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006<br />
<br />
<br />
<br />
[[Category:Group Projects]]<br />
[[Category:Sulfiknights]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights&diff=7155Sulfiknights2019-11-21T03:33:25Z<p>Ntesfaio: /* Week 12/13 Milestones */ added to week 12/13</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Week 12/13 Milestones==<br />
<br />
==Project Manager==<br />
<br />
=== Milestone 1: Project “Scaffolding” ===<br />
<br />
This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.<br />
<br />
# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 11]], [[Week 12/13]], and [[Week 15]].<br />
# Organize management tools for your team:<br />
#* Communication tools<br />
#* Workflow narratives<br />
#* Action items<br />
#* Testing results/reports<br />
#** Bugs/feature requests<br />
#** Question/answer sequences<br />
<br />
=== Milestone 2: Periodic Updates ===<br />
<br />
Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.<br />
<br />
# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructor will expect you to know and be able to report on the status of each member of your team at any time.<br />
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder/Designer|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.<br />
# Monitor the status of the report-in-progress and other related documentation.<br />
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.<br />
<br />
==Quality Assurance==<br />
<br />
=== Milestone 1: Annotated Bibliography ===<br />
<br />
* The QA's will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.<br />
<br />
=== Milestone 2: Journal Club Presentation ===<br />
<br />
* The QA's will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.<br />
<br />
=== Milestone 3: Working with Data Analysts to understand microarray dataset ===<br />
<br />
As an overview, the QA team member is the link between the Coder/Designer and the Data Analyst. He or she needs to know the details of the microarray dataset being analyzed so that the database being designed and populated by the Coder/Designer is correct and useful for the Data Analyst. The QA will independently check that all of the data retrieved from SGD is present and accurately represented in the MS Access database. The QA will also provide assistance to the Data Analyst, making sure that the data analysis steps are being performed correctly and are being correctly documented.<br />
<br />
Initially, the QA's will need to do the following:<br />
* Along with the Data Analysts, download the microarray data associated with your group's article.<br />
** [https://sgd-prod-upload.s3.amazonaws.com/S000204227/Barreto_2012_PMID_23039231.zip Barreto et al. (2012)]<br />
** [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]<br />
** [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]<br />
** Along with the Data Analysts, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.<br />
** Are all the samples described in the paper in the dataset?<br />
** Are all the samples in the dataset described in the paper?<br />
* Come up with consistent column headers that summarize this information<br />
** For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.<br />
* Organize the data in a worksheet in an Excel workbook so that:<br />
* ID is in the first column<br />
* Data columns are to the right, in increasing chronological order, using the column header pattern you created<br />
* Replicates are grouped together<br />
<br />
=== Milestone 4: Making sure expression data has both Sytematic Name and Standard Name ID's ===<br />
<br />
* The design of the expression tables in the final database will need both an ID field (yeast systematic name) and Standard Name fields. <br />
* You will need to check the IDs in the expression data and potentially populate one or both of these fields.<br />
* One way to do this is use the [http://www.yeastract.com/formorftogene.php "ORF List <-> Gene List"] tool at YEASTRACT.<br />
* The [http://llama.mshri.on.ca/synergizer/translate/ Synergizer] website may also be helpful.<br />
* Here is a [https://rdrr.io/bioc/ClusterJudge/man/convert_Yeast_SGDId_2_systematic.html Bioconductor package] for it, too.<br />
<br />
=== Milestone 5: Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from four sources ===<br />
<br />
* Databases created by the teams will be kept in a [https://lmu.box.com/s/gutpb5qm0a6b2pvjn1j6moqb6y47e903 "BIOL367_Fall2019 > Final Project Database" Box folder].<br />
* Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.<br />
* This folder will serve as as the version control mechanism for the Coder/Designer guild.<br />
* Designer/Coders will work with the QA's to create a MS Access Database to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts.<br />
* The starting point will be the database already used for the [[Week 10]] assignment, which can be found [https://lmu.box.com/s/kn8l6r639af683ioojqoce5w1g3z7kd2 here] on Box.<br />
** This database is already populated with tables for the Dahlquist Lab microarray data, degradation rates from Neymotin et al. (2014), and initial guesses for production rates.<br />
*** You may need to change the table names of these existing tables so that they make sense with the overall database design.<br />
** You will need to add one or more expression tables for the expression data from your team's article.<br />
*** Work with your team's QA and Data Analysts to determine appropriate column headings for the expression table.<br />
** You will also need to create one or more tables with metadata about the other tables because now the database will contain data from multiple sources, not just one.<br />
*** A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.<br />
<br />
=== Milestone 6: Validation and Quality Assurance on Database ===<br />
<br />
* After the Access database is built by the Coder/Designer, the QA will perform quality assurance to make sure that the database is correct and accurate.<br />
** In particular, the QA needs to make sure that all of the rows of data were imported into the database for the expression table(s).<br />
** The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.<br />
* QA's will communicate to the Coder/Designers any changes needed to the database.<br />
<br />
=== Milestone 7: Final Documentation ===<br />
<br />
* With the Coder/Designer, finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]<br />
<br />
==Data Analysis==<br />
<br />
=== Milestone 1: Annotated Bibliography ===<br />
<br />
* The Data Analysts will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.<br />
<br />
=== Milestone 2: Journal Club Presentation ===<br />
<br />
* The Data Analysts will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.<br />
<br />
=== Milestone 3: Getting the data ready for analysis ===<br />
<br />
# Download and examine the microarray dataset, comparing it to the samples and experiment described in your journal club article.<br />
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204227/Barreto_2012_PMID_23039231.zip Barreto et al. (2012)]<br />
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]<br />
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]<br />
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.<br />
#* Come up with consistent column headers that summarize this information<br />
#** For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.<br />
# Organize the data in a worksheet in an Excel workbook so that:<br />
#* ID is in the first column<br />
#* Data columns are to the right, in increasing chronological order, using the column header pattern you created<br />
#* Replicates are grouped together<br />
<br />
=== Milestone 4: ANOVA analysis ===<br />
<br />
# Perform an ANOVA analysis of the data, as you did on [[Week 8]] for the Dahlquist lab data.<br />
#* Note that you will need to adjust your formulas to take into account the different number of timepoints and replicates in your article's dataset.<br />
<br />
=== Milestone 5: Clustering with stem and YEASTRACT ===<br />
<br />
# Cluster the data with stem, as you did on [[Week 9]].<br />
#* Note that we will make some adjustments to the GO term analysis because stem was not providing GO term names.<br />
# Use YEASTRACT to generate a candidate gene regulatory network as you did on [[Week 9]].<br />
<br />
=== Milestone 6: Create an input workbook for GRNmap using MS Access database ===<br />
<br />
# Create an input workbook for GRNmap based on a Microsoft Access database that the Coder/Designer and QA's make, following protocol in [[Week 10]]<br />
# Run GRNmap and interpret data.<br />
# As the end-user of the Access database, the Data Analysts will provide feedback to the QAs and Coder/Designer about the usability of database.<br />
<br />
==Coder/Designer==<br />
<br />
=== Milestone 1: Annotated Bibliography ===<br />
<br />
* The Coder/Designer will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.<br />
<br />
=== Milestone 2: Journal Club Presentation ===<br />
<br />
* The Coder/Designer will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.<br />
<br />
=== Milestone 3: Working Environment Setup ===<br />
<br />
Coder/Designer work will require the following software/accounts. The Seaver 120 lab computers are already set up for this; this list is provided for Coders/Designers who need to work on a different computer or outside of the lab.<br />
* Microsoft Access<br />
* Box account (provided by LMU)<br />
** Databases created by the teams will be kept in a [https://lmu.box.com/s/gutpb5qm0a6b2pvjn1j6moqb6y47e903 "BIOL367_Fall2019 > Final Project Database" Box folder].<br />
** Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.<br />
** This folder will serve as as the version control mechanism for the Coder/Designer guild.<br />
<br />
=== Milestone 4: Design a Database to Store Time-course Microarray Data from four sources ===<br />
<br />
* Designer/Coders will work with the QA's to create a MS Access Database to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts.<br />
* The starting point will be the database already used for the [[Week 10]] assignment, which can be found [https://lmu.box.com/s/kn8l6r639af683ioojqoce5w1g3z7kd2 here] on Box.<br />
** This database is already populated with tables for the Dahlquist Lab microarray data, degradation rates from Neymotin et al. (2014), and initial guesses for production rates.<br />
*** You may need to change the table names of these existing tables so that they make sense with the overall database design.<br />
** You will need to add one or more expression tables for the expression data from your team's article.<br />
*** Work with your team's QA and Data Analysts to determine appropriate column headings for the expression table.<br />
** You will also need to create one or more tables with metadata about the other tables because now the database will contain data from multiple sources, not just one.<br />
*** A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.<br />
*** Think about what information would someone need to know to be able to understand how the dataset works. Consult with the QA and Data Analysts to figure out the sample-data relationships and how that should be encoded.<br />
<br />
=== Milestone 5: Build an individual database for your team ===<br />
<br />
* Once the design work has been completed, you need to actually import the data into the database.<br />
* Initially, each team will have their own database so that the QA and Data analysts can validate and use the database.<br />
<br />
=== Milestone 6: Validation and Quality Assurance on Database ===<br />
<br />
* The QA will perform quality assurance to make sure that the database is correct and accurate.<br />
** In particular, the QA needs to make sure that all of the rows of data were imported into the database for the expression table(s).<br />
** The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.<br />
* QA's will communicate to the Coder/Designers any changes needed to the database.<br />
<br />
=== Milestone 7: Merge completed databases into a single database for the class ===<br />
<br />
* As a guild, the Coder/Designers will merge their separate databases into a final product.<br />
* With the QA's finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]<br />
<br />
==Data/Files==<br />
'''[[Sulfiknights Deliverables]]'''<br />
<br />
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]<br />
<br />
==Team Feedback==<br />
===Naomi Tesfaiohannes===<br />
Each team member should reflect on the team's progress:<br />
<br />
*What worked?<br />
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure. <br />
<br />
*What didn't work?<br />
My time management due to other coursework<br />
<br />
*What will I do next to fix what didn't work?<br />
Have a better control of what work I put in each day for this assignment<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Joey Nimmers-Minor===<br />
*What worked?<br />
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.<br />
*What didn't work?<br />
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week<br />
*What will I do next to fix what didn't work?<br />
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.<br />
<br />
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Marcus Avila===<br />
# What worked?<br />
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.<br />
# What didn't work?<br />
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.<br />
# What will I do next to fix what didn't work?<br />
#* Next time I will allocate more time to the assignment.<br />
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)<br />
<br />
===DeLisa Madere===<br />
<br />
'''What Worked?'''<br />
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.<br />
<br />
'''What didn't work?'''<br />
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.<br />
<br />
'''What will I do next to fix what didn't work?'''<br />
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.<br />
<br />
===Ivy Macaraeg===<br />
*What worked?<br />
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out. <br />
*What didn't work?<br />
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it. <br />
*What will I do next to fix what didn't work?<br />
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.<br />
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)<br />
<br />
==Annotated Bibliography Sources==<br />
<br />
===DeLisa Madere===<br />
<br />
1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938<br />
<br />
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013<br />
<br />
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003<br />
<br />
===Ivy Macaraeg===<br />
<br />
1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712<br />
<br />
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5<br />
<br />
===Marcus Avila===<br />
<br />
1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98<br />
<br />
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0<br />
<br />
===John Nimmers-Minor===<br />
<br />
1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005<br />
<br />
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x<br />
<br />
==References==<br />
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006<br />
<br />
<br />
<br />
[[Category:Group Projects]]<br />
[[Category:Sulfiknights]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7154Ntesfaio Week 12/132019-11-21T03:31:56Z<p>Ntesfaio: made sections for each guild</p>
<hr />
<div>==Electronic Lab Notebook==<br />
<br />
==Project Manager==<br />
<br />
=== Milestone 1: Project “Scaffolding” ===<br />
<br />
This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.<br />
<br />
# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 11]], [[Week 12/13]], and [[Week 15]].<br />
# Organize management tools for your team:<br />
#* Communication tools<br />
#* Workflow narratives<br />
#* Action items<br />
#* Testing results/reports<br />
#** Bugs/feature requests<br />
#** Question/answer sequences<br />
<br />
=== Milestone 2: Periodic Updates ===<br />
<br />
Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.<br />
<br />
# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructor will expect you to know and be able to report on the status of each member of your team at any time.<br />
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder/Designer|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.<br />
# Monitor the status of the report-in-progress and other related documentation.<br />
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.<br />
<br />
==Quality Assurance==<br />
<br />
=== Milestone 1: Annotated Bibliography ===<br />
<br />
* The QA's will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.<br />
<br />
=== Milestone 2: Journal Club Presentation ===<br />
<br />
* The QA's will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.<br />
<br />
=== Milestone 3: Working with Data Analysts to understand microarray dataset ===<br />
<br />
As an overview, the QA team member is the link between the Coder/Designer and the Data Analyst. He or she needs to know the details of the microarray dataset being analyzed so that the database being designed and populated by the Coder/Designer is correct and useful for the Data Analyst. The QA will independently check that all of the data retrieved from SGD is present and accurately represented in the MS Access database. The QA will also provide assistance to the Data Analyst, making sure that the data analysis steps are being performed correctly and are being correctly documented.<br />
<br />
Initially, the QA's will need to do the following:<br />
* Along with the Data Analysts, download the microarray data associated with your group's article.<br />
** [https://sgd-prod-upload.s3.amazonaws.com/S000204227/Barreto_2012_PMID_23039231.zip Barreto et al. (2012)]<br />
** [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]<br />
** [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]<br />
** Along with the Data Analysts, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.<br />
** Are all the samples described in the paper in the dataset?<br />
** Are all the samples in the dataset described in the paper?<br />
* Come up with consistent column headers that summarize this information<br />
** For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.<br />
* Organize the data in a worksheet in an Excel workbook so that:<br />
* ID is in the first column<br />
* Data columns are to the right, in increasing chronological order, using the column header pattern you created<br />
* Replicates are grouped together<br />
<br />
=== Milestone 4: Making sure expression data has both Sytematic Name and Standard Name ID's ===<br />
<br />
* The design of the expression tables in the final database will need both an ID field (yeast systematic name) and Standard Name fields. <br />
* You will need to check the IDs in the expression data and potentially populate one or both of these fields.<br />
* One way to do this is use the [http://www.yeastract.com/formorftogene.php "ORF List <-> Gene List"] tool at YEASTRACT.<br />
* The [http://llama.mshri.on.ca/synergizer/translate/ Synergizer] website may also be helpful.<br />
* Here is a [https://rdrr.io/bioc/ClusterJudge/man/convert_Yeast_SGDId_2_systematic.html Bioconductor package] for it, too.<br />
<br />
=== Milestone 5: Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from four sources ===<br />
<br />
* Databases created by the teams will be kept in a [https://lmu.box.com/s/gutpb5qm0a6b2pvjn1j6moqb6y47e903 "BIOL367_Fall2019 > Final Project Database" Box folder].<br />
* Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.<br />
* This folder will serve as as the version control mechanism for the Coder/Designer guild.<br />
* Designer/Coders will work with the QA's to create a MS Access Database to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts.<br />
* The starting point will be the database already used for the [[Week 10]] assignment, which can be found [https://lmu.box.com/s/kn8l6r639af683ioojqoce5w1g3z7kd2 here] on Box.<br />
** This database is already populated with tables for the Dahlquist Lab microarray data, degradation rates from Neymotin et al. (2014), and initial guesses for production rates.<br />
*** You may need to change the table names of these existing tables so that they make sense with the overall database design.<br />
** You will need to add one or more expression tables for the expression data from your team's article.<br />
*** Work with your team's QA and Data Analysts to determine appropriate column headings for the expression table.<br />
** You will also need to create one or more tables with metadata about the other tables because now the database will contain data from multiple sources, not just one.<br />
*** A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.<br />
<br />
=== Milestone 6: Validation and Quality Assurance on Database ===<br />
<br />
* After the Access database is built by the Coder/Designer, the QA will perform quality assurance to make sure that the database is correct and accurate.<br />
** In particular, the QA needs to make sure that all of the rows of data were imported into the database for the expression table(s).<br />
** The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.<br />
* QA's will communicate to the Coder/Designers any changes needed to the database.<br />
<br />
=== Milestone 7: Final Documentation ===<br />
<br />
* With the Coder/Designer, finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]<br />
<br />
==Data Analysis==<br />
<br />
=== Milestone 1: Annotated Bibliography ===<br />
<br />
* The Data Analysts will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.<br />
<br />
=== Milestone 2: Journal Club Presentation ===<br />
<br />
* The Data Analysts will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.<br />
<br />
=== Milestone 3: Getting the data ready for analysis ===<br />
<br />
# Download and examine the microarray dataset, comparing it to the samples and experiment described in your journal club article.<br />
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204227/Barreto_2012_PMID_23039231.zip Barreto et al. (2012)]<br />
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]<br />
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]<br />
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.<br />
#* Come up with consistent column headers that summarize this information<br />
#** For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.<br />
# Organize the data in a worksheet in an Excel workbook so that:<br />
#* ID is in the first column<br />
#* Data columns are to the right, in increasing chronological order, using the column header pattern you created<br />
#* Replicates are grouped together<br />
<br />
=== Milestone 4: ANOVA analysis ===<br />
<br />
# Perform an ANOVA analysis of the data, as you did on [[Week 8]] for the Dahlquist lab data.<br />
#* Note that you will need to adjust your formulas to take into account the different number of timepoints and replicates in your article's dataset.<br />
<br />
=== Milestone 5: Clustering with stem and YEASTRACT ===<br />
<br />
# Cluster the data with stem, as you did on [[Week 9]].<br />
#* Note that we will make some adjustments to the GO term analysis because stem was not providing GO term names.<br />
# Use YEASTRACT to generate a candidate gene regulatory network as you did on [[Week 9]].<br />
<br />
=== Milestone 6: Create an input workbook for GRNmap using MS Access database ===<br />
<br />
# Create an input workbook for GRNmap based on a Microsoft Access database that the Coder/Designer and QA's make, following protocol in [[Week 10]]<br />
# Run GRNmap and interpret data.<br />
# As the end-user of the Access database, the Data Analysts will provide feedback to the QAs and Coder/Designer about the usability of database.<br />
<br />
==Coder/Designer==<br />
<br />
=== Milestone 1: Annotated Bibliography ===<br />
<br />
* The Coder/Designer will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.<br />
<br />
=== Milestone 2: Journal Club Presentation ===<br />
<br />
* The Coder/Designer will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.<br />
<br />
=== Milestone 3: Working Environment Setup ===<br />
<br />
Coder/Designer work will require the following software/accounts. The Seaver 120 lab computers are already set up for this; this list is provided for Coders/Designers who need to work on a different computer or outside of the lab.<br />
* Microsoft Access<br />
* Box account (provided by LMU)<br />
** Databases created by the teams will be kept in a [https://lmu.box.com/s/gutpb5qm0a6b2pvjn1j6moqb6y47e903 "BIOL367_Fall2019 > Final Project Database" Box folder].<br />
** Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.<br />
** This folder will serve as as the version control mechanism for the Coder/Designer guild.<br />
<br />
=== Milestone 4: Design a Database to Store Time-course Microarray Data from four sources ===<br />
<br />
* Designer/Coders will work with the QA's to create a MS Access Database to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts.<br />
* The starting point will be the database already used for the [[Week 10]] assignment, which can be found [https://lmu.box.com/s/kn8l6r639af683ioojqoce5w1g3z7kd2 here] on Box.<br />
** This database is already populated with tables for the Dahlquist Lab microarray data, degradation rates from Neymotin et al. (2014), and initial guesses for production rates.<br />
*** You may need to change the table names of these existing tables so that they make sense with the overall database design.<br />
** You will need to add one or more expression tables for the expression data from your team's article.<br />
*** Work with your team's QA and Data Analysts to determine appropriate column headings for the expression table.<br />
** You will also need to create one or more tables with metadata about the other tables because now the database will contain data from multiple sources, not just one.<br />
*** A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.<br />
*** Think about what information would someone need to know to be able to understand how the dataset works. Consult with the QA and Data Analysts to figure out the sample-data relationships and how that should be encoded.<br />
<br />
=== Milestone 5: Build an individual database for your team ===<br />
<br />
* Once the design work has been completed, you need to actually import the data into the database.<br />
* Initially, each team will have their own database so that the QA and Data analysts can validate and use the database.<br />
<br />
=== Milestone 6: Validation and Quality Assurance on Database ===<br />
<br />
* The QA will perform quality assurance to make sure that the database is correct and accurate.<br />
** In particular, the QA needs to make sure that all of the rows of data were imported into the database for the expression table(s).<br />
** The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.<br />
* QA's will communicate to the Coder/Designers any changes needed to the database.<br />
<br />
=== Milestone 7: Merge completed databases into a single database for the class ===<br />
<br />
* As a guild, the Coder/Designers will merge their separate databases into a final product.<br />
* With the QA's finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]<br />
<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights&diff=7152Sulfiknights2019-11-21T03:30:46Z<p>Ntesfaio: /* Week 12/13 Milestones */ deleted section</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Week 12/13 Milestones==<br />
<br />
==Data/Files==<br />
'''[[Sulfiknights Deliverables]]'''<br />
<br />
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]<br />
<br />
==Team Feedback==<br />
===Naomi Tesfaiohannes===<br />
Each team member should reflect on the team's progress:<br />
<br />
*What worked?<br />
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure. <br />
<br />
*What didn't work?<br />
My time management due to other coursework<br />
<br />
*What will I do next to fix what didn't work?<br />
Have a better control of what work I put in each day for this assignment<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Joey Nimmers-Minor===<br />
*What worked?<br />
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.<br />
*What didn't work?<br />
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week<br />
*What will I do next to fix what didn't work?<br />
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.<br />
<br />
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Marcus Avila===<br />
# What worked?<br />
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.<br />
# What didn't work?<br />
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.<br />
# What will I do next to fix what didn't work?<br />
#* Next time I will allocate more time to the assignment.<br />
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)<br />
<br />
===DeLisa Madere===<br />
<br />
'''What Worked?'''<br />
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.<br />
<br />
'''What didn't work?'''<br />
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.<br />
<br />
'''What will I do next to fix what didn't work?'''<br />
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.<br />
<br />
===Ivy Macaraeg===<br />
*What worked?<br />
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out. <br />
*What didn't work?<br />
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it. <br />
*What will I do next to fix what didn't work?<br />
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.<br />
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)<br />
<br />
==Annotated Bibliography Sources==<br />
<br />
===DeLisa Madere===<br />
<br />
1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938<br />
<br />
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013<br />
<br />
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003<br />
<br />
===Ivy Macaraeg===<br />
<br />
1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712<br />
<br />
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5<br />
<br />
===Marcus Avila===<br />
<br />
1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98<br />
<br />
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0<br />
<br />
===John Nimmers-Minor===<br />
<br />
1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005<br />
<br />
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x<br />
<br />
==References==<br />
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006<br />
<br />
<br />
<br />
[[Category:Group Projects]]<br />
[[Category:Sulfiknights]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights&diff=7151Sulfiknights2019-11-21T03:29:40Z<p>Ntesfaio: added milestones</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Week 12/13 Milestones==<br />
<br />
=== Milestone 1: Annotated Bibliography ===<br />
<br />
* The Coder/Designer will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.<br />
<br />
=== Milestone 2: Journal Club Presentation ===<br />
<br />
* The Coder/Designer will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.<br />
<br />
=== Milestone 3: Working Environment Setup ===<br />
<br />
Coder/Designer work will require the following software/accounts. The Seaver 120 lab computers are already set up for this; this list is provided for Coders/Designers who need to work on a different computer or outside of the lab.<br />
* Microsoft Access<br />
* Box account (provided by LMU)<br />
** Databases created by the teams will be kept in a [https://lmu.box.com/s/gutpb5qm0a6b2pvjn1j6moqb6y47e903 "BIOL367_Fall2019 > Final Project Database" Box folder].<br />
** Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.<br />
** This folder will serve as as the version control mechanism for the Coder/Designer guild.<br />
<br />
=== Milestone 4: Design a Database to Store Time-course Microarray Data from four sources ===<br />
<br />
* Designer/Coders will work with the QA's to create a MS Access Database to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts.<br />
* The starting point will be the database already used for the [[Week 10]] assignment, which can be found [https://lmu.box.com/s/kn8l6r639af683ioojqoce5w1g3z7kd2 here] on Box.<br />
** This database is already populated with tables for the Dahlquist Lab microarray data, degradation rates from Neymotin et al. (2014), and initial guesses for production rates.<br />
*** You may need to change the table names of these existing tables so that they make sense with the overall database design.<br />
** You will need to add one or more expression tables for the expression data from your team's article.<br />
*** Work with your team's QA and Data Analysts to determine appropriate column headings for the expression table.<br />
** You will also need to create one or more tables with metadata about the other tables because now the database will contain data from multiple sources, not just one.<br />
*** A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.<br />
*** Think about what information would someone need to know to be able to understand how the dataset works. Consult with the QA and Data Analysts to figure out the sample-data relationships and how that should be encoded.<br />
<br />
=== Milestone 5: Build an individual database for your team ===<br />
<br />
* Once the design work has been completed, you need to actually import the data into the database.<br />
* Initially, each team will have their own database so that the QA and Data analysts can validate and use the database.<br />
<br />
=== Milestone 6: Validation and Quality Assurance on Database ===<br />
<br />
* The QA will perform quality assurance to make sure that the database is correct and accurate.<br />
** In particular, the QA needs to make sure that all of the rows of data were imported into the database for the expression table(s).<br />
** The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.<br />
* QA's will communicate to the Coder/Designers any changes needed to the database.<br />
<br />
=== Milestone 7: Merge completed databases into a single database for the class ===<br />
<br />
* As a guild, the Coder/Designers will merge their separate databases into a final product.<br />
* With the QA's finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]<br />
<br />
==Data/Files==<br />
'''[[Sulfiknights Deliverables]]'''<br />
<br />
[[Media:Biolpresentation_IM.pptx|Journal Club Presentation 11/14/19]]<br />
<br />
==Team Feedback==<br />
===Naomi Tesfaiohannes===<br />
Each team member should reflect on the team's progress:<br />
<br />
*What worked?<br />
Breaking up the sections of the paper to understand the transcription factors and cells affected by the arsenite exposure. <br />
<br />
*What didn't work?<br />
My time management due to other coursework<br />
<br />
*What will I do next to fix what didn't work?<br />
Have a better control of what work I put in each day for this assignment<br />
<br />
[[User:Ntesfaio|Ntesfaio]] ([[User talk:Ntesfaio|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Joey Nimmers-Minor===<br />
*What worked?<br />
Dividing up responsibilities and meeting in person in order to avoid missed texts and simply make communication simpler and smoother.<br />
*What didn't work?<br />
Waiting until the last minute to do the assignment because every member of the team had tests to get through this week<br />
*What will I do next to fix what didn't work?<br />
I'll make sure to begin the assignments much sooner and communicate responsibilities with the rest of my team pomtply so we don't have to worry about rushing/procrastinating regardless of what assignments or tests we have the next week.<br />
<br />
[[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 00:08, 14 November 2019 (PST)<br />
<br />
===Marcus Avila===<br />
# What worked?<br />
#* The team dynamic and communication worked out very well. I feel that we each did our part and were even able to help each other out in some places.<br />
# What didn't work?<br />
#* I believe the amount of time given to complete the individual outline and group presentation was insufficient.<br />
# What will I do next to fix what didn't work?<br />
#* Next time I will allocate more time to the assignment.<br />
[[User:Mavila9|Mavila9]] ([[User talk:Mavila9|talk]]) 17:24, 15 November 2019 (PST)<br />
<br />
===DeLisa Madere===<br />
<br />
'''What Worked?'''<br />
*Being able to come together as a group and collaborate our ideas of the paper really allowed us to efficiently break up the work. We all assisted each other if we needed help.<br />
<br />
'''What didn't work?'''<br />
*This week there was a lot of work going into this assignment along with the tests we have had from our other class, so we did not have a great amount of delegated time due to the workload.<br />
<br />
'''What will I do next to fix what didn't work?'''<br />
*Next time, there will not be any other tests, therefore, more time can be delegated to this assignment.<br />
<br />
===Ivy Macaraeg===<br />
*What worked?<br />
*:-I think we worked together well, even under pressure. We were able to coordinate with each other and help each other out. <br />
*What didn't work?<br />
*:-All of us were under a lot of pressure concerning other classes, so the amount of time we had to come together and work on this project was limited. Therefore, what didn't work was the timing we had to complete it. <br />
*What will I do next to fix what didn't work?<br />
*:-Next time, I will try to get ahead on my individual page more, so that I will be able to allocate more time to group areas.<br />
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 00:12, 14 November 2019 (PST)<br />
<br />
==Annotated Bibliography Sources==<br />
<br />
===DeLisa Madere===<br />
<br />
1. Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. https://doi.org/10.1242/bio.20148938<br />
<br />
2. Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: https://doi.org/10.1002/j.1460-2075.1992.tb05295.x<br />
<br />
===Naomi Tesfaiohannes===<br />
<br />
1. Tsai, S. L., Singh, S., & Chen, W. (2009). Arsenic metabolism by microbes in nature and the impact on arsenic remediation. Current Opinion in Biotechnology, 20(6), 659-667. https://doi.org/10.1016/j.copbio.2009.09.013<br />
<br />
2. Zhou, X., Arita, A., Ellen, T. P., Liu, X., Bai, J., Rooney, J. P., ... & Costa, M. (2009). A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity. Genomics, 94(5), 294-307. https://doi.org/10.1016/j.ygeno.2009.07.003<br />
<br />
===Ivy Macaraeg===<br />
<br />
1. Khullar, S., & Sudhakara Reddy, M. (2019). Cadmium and arsenic responses in the ectomycorrhizal fungus Laccaria bicolor: glutathione metabolism and its role in metal (loid) homeostasis. Environmental microbiology reports, 11(2), 53-61. https://doi.org/10.1111/1758-2229.12712<br />
<br />
2. Das, S., Majumder, B., & Biswas, A. K. (2018). Modulation of growth, ascorbate-glutathione cycle and thiol metabolism in rice (Oryza sativa L. cv. MTU-1010) seedlings by arsenic and silicon. Ecotoxicology, 27(10), 1387-1403. 10.1007/s10646-018-1994-5<br />
<br />
===Marcus Avila===<br />
<br />
1. Parrish, A. R., Zheng, X. H., Turney, K. D., Younis, H. S., & Gandolfi, A. J. (1999). Enhanced transcription factor DNA binding and gene expression induced by arsenite or arsenate in renal slices. Toxicological sciences: an official journal of the Society of Toxicology, 50(1), 98-105. https://doi.org/10.1093/toxsci/50.1.98<br />
<br />
2. Tang, L., Wang, W., Zhou, W., Cheng, K., Yang, Y., Liu, M., ... & Wang, W. (2015). Three-pathway combination for glutathione biosynthesis in Saccharomyces cerevisiae. Microbial cell factories, 14(1), 139. https://doi.org/139. 10.1186/s12934-015-0327-0<br />
<br />
===John Nimmers-Minor===<br />
<br />
1.Silver, S., & Phung, L. T. (2005). Genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic. Appl. Environ. Microbiol., 71(2), 599-608. DOI: https://doi.org/10.1128/AEM.71.2.599-608.2005<br />
<br />
2.Hayakawa, T., Kobayashi, Y., Cui, X. et al. Arch Toxicol (2005) 79: 183. https://doi.org/10.1007/s00204-004-0620-x<br />
<br />
==References==<br />
*Thorsen, M., Lagniel, G., Kristiansson, E., Junot, C., Nerman, O., Labarre, J., & Tamás, M. J. (2007). Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiological genomics, 30(1), 35-43. DOI: 10.1152/physiolgenomics.00236.2006<br />
<br />
<br />
<br />
[[Category:Group Projects]]<br />
[[Category:Sulfiknights]]</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7150Ntesfaio Week 12/132019-11-21T03:26:34Z<p>Ntesfaio: /* Electronic Lab Notebook */ added sections for each person</p>
<hr />
<div>==Electronic Lab Notebook==<br />
<br />
===Project Manager===<br />
<br />
=== Milestone 1: Project “Scaffolding” ===<br />
<br />
This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.<br />
<br />
# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 11]], [[Week 12/13]], and [[Week 15]].<br />
# Organize management tools for your team:<br />
#* Communication tools<br />
#* Workflow narratives<br />
#* Action items<br />
#* Testing results/reports<br />
#** Bugs/feature requests<br />
#** Question/answer sequences<br />
<br />
=== Milestone 2: Periodic Updates ===<br />
<br />
Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.<br />
<br />
# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructor will expect you to know and be able to report on the status of each member of your team at any time.<br />
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder/Designer|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.<br />
# Monitor the status of the report-in-progress and other related documentation.<br />
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.<br />
<br />
===Quality Assurance===<br />
<br />
=== Milestone 1: Annotated Bibliography ===<br />
<br />
* The QA's will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.<br />
<br />
=== Milestone 2: Journal Club Presentation ===<br />
<br />
* The QA's will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.<br />
<br />
=== Milestone 3: Working with Data Analysts to understand microarray dataset ===<br />
<br />
As an overview, the QA team member is the link between the Coder/Designer and the Data Analyst. He or she needs to know the details of the microarray dataset being analyzed so that the database being designed and populated by the Coder/Designer is correct and useful for the Data Analyst. The QA will independently check that all of the data retrieved from SGD is present and accurately represented in the MS Access database. The QA will also provide assistance to the Data Analyst, making sure that the data analysis steps are being performed correctly and are being correctly documented.<br />
<br />
Initially, the QA's will need to do the following:<br />
* Along with the Data Analysts, download the microarray data associated with your group's article.<br />
** [https://sgd-prod-upload.s3.amazonaws.com/S000204227/Barreto_2012_PMID_23039231.zip Barreto et al. (2012)]<br />
** [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]<br />
** [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]<br />
** Along with the Data Analysts, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.<br />
** Are all the samples described in the paper in the dataset?<br />
** Are all the samples in the dataset described in the paper?<br />
* Come up with consistent column headers that summarize this information<br />
** For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.<br />
* Organize the data in a worksheet in an Excel workbook so that:<br />
* ID is in the first column<br />
* Data columns are to the right, in increasing chronological order, using the column header pattern you created<br />
* Replicates are grouped together<br />
<br />
=== Milestone 4: Making sure expression data has both Sytematic Name and Standard Name ID's ===<br />
<br />
* The design of the expression tables in the final database will need both an ID field (yeast systematic name) and Standard Name fields. <br />
* You will need to check the IDs in the expression data and potentially populate one or both of these fields.<br />
* One way to do this is use the [http://www.yeastract.com/formorftogene.php "ORF List <-> Gene List"] tool at YEASTRACT.<br />
* The [http://llama.mshri.on.ca/synergizer/translate/ Synergizer] website may also be helpful.<br />
* Here is a [https://rdrr.io/bioc/ClusterJudge/man/convert_Yeast_SGDId_2_systematic.html Bioconductor package] for it, too.<br />
<br />
=== Milestone 5: Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from four sources ===<br />
<br />
* Databases created by the teams will be kept in a [https://lmu.box.com/s/gutpb5qm0a6b2pvjn1j6moqb6y47e903 "BIOL367_Fall2019 > Final Project Database" Box folder].<br />
* Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.<br />
* This folder will serve as as the version control mechanism for the Coder/Designer guild.<br />
* Designer/Coders will work with the QA's to create a MS Access Database to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts.<br />
* The starting point will be the database already used for the [[Week 10]] assignment, which can be found [https://lmu.box.com/s/kn8l6r639af683ioojqoce5w1g3z7kd2 here] on Box.<br />
** This database is already populated with tables for the Dahlquist Lab microarray data, degradation rates from Neymotin et al. (2014), and initial guesses for production rates.<br />
*** You may need to change the table names of these existing tables so that they make sense with the overall database design.<br />
** You will need to add one or more expression tables for the expression data from your team's article.<br />
*** Work with your team's QA and Data Analysts to determine appropriate column headings for the expression table.<br />
** You will also need to create one or more tables with metadata about the other tables because now the database will contain data from multiple sources, not just one.<br />
*** A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.<br />
<br />
=== Milestone 6: Validation and Quality Assurance on Database ===<br />
<br />
* After the Access database is built by the Coder/Designer, the QA will perform quality assurance to make sure that the database is correct and accurate.<br />
** In particular, the QA needs to make sure that all of the rows of data were imported into the database for the expression table(s).<br />
** The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.<br />
* QA's will communicate to the Coder/Designers any changes needed to the database.<br />
<br />
=== Milestone 7: Final Documentation ===<br />
<br />
* With the Coder/Designer, finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]<br />
<br />
===Data Analysis===<br />
<br />
=== Milestone 1: Annotated Bibliography ===<br />
<br />
* The Data Analysts will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.<br />
<br />
=== Milestone 2: Journal Club Presentation ===<br />
<br />
* The Data Analysts will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.<br />
<br />
=== Milestone 3: Getting the data ready for analysis ===<br />
<br />
# Download and examine the microarray dataset, comparing it to the samples and experiment described in your journal club article.<br />
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204227/Barreto_2012_PMID_23039231.zip Barreto et al. (2012)]<br />
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]<br />
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204367/Thorsen_2007_PMID_17327492.zip Thorsen et al. (2007)]<br />
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, and replicate number.<br />
#* Come up with consistent column headers that summarize this information<br />
#** For example, the Dahlquist Lab microarray data used strain_LogFC_timepoint-replicate number, as in wt_LogFC_t15-1.<br />
# Organize the data in a worksheet in an Excel workbook so that:<br />
#* ID is in the first column<br />
#* Data columns are to the right, in increasing chronological order, using the column header pattern you created<br />
#* Replicates are grouped together<br />
<br />
=== Milestone 4: ANOVA analysis ===<br />
<br />
# Perform an ANOVA analysis of the data, as you did on [[Week 8]] for the Dahlquist lab data.<br />
#* Note that you will need to adjust your formulas to take into account the different number of timepoints and replicates in your article's dataset.<br />
<br />
=== Milestone 5: Clustering with stem and YEASTRACT ===<br />
<br />
# Cluster the data with stem, as you did on [[Week 9]].<br />
#* Note that we will make some adjustments to the GO term analysis because stem was not providing GO term names.<br />
# Use YEASTRACT to generate a candidate gene regulatory network as you did on [[Week 9]].<br />
<br />
=== Milestone 6: Create an input workbook for GRNmap using MS Access database ===<br />
<br />
# Create an input workbook for GRNmap based on a Microsoft Access database that the Coder/Designer and QA's make, following protocol in [[Week 10]]<br />
# Run GRNmap and interpret data.<br />
# As the end-user of the Access database, the Data Analysts will provide feedback to the QAs and Coder/Designer about the usability of database.<br />
<br />
===Coder/Designer===<br />
<br />
=== Milestone 1: Annotated Bibliography ===<br />
<br />
* The Coder/Designer will work with their teams to develop an annotated bibliography of papers relating to their team's assigned paper.<br />
<br />
=== Milestone 2: Journal Club Presentation ===<br />
<br />
* The Coder/Designer will work with their teams to create and deliver a Journal Club presentation about to their team's assigned paper.<br />
<br />
=== Milestone 3: Working Environment Setup ===<br />
<br />
Coder/Designer work will require the following software/accounts. The Seaver 120 lab computers are already set up for this; this list is provided for Coders/Designers who need to work on a different computer or outside of the lab.<br />
* Microsoft Access<br />
* Box account (provided by LMU)<br />
** Databases created by the teams will be kept in a [https://lmu.box.com/s/gutpb5qm0a6b2pvjn1j6moqb6y47e903 "BIOL367_Fall2019 > Final Project Database" Box folder].<br />
** Coder/Designer guild members have rights as editor to this folder; all others in the class can only view/download.<br />
** This folder will serve as as the version control mechanism for the Coder/Designer guild.<br />
<br />
=== Milestone 4: Design a Database to Store Time-course Microarray Data from four sources ===<br />
<br />
* Designer/Coders will work with the QA's to create a MS Access Database to store the yeast time-course microarray data for the dataset being analyzed by the Data Analysts.<br />
* The starting point will be the database already used for the [[Week 10]] assignment, which can be found [https://lmu.box.com/s/kn8l6r639af683ioojqoce5w1g3z7kd2 here] on Box.<br />
** This database is already populated with tables for the Dahlquist Lab microarray data, degradation rates from Neymotin et al. (2014), and initial guesses for production rates.<br />
*** You may need to change the table names of these existing tables so that they make sense with the overall database design.<br />
** You will need to add one or more expression tables for the expression data from your team's article.<br />
*** Work with your team's QA and Data Analysts to determine appropriate column headings for the expression table.<br />
** You will also need to create one or more tables with metadata about the other tables because now the database will contain data from multiple sources, not just one.<br />
*** A major part of the design work will be to figure out what information needs to be in the metadata table so that queries can be easily and uniquely performed on the data.<br />
*** Think about what information would someone need to know to be able to understand how the dataset works. Consult with the QA and Data Analysts to figure out the sample-data relationships and how that should be encoded.<br />
<br />
=== Milestone 5: Build an individual database for your team ===<br />
<br />
* Once the design work has been completed, you need to actually import the data into the database.<br />
* Initially, each team will have their own database so that the QA and Data analysts can validate and use the database.<br />
<br />
=== Milestone 6: Validation and Quality Assurance on Database ===<br />
<br />
* The QA will perform quality assurance to make sure that the database is correct and accurate.<br />
** In particular, the QA needs to make sure that all of the rows of data were imported into the database for the expression table(s).<br />
** The QA will make sure that both the ID (SGD systematic name) and Standard Names are included in each expression table and are correct.<br />
* QA's will communicate to the Coder/Designers any changes needed to the database.<br />
<br />
=== Milestone 7: Merge completed databases into a single database for the class ===<br />
<br />
* As a guild, the Coder/Designers will merge their separate databases into a final product.<br />
* With the QA's finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]<br />
<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7149Ntesfaio Week 12/132019-11-21T03:24:05Z<p>Ntesfaio: /* Individual Journal Assignment */ added to the electronic lab notebook</p>
<hr />
<div>==Electronic Lab Notebook==<br />
<br />
===Project Manager===<br />
<br />
=== Milestone 1: Project “Scaffolding” ===<br />
<br />
This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.<br />
<br />
# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 11]], [[Week 12/13]], and [[Week 15]].<br />
# Organize management tools for your team:<br />
#* Communication tools<br />
#* Workflow narratives<br />
#* Action items<br />
#* Testing results/reports<br />
#** Bugs/feature requests<br />
#** Question/answer sequences<br />
<br />
=== Milestone 2: Periodic Updates ===<br />
<br />
Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.<br />
<br />
# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructor will expect you to know and be able to report on the status of each member of your team at any time.<br />
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder/Designer|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.<br />
# Monitor the status of the report-in-progress and other related documentation.<br />
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7148Ntesfaio Week 12/132019-11-21T03:23:43Z<p>Ntesfaio: /* Electric Lab Notebook */ deleted extra text</p>
<hr />
<div>==Individual Journal Assignment==<br />
<br />
===Project Manager===<br />
<br />
=== Milestone 1: Project “Scaffolding” ===<br />
<br />
This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.<br />
<br />
# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 11]], [[Week 12/13]], and [[Week 15]].<br />
# Organize management tools for your team:<br />
#* Communication tools<br />
#* Workflow narratives<br />
#* Action items<br />
#* Testing results/reports<br />
#** Bugs/feature requests<br />
#** Question/answer sequences<br />
<br />
=== Milestone 2: Periodic Updates ===<br />
<br />
Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.<br />
<br />
# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructor will expect you to know and be able to report on the status of each member of your team at any time.<br />
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder/Designer|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.<br />
# Monitor the status of the report-in-progress and other related documentation.<br />
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaiohttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_12/13&diff=7147Ntesfaio Week 12/132019-11-21T03:23:27Z<p>Ntesfaio: /* Electric Lab Notebook */ added two milestones</p>
<hr />
<div>==Individual Journal Assignment==<br />
<br />
===Electric Lab Notebook===<br />
<br />
===Project Manager===<br />
<br />
=== Milestone 1: Project “Scaffolding” ===<br />
<br />
This milestone pertains to setting up an initial schedule and any resources that your team will use for the duration of the project. It will be useful to get an overview of every team member’s own milestones so that you have an accurate big picture view.<br />
<br />
# In consultation with your team, work backward from the final deadline to set intermediate deadlines for each deliverable. In particular you need to set deadlines for what you will accomplish by the journal deadline for [[Week 11]], [[Week 12/13]], and [[Week 15]].<br />
# Organize management tools for your team:<br />
#* Communication tools<br />
#* Workflow narratives<br />
#* Action items<br />
#* Testing results/reports<br />
#** Bugs/feature requests<br />
#** Question/answer sequences<br />
<br />
=== Milestone 2: Periodic Updates ===<br />
<br />
Not as much a milestone as an on-going task, once the project is up and running the Project Manager is responsible for keeping track of everyone’s progress.<br />
<br />
# Get periodic updates on progress; in particular, the project’s “place” in the overall flow should be known at all times (transparency). Team members will be giving a status reports in class for the rest of the semester. However, the instructor will expect you to know and be able to report on the status of each member of your team at any time.<br />
# Familiarize yourselves with the specific milestones of [[Quality Assurance|each]] [[Coder/Designer|team]] [[Data Analysis|member]] so that you know how to monitor the team’s overall progress.<br />
# Monitor the status of the report-in-progress and other related documentation.<br />
# Coordinate team decisions and action items addressing any unforeseen delays or roadblocks.<br />
<br />
{{Template:Ntesfaio}}<br />
<br />
==Acknowledgments==<br />
<br />
==References==</div>Ntesfaio