https://xmlpipedb2024.lmucs.io/biodb/fall2019/api.php?action=feedcontributions&feedformat=atom&user=ImacaraeLMU BioDB 2019 - User contributions [en]2026-04-08T08:00:00ZUser contributionsMediaWiki 1.32.1https://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7848Sulfiknights Deliverables2019-12-13T23:04:46Z<p>Imacarae: /* Ivy Macaraeg's Final Reflection */ signed</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Checklist:==<br />
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''COMPLETE'''<br />
#Group Report (.doc, .docx or .pdf file) '''COMPLETE'''<br />
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''COMPLETE'''<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. '''COMPLETE'''<br />
<br />
==Group Report==<br />
==Individual Statements of Work, Assessments, Reflections==<br />
===Joey Nimmers-Minor's Final Reflection===<br />
====Individual Assessment and Reflection====<br />
=====Statement of Work=====<br />
<br />
*Describe exactly what you did on the project.<br />
**For this project, I worked in my role as Quality Assurance. I worked along with the rest of my team to understand the data provided by the original journal paper, working alongside Naomi and Delisa to convert and format the data sets to create a uniform set of databases with the other groups. I created and was assisted in the creation and editing of the Access database, as well as the original query done on that database (not to be confused with the finalized schema carried out by Delisa). I assisted my fellow QA with any work she requiremed my help on as well as created/assisted in the creation of the final presentation, namely the materials and methods portion of it. <br />
*Provide references or links to artifacts of your work<br />
**[[Media:SK_Expression-and-Degradation-rate-database_2019.zip | Expression and Degradation Sheet of Thorsen & Dahlquist Data]]<br />
**[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
<br />
===== Assessment of Project =====<br />
<br />
===== Reflection on the Process =====<br />
<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 />
===DeLisa Madere's Final Reflection===<br />
====Statement of Work====<br />
#'''Role as Designer'''<br />
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.<br />
#'''Links to Artifacts'''<br />
#*[[Sulfiknights]]<br />
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip]]<br />
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]<br />
<br />
====Assessment of Project====<br />
#'''Objective Assessment'''<br />
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.<br />
#'''What worked and didn't work?'''<br />
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.<br />
#'''What would you do differently?'''<br />
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.<br />
#'''Team Evaluation'''<br />
#*'''Content'''<br />
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.<br />
#*'''Organization'''<br />
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.<br />
#*'''Completedness'''<br />
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.<br />
<br />
====Reflection on the Process====<br />
#'''What did you learn?'''<br />
#*'''With your Head'''<br />
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.<br />
#*'''With your Heart'''<br />
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules. <br />
#*'''With your Hands'''<br />
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data. <br />
#'''What lessons did you take away from this project that you will still use a year from now?'''<br />
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.<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)<br />
<br />
===Ivy Macaraeg's Final Reflection===<br />
==== Statement of Work ====<br />
<br />
* Describe exactly what you did on the project.<br />
:-For this project, I worked with Marcus to organize and analyze the data. We worked together during and outside of class time to figure out what we needed to do so that the other members of our team could complete their jobs. I also worked with the other groups to better understand my role and the project in general. I helped do the ANOVA, STEM, GO, GRNsight, and GRNmap analyses. I also helped put together the final project and the final report. <br />
* Provide references or links to artifacts of my work:<br />
:-[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
:-[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
:-[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
:-[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]] <br />
:-[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]] <br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
:-[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
:-[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
:-[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
:-[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
:-[[Sulfiknights DA Week 12/13]]<br />
:-[[Sulfiknights DA Week 14]]<br />
<br />
==== Assessment of Project ====<br />
<br />
* Give an objective assessment of the success of your project workflow and teamwork. <br />
:-At first, I think we were a little uneasy and going about our tasks was a little rough because we didn't really know what we were doing. As time moved on, and we remembered the methods of previous weeks, it got easier to complete our tasks. I thought the team work was good. Even though it felt like there was a lot more work for the Data Analysts, everyone was able to do what they needed to and we always offered to help each other out if we needed help. <br />
* What worked and what didn't work? <br />
:-I think what worked the best was how willing everyone was to work together and offer help. Communication between all of us was good, and we helped each other understand what needed to be done. <br />
* What would you do differently if you could do it all over again?<br />
:-If I could do it all over again, I would not be data analyst, not because I did not enjoy the work, but because I would like to see what the coders/designers did and how the schema worked. <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 />
*#:-I think I did well in terms of doing what needed to be done. I think I was pretty thorough, but I probably could have been a little bit neater in terms of getting my files together in an organized spot and formatting everything correctly.<br />
*# Organization: Comment on the organization of the project and of your group's wiki pages.<br />
*#:- I got confused from time to time about what needed to be where. I felt like there were a lot of wiki pages to be managed (Group, individual, deliverables), and I wasn't sure about what exactly had to go on what page. Each page had a lot of components to it and I felt as though it got a little messy.<br />
*# Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
*#:-Yes, we did achieve all of the project objectives because we were able to work efficiently together.<br />
<br />
==== Reflection on the Process ====<br />
<br />
* What did you learn?<br />
** With your head (biological or computer science principles)<br />
**:-I learned how database worked because I had no idea how the technology was organized. I wasn't even familiar with how wiki worked. Biologically related, the biggest takeaway was how microarray data was relevant to biology. I did not know that that method existed. <br />
** With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
**:- I learned that communication is absolutely key. I feel very lucky that I had a team that was dedicated to understanding what we had to do and was able to effectively do their jobs and help me too. I learned that I don't neccesary like the "number crunching" but it makes me pay attention to the directions more. <br />
** With your hands (technical skills)?<br />
**:- I became really familiar with Excel and statistical analysis, more so than I have done before. I also learned how wiki work, and even though it was hard at first, I got the hang of it by the end of the semester. Both of these things were pretty overwhelming at first but I think I just needed more time and practice. <br />
* What lesson will you take away from this project that you will still use a year from now?<br />
**:- Even though this was a very dense project, I think the biggest thing for me was how well my team worked together. I've been in other group projects before, but I think this one worked really well, and I want to learn from it and keep practicing these skills as I go on to work with other people in the future.<br />
<br />
[[User:Imacarae|Imacarae]] ([[User talk:Imacarae|talk]]) 15:04, 13 December 2019 (PST)<br />
<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 />
[[Media:DM_Metadata_Sheet.xlsx|Metadata Sheet]]<br />
<br />
[[Media:DM_ReadMe_Database_Design.docx|Design of Database]]<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|500px]]<br />
[[Image:Degradationrates_923_querydesign.PNG|500px]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG|1000px]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG|1000px]]<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 />
[[Dmadere Week 12|Dmadere Week 12/13]]<br />
<br />
[[Dmadere Week 15]]<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7843Sulfiknights Deliverables2019-12-13T22:48:07Z<p>Imacarae: /* Ivy Macaraeg's Final Reflection */ saved</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Checklist:==<br />
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''COMPLETE'''<br />
#Group Report (.doc, .docx or .pdf file) '''COMPLETE'''<br />
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''COMPLETE'''<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. '''COMPLETE'''<br />
<br />
==Group Report==<br />
==Individual Statements of Work, Assessments, Reflections==<br />
===Joey Nimmers-Minor's Final Reflection===<br />
====Individual Assessment and Reflection====<br />
=====Statement of Work=====<br />
<br />
*Describe exactly what you did on the project.<br />
**For this project, I worked in my role as Quality Assurance. I worked along with the rest of my team to understand the data provided by the original journal paper, working alongside Naomi and Delisa to convert and format the data sets to create a uniform set of databases with the other groups. I created and was assisted in the creation and editing of the Access database, as well as the original query done on that database (not to be confused with the finalized schema carried out by Delisa). I assisted my fellow QA with any work she requiremed my help on as well as created/assisted in the creation of the final presentation, namely the materials and methods portion of it. <br />
*Provide references or links to artifacts of your work<br />
**[[Media:SK_Expression-and-Degradation-rate-database_2019.zip | Expression and Degradation Sheet of Thorsen & Dahlquist Data]]<br />
**[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
<br />
===== Assessment of Project =====<br />
<br />
===== Reflection on the Process =====<br />
<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 />
===DeLisa Madere's Final Reflection===<br />
====Statement of Work====<br />
#'''Role as Designer'''<br />
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.<br />
#'''Links to Artifacts'''<br />
#*[[Sulfiknights]]<br />
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip]]<br />
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]<br />
<br />
====Assessment of Project====<br />
#'''Objective Assessment'''<br />
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.<br />
#'''What worked and didn't work?'''<br />
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.<br />
#'''What would you do differently?'''<br />
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.<br />
#'''Team Evaluation'''<br />
#*'''Content'''<br />
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.<br />
#*'''Organization'''<br />
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.<br />
#*'''Completedness'''<br />
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.<br />
<br />
====Reflection on the Process====<br />
#'''What did you learn?'''<br />
#*'''With your Head'''<br />
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.<br />
#*'''With your Heart'''<br />
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules. <br />
#*'''With your Hands'''<br />
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data. <br />
#'''What lessons did you take away from this project that you will still use a year from now?'''<br />
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.<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)<br />
<br />
===Ivy Macaraeg's Final Reflection===<br />
==== Statement of Work ====<br />
<br />
* Describe exactly what you did on the project.<br />
:-For this project, I worked with Marcus to organize and analyze the data. We worked together during and outside of class time to figure out what we needed to do so that the other members of our team could complete their jobs. I also worked with the other groups to better understand my role and the project in general. I helped do the ANOVA, STEM, GO, GRNsight, and GRNmap analyses. I also helped put together the final project and the final report. <br />
* Provide references or links to artifacts of my work:<br />
:-[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
:-[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
:-[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
:-[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]] <br />
:-[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]] <br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
:-[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
:-[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
:-[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
:-[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
:-[[Sulfiknights DA Week 12/13]]<br />
:-[[Sulfiknights DA Week 14]]<br />
<br />
==== Assessment of Project ====<br />
<br />
* Give an objective assessment of the success of your project workflow and teamwork. <br />
:-At first, I think we were a little uneasy and going about our tasks was a little rough because we didn't really know what we were doing. As time moved on, and we remembered the methods of previous weeks, it got easier to complete our tasks. I thought the team work was good. Even though it felt like there was a lot more work for the Data Analysts, everyone was able to do what they needed to and we always offered to help each other out if we needed help. <br />
* What worked and what didn't work? <br />
:-I think what worked the best was how willing everyone was to work together and offer help. Communication between all of us was good, and we helped each other understand what needed to be done. <br />
* What would you do differently if you could do it all over again?<br />
:-If I could do it all over again, I would not be data analyst, not because I did not enjoy the work, but because I would like to see what the coders/designers did and how the schema worked. <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 />
*#:-I think I did well in terms of doing what needed to be done. I think I was pretty thorough, but I probably could have been a little bit neater in terms of getting my files together in an organized spot and formatting everything correctly.<br />
*# Organization: Comment on the organization of the project and of your group's wiki pages.<br />
*#:- I got confused from time to time about what needed to be where. I felt like there were a lot of wiki pages to be managed (Group, individual, deliverables), and I wasn't sure about what exactly had to go on what page. Each page had a lot of components to it and I felt as though it got a little messy.<br />
*# Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
*#:-Yes, we did achieve all of the project objectives because we were able to work efficiently together.<br />
<br />
==== Reflection on the Process ====<br />
<br />
* What did you learn?<br />
** With your head (biological or computer science principles)<br />
**:-I learned how database worked because I had no idea how the technology was organized. I wasn't even familiar with how wiki worked. Biologically related, the biggest takeaway was how microarray data was relevant to biology. I did not know that that method existed. <br />
** With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
**:- I learned that communication is absolutely key. I feel very lucky that I had a team that was dedicated to understanding what we had to do and was able to effectively do their jobs and help me too. I learned that I don't neccesary like the "number crunching" but it makes me pay attention to the directions more. <br />
** With your hands (technical skills)?<br />
**:- I became really familiar with Excel and statistical analysis, more so than I have done before. I also learned how wiki work, and even though it was hard at first, I got the hang of it by the end of the semester. Both of these things were pretty overwhelming at first but I think I just needed more time and practice. <br />
* What lesson will you take away from this project that you will still use a year from now?<br />
**:- Even though this was a very dense project, I think the biggest thing for me was how well my team worked together. I've been in other group projects before, but I think this one worked really well, and I want to learn from it and keep practicing these skills as I go on to work with other people in the future.<br />
<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|500px]]<br />
[[Image:Degradationrates_923_querydesign.PNG|500px]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG|1000px]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG|1000px]]<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 />
[[Dmadere Week 12|Dmadere Week 12/13]]<br />
<br />
[[Dmadere Week 15]]<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:DM_Metadata_Sheet.xlsx|Metadata Sheet]]<br />
<br />
[[Image:Access_Database_Schema_Screenshot.PNG|1000px|Access_Database_Schema_Screenshot.PNG]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7842Sulfiknights Deliverables2019-12-13T22:44:41Z<p>Imacarae: /* Checklist: */ marked complete</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Checklist:==<br />
#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) '''COMPLETE'''<br />
#Group Report (.doc, .docx or .pdf file) '''COMPLETE'''<br />
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)'''COMPLETE'''<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. '''COMPLETE'''<br />
<br />
==Group Report==<br />
==Individual Statements of Work, Assessments, Reflections==<br />
===Joey Nimmers-Minor's Final Reflection===<br />
====Individual Assessment and Reflection====<br />
=====Statement of Work=====<br />
<br />
*Describe exactly what you did on the project.<br />
**For this project, I worked in my role as Quality Assurance. I worked along with the rest of my team to understand the data provided by the original journal paper, working alongside Naomi and Delisa to convert and format the data sets to create a uniform set of databases with the other groups. I created and was assisted in the creation and editing of the Access database, as well as the original query done on that database (not to be confused with the finalized schema carried out by Delisa). I assisted my fellow QA with any work she requiremed my help on as well as created/assisted in the creation of the final presentation, namely the materials and methods portion of it. <br />
*Provide references or links to artifacts of your work<br />
**[[Media:SK_Expression-and-Degradation-rate-database_2019.zip | Expression and Degradation Sheet of Thorsen & Dahlquist Data]]<br />
**[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
<br />
===== Assessment of Project =====<br />
<br />
===== Reflection on the Process =====<br />
<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 />
===DeLisa Madere's Final Reflection===<br />
====Statement of Work====<br />
#'''Role as Designer'''<br />
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.<br />
#'''Links to Artifacts'''<br />
#*[[Sulfiknights]]<br />
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip]]<br />
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]<br />
<br />
====Assessment of Project====<br />
#'''Objective Assessment'''<br />
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.<br />
#'''What worked and didn't work?'''<br />
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.<br />
#'''What would you do differently?'''<br />
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.<br />
#'''Team Evaluation'''<br />
#*'''Content'''<br />
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.<br />
#*'''Organization'''<br />
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.<br />
#*'''Completedness'''<br />
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.<br />
<br />
====Reflection on the Process====<br />
#'''What did you learn?'''<br />
#*'''With your Head'''<br />
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.<br />
#*'''With your Heart'''<br />
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules. <br />
#*'''With your Hands'''<br />
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data. <br />
#'''What lessons did you take away from this project that you will still use a year from now?'''<br />
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.<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)<br />
<br />
===Ivy Macaraeg's Final Reflection===<br />
==== Statement of Work ====<br />
<br />
* Describe exactly what you did on the project.<br />
:-For this project, I worked with Marcus to organize and analyze the data. We worked together during and outside of class time to figure out what we needed to do so that the other members of our team could complete their jobs. I also worked with the other groups to better understand my role and the project in general. I helped do the ANOVA, STEM, GO, GRNsight, and GRNmap analyses. I also helped put together the final project and the final report. <br />
* Provide references or links to artifacts of my work:<br />
:-[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
:-[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
:-[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
:-[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]], [[Media:Profil923_GRNsight_matrix.PNG]]<br />
:-[[Media:Colored_GRNsight_923.PNG]]<br />
:-[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
:-[[Media:Profile4048_GRNsight_matrix.PNG]], [[Media:Colored GRNsight 4048.PNG]]<br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]] <br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
:-[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
:-[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
:-[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
:-[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
:-[[Sulfiknights DA Week 12/13]]<br />
:-[[Sulfiknights DA Week 14]]<br />
<br />
==== Assessment of Project ====<br />
<br />
* Give an objective assessment of the success of your project workflow and teamwork. <br />
:-At first, I think we were a little uneasy and going about our tasks was a little rough because we didn't really know what we were doing. As time moved on, and we remembered the methods of previous weeks, it got easier to complete our tasks. I thought the team work was good. Even though it felt like there was a lot more work for the Data Analysts, everyone was able to do what they needed to and we always offered to help each other out if we needed help. <br />
* What worked and what didn't work? <br />
:-I think what worked the best was how willing everyone was to work together and offer help. Communication between all of us was good, and we helped each other understand what needed to be done. <br />
* What would you do differently if you could do it all over again?<br />
:-If I could do it all over again, I would not be data analyst, not because I did not enjoy the work, but because I would like to see what the coders/designers did and how the schema worked. <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 />
*#:-I think I did well in terms of doing what needed to be done. I think I was pretty thorough, but I probably could have been a little bit neater in terms of getting my files together in an organized spot and formatting everything correctly.<br />
*# Organization: Comment on the organization of the project and of your group's wiki pages.<br />
*#:- I got confused from time to time about what needed to be where. I felt like there were a lot of wiki pages to be managed (Group, individual, deliverables), and I wasn't sure about what exactly had to go on what page. Each page had a lot of components to it and I felt as though it got a little messy.<br />
*# Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
*#:-Yes, we did achieve all of the project objectives because we were able to work efficiently together.<br />
<br />
==== Reflection on the Process ====<br />
<br />
* What did you learn?<br />
** With your head (biological or computer science principles)<br />
**:-I learned how database worked because I had no idea how the technology was organized. I wasn't even familiar with how wiki worked. Biologically related, the biggest takeaway was how microarray data was relevant to biology. I did not know that that method existed. <br />
** With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
**:- I learned that communication is absolutely key. I feel very lucky that I had a team that was dedicated to understanding what we had to do and was able to effectively do their jobs and help me too. I learned that I don't neccesary like the "number crunching" but it makes me pay attention to the directions more. <br />
** With your hands (technical skills)?<br />
**:- I became really familiar with Excel and statistical analysis, more so than I have done before. I also learned how wiki work, and even though it was hard at first, I got the hang of it by the end of the semester. Both of these things were pretty overwhelming at first but I think I just needed more time and practice. <br />
* What lesson will you take away from this project that you will still use a year from now?<br />
**:- Even though this was a very dense project, I think the biggest thing for me was how well my team worked together. I've been in other group projects before, but I think this one worked really well, and I want to learn from it and keep practicing these skills as I go on to work with other people in the future.<br />
<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|500px]]<br />
[[Image:Degradationrates_923_querydesign.PNG|500px]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG|1000px]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG|1000px]]<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 />
[[Dmadere Week 12|Dmadere Week 12/13]]<br />
<br />
[[Dmadere Week 15]]<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:DM_Metadata_Sheet.xlsx|Metadata Sheet]]<br />
<br />
[[Image:Access_Database_Schema_Screenshot.PNG|1000px|Access_Database_Schema_Screenshot.PNG]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7841Sulfiknights Deliverables2019-12-13T22:44:11Z<p>Imacarae: /* Reflection on the Process */ answered questions</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 />
===Joey Nimmers-Minor's Final Reflection===<br />
====Individual Assessment and Reflection====<br />
=====Statement of Work=====<br />
<br />
*Describe exactly what you did on the project.<br />
**For this project, I worked in my role as Quality Assurance. I worked along with the rest of my team to understand the data provided by the original journal paper, working alongside Naomi and Delisa to convert and format the data sets to create a uniform set of databases with the other groups. I created and was assisted in the creation and editing of the Access database, as well as the original query done on that database (not to be confused with the finalized schema carried out by Delisa). I assisted my fellow QA with any work she requiremed my help on as well as created/assisted in the creation of the final presentation, namely the materials and methods portion of it. <br />
*Provide references or links to artifacts of your work<br />
**[[Media:SK_Expression-and-Degradation-rate-database_2019.zip | Expression and Degradation Sheet of Thorsen & Dahlquist Data]]<br />
**[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
<br />
===== Assessment of Project =====<br />
<br />
===== Reflection on the Process =====<br />
<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 />
===DeLisa Madere's Final Reflection===<br />
====Statement of Work====<br />
#'''Role as Designer'''<br />
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.<br />
#'''Links to Artifacts'''<br />
#*[[Sulfiknights]]<br />
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip]]<br />
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]<br />
<br />
====Assessment of Project====<br />
#'''Objective Assessment'''<br />
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.<br />
#'''What worked and didn't work?'''<br />
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.<br />
#'''What would you do differently?'''<br />
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.<br />
#'''Team Evaluation'''<br />
#*'''Content'''<br />
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.<br />
#*'''Organization'''<br />
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.<br />
#*'''Completedness'''<br />
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.<br />
<br />
====Reflection on the Process====<br />
#'''What did you learn?'''<br />
#*'''With your Head'''<br />
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.<br />
#*'''With your Heart'''<br />
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules. <br />
#*'''With your Hands'''<br />
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data. <br />
#'''What lessons did you take away from this project that you will still use a year from now?'''<br />
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.<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)<br />
<br />
===Ivy Macaraeg's Final Reflection===<br />
==== Statement of Work ====<br />
<br />
* Describe exactly what you did on the project.<br />
:-For this project, I worked with Marcus to organize and analyze the data. We worked together during and outside of class time to figure out what we needed to do so that the other members of our team could complete their jobs. I also worked with the other groups to better understand my role and the project in general. I helped do the ANOVA, STEM, GO, GRNsight, and GRNmap analyses. I also helped put together the final project and the final report. <br />
* Provide references or links to artifacts of my work:<br />
:-[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
:-[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
:-[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
:-[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]], [[Media:Profil923_GRNsight_matrix.PNG]]<br />
:-[[Media:Colored_GRNsight_923.PNG]]<br />
:-[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
:-[[Media:Profile4048_GRNsight_matrix.PNG]], [[Media:Colored GRNsight 4048.PNG]]<br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]] <br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
:-[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
:-[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
:-[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
:-[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
:-[[Sulfiknights DA Week 12/13]]<br />
:-[[Sulfiknights DA Week 14]]<br />
<br />
==== Assessment of Project ====<br />
<br />
* Give an objective assessment of the success of your project workflow and teamwork. <br />
:-At first, I think we were a little uneasy and going about our tasks was a little rough because we didn't really know what we were doing. As time moved on, and we remembered the methods of previous weeks, it got easier to complete our tasks. I thought the team work was good. Even though it felt like there was a lot more work for the Data Analysts, everyone was able to do what they needed to and we always offered to help each other out if we needed help. <br />
* What worked and what didn't work? <br />
:-I think what worked the best was how willing everyone was to work together and offer help. Communication between all of us was good, and we helped each other understand what needed to be done. <br />
* What would you do differently if you could do it all over again?<br />
:-If I could do it all over again, I would not be data analyst, not because I did not enjoy the work, but because I would like to see what the coders/designers did and how the schema worked. <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 />
*#:-I think I did well in terms of doing what needed to be done. I think I was pretty thorough, but I probably could have been a little bit neater in terms of getting my files together in an organized spot and formatting everything correctly.<br />
*# Organization: Comment on the organization of the project and of your group's wiki pages.<br />
*#:- I got confused from time to time about what needed to be where. I felt like there were a lot of wiki pages to be managed (Group, individual, deliverables), and I wasn't sure about what exactly had to go on what page. Each page had a lot of components to it and I felt as though it got a little messy.<br />
*# Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
*#:-Yes, we did achieve all of the project objectives because we were able to work efficiently together.<br />
<br />
==== Reflection on the Process ====<br />
<br />
* What did you learn?<br />
** With your head (biological or computer science principles)<br />
**:-I learned how database worked because I had no idea how the technology was organized. I wasn't even familiar with how wiki worked. Biologically related, the biggest takeaway was how microarray data was relevant to biology. I did not know that that method existed. <br />
** With your heart (personal qualities and teamwork qualities that make things work or not work)?<br />
**:- I learned that communication is absolutely key. I feel very lucky that I had a team that was dedicated to understanding what we had to do and was able to effectively do their jobs and help me too. I learned that I don't neccesary like the "number crunching" but it makes me pay attention to the directions more. <br />
** With your hands (technical skills)?<br />
**:- I became really familiar with Excel and statistical analysis, more so than I have done before. I also learned how wiki work, and even though it was hard at first, I got the hang of it by the end of the semester. Both of these things were pretty overwhelming at first but I think I just needed more time and practice. <br />
* What lesson will you take away from this project that you will still use a year from now?<br />
**:- Even though this was a very dense project, I think the biggest thing for me was how well my team worked together. I've been in other group projects before, but I think this one worked really well, and I want to learn from it and keep practicing these skills as I go on to work with other people in the future.<br />
<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|500px]]<br />
[[Image:Degradationrates_923_querydesign.PNG|500px]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG|1000px]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG|1000px]]<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 />
[[Dmadere Week 12|Dmadere Week 12/13]]<br />
<br />
[[Dmadere Week 15]]<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:DM_Metadata_Sheet.xlsx|Metadata Sheet]]<br />
<br />
[[Image:Access_Database_Schema_Screenshot.PNG|1000px|Access_Database_Schema_Screenshot.PNG]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7837Sulfiknights Deliverables2019-12-13T22:37:12Z<p>Imacarae: /* Assessment of Project */ edited</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 />
===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 />
===DeLisa Madere's Final Reflection===<br />
====Statement of Work====<br />
#'''Role as Designer'''<br />
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.<br />
#'''Links to Artifacts'''<br />
#*[[Sulfiknights]]<br />
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip]]<br />
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]<br />
<br />
====Assessment of Project====<br />
#'''Objective Assessment'''<br />
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.<br />
#'''What worked and didn't work?'''<br />
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.<br />
#'''What would you do differently?'''<br />
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.<br />
#'''Team Evaluation'''<br />
#*'''Content'''<br />
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.<br />
#*'''Organization'''<br />
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.<br />
#*'''Completedness'''<br />
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.<br />
<br />
====Reflection on the Process====<br />
#'''What did you learn?'''<br />
#*'''With your Head'''<br />
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.<br />
#*'''With your Heart'''<br />
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules. <br />
#*'''With your Hands'''<br />
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data. <br />
#'''What lessons did you take away from this project that you will still use a year from now?'''<br />
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.<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)<br />
<br />
===Ivy Macaraeg's Final Reflection===<br />
==== Statement of Work ====<br />
<br />
* Describe exactly what you did on the project.<br />
:-For this project, I worked with Marcus to organize and analyze the data. We worked together during and outside of class time to figure out what we needed to do so that the other members of our team could complete their jobs. I also worked with the other groups to better understand my role and the project in general. I helped do the ANOVA, STEM, GO, GRNsight, and GRNmap analyses. I also helped put together the final project and the final report. <br />
* Provide references or links to artifacts of my work:<br />
:-[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
:-[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
:-[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
:-[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]], [[Media:Profil923_GRNsight_matrix.PNG]]<br />
:-[[Media:Colored_GRNsight_923.PNG]]<br />
:-[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
:-[[Media:Profile4048_GRNsight_matrix.PNG]], [[Media:Colored GRNsight 4048.PNG]]<br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]] <br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
:-[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
:-[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
:-[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
:-[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
:-[[Sulfiknights DA Week 12/13]]<br />
:-[[Sulfiknights DA Week 14]]<br />
<br />
==== Assessment of Project ====<br />
<br />
* Give an objective assessment of the success of your project workflow and teamwork. <br />
:-At first, I think we were a little uneasy and going about our tasks was a little rough because we didn't really know what we were doing. As time moved on, and we remembered the methods of previous weeks, it got easier to complete our tasks. I thought the team work was good. Even though it felt like there was a lot more work for the Data Analysts, everyone was able to do what they needed to and we always offered to help each other out if we needed help. <br />
* What worked and what didn't work? <br />
:-I think what worked the best was how willing everyone was to work together and offer help. Communication between all of us was good, and we helped each other understand what needed to be done. <br />
* What would you do differently if you could do it all over again?<br />
:-If I could do it all over again, I would not be data analyst, not because I did not enjoy the work, but because I would like to see what the coders/designers did and how the schema worked. <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 />
*#:-I think I did well in terms of doing what needed to be done. I think I was pretty thorough, but I probably could have been a little bit neater in terms of getting my files together in an organized spot and formatting everything correctly.<br />
*# Organization: Comment on the organization of the project and of your group's wiki pages.<br />
*#:- I got confused from time to time about what needed to be where. I felt like there were a lot of wiki pages to be managed (Group, individual, deliverables), and I wasn't sure about what exactly had to go on what page. Each page had a lot of components to it and I felt as though it got a little messy.<br />
*# Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
*#:-Yes, we did achieve all of the project objectives because we were able to work efficiently together.<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 />
==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|500px]]<br />
[[Image:Degradationrates_923_querydesign.PNG|500px]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG|1000px]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG|1000px]]<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 />
[[Dmadere Week 12|Dmadere Week 12/13]]<br />
<br />
[[Dmadere Week 15]]<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:DM_Metadata_Sheet.xlsx|Metadata Sheet]]<br />
<br />
[[Image:Access_Database_Schema_Screenshot.PNG|1000px|Access_Database_Schema_Screenshot.PNG]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7835Sulfiknights Deliverables2019-12-13T22:33:09Z<p>Imacarae: /* Assessment of Project */ answered qs</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 />
===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 />
===DeLisa Madere's Final Reflection===<br />
====Statement of Work====<br />
#'''Role as Designer'''<br />
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.<br />
#'''Links to Artifacts'''<br />
#*[[Sulfiknights]]<br />
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip]]<br />
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]<br />
<br />
====Assessment of Project====<br />
#'''Objective Assessment'''<br />
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.<br />
#'''What worked and didn't work?'''<br />
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.<br />
#'''What would you do differently?'''<br />
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.<br />
#'''Team Evaluation'''<br />
#*'''Content'''<br />
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.<br />
#*'''Organization'''<br />
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.<br />
#*'''Completedness'''<br />
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.<br />
<br />
====Reflection on the Process====<br />
#'''What did you learn?'''<br />
#*'''With your Head'''<br />
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.<br />
#*'''With your Heart'''<br />
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules. <br />
#*'''With your Hands'''<br />
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data. <br />
#'''What lessons did you take away from this project that you will still use a year from now?'''<br />
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.<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)<br />
<br />
===Ivy Macaraeg's Final Reflection===<br />
==== Statement of Work ====<br />
<br />
* Describe exactly what you did on the project.<br />
:-For this project, I worked with Marcus to organize and analyze the data. We worked together during and outside of class time to figure out what we needed to do so that the other members of our team could complete their jobs. I also worked with the other groups to better understand my role and the project in general. I helped do the ANOVA, STEM, GO, GRNsight, and GRNmap analyses. I also helped put together the final project and the final report. <br />
* Provide references or links to artifacts of my work:<br />
:-[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
:-[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
:-[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
:-[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]], [[Media:Profil923_GRNsight_matrix.PNG]]<br />
:-[[Media:Colored_GRNsight_923.PNG]]<br />
:-[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
:-[[Media:Profile4048_GRNsight_matrix.PNG]], [[Media:Colored GRNsight 4048.PNG]]<br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]] <br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
:-[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
:-[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
:-[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
:-[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
:-[[Sulfiknights DA Week 12/13]]<br />
:-[[Sulfiknights DA Week 14]]<br />
<br />
==== Assessment of Project ====<br />
<br />
* Give an objective assessment of the success of your project workflow and teamwork. <br />
:-At first, I think we were a little uneasy and going about our tasks was a little rough because we didn't really know what we were doing. As time moved on, and we remembered the methods of previous weeks, it got easier to complete our tasks. I thought the team work was good. Even though it felt like there was a lot more work for the Data Analysts, everyone was able to do what they needed to and we always offered to help each other out if we needed help. <br />
* What worked and what didn't work? <br />
:-I think what worked the best was how willing everyone was to work together and offer help. Communication between all of us was good, and we helped each other understand what needed to be done. <br />
* What would you do differently if you could do it all over again?<br />
:-If I could do it all over again, I would not be data analyst, not because I did not enjoy the work, but because I would like to see what the coders/designers did and how the schema worked. <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 />
*:-I think I did well in terms of doing what needed to be done. I think I was pretty thorough, but I probably could have been a little bit neater in terms of getting my files together in an organized spot and formatting everything correctly.<br />
*# Organization: Comment on the organization of the project and of your group's wiki pages.<br />
*:- I got confused from time to time about what needed to be where. I felt like there were a lot of wiki pages to be managed (Group, individual, deliverables), and I wasn't sure about what exactly had to go on what page. Each page had a lot of components to it and I felt as though it got a little messy.<br />
*# Completeness: Did your team achieve all of the project objectives? Why or why not?<br />
*:-Yes, we did achieve all of the project objectives because we were able to work efficiently together.<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 />
==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|500px]]<br />
[[Image:Degradationrates_923_querydesign.PNG|500px]]<br />
[[Image:Thorsen_2007_log2_expression_923_querydesign.PNG|1000px]]<br />
<br />
'''Profiles 40 and 48:'''<br />
<br />
[[Image:ProductionRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:DegradationRates 4048 QueryDesign.PNG|500px]]<br />
[[Image:Thorsen 2007 log2 expression QueryDesign.PNG|1000px]]<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 />
[[Dmadere Week 12|Dmadere Week 12/13]]<br />
<br />
[[Dmadere Week 15]]<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:DM_Metadata_Sheet.xlsx|Metadata Sheet]]<br />
<br />
[[Image:Access_Database_Schema_Screenshot.PNG|1000px|Access_Database_Schema_Screenshot.PNG]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7832Sulfiknights Deliverables2019-12-13T22:13:16Z<p>Imacarae: /* Statement of Work */ edited</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 />
===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 />
===DeLisa Madere's Final Reflection===<br />
====Statement of Work====<br />
#'''Role as Designer'''<br />
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.<br />
#'''Links to Artifacts'''<br />
#*[[Sulfiknights]]<br />
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip]]<br />
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]<br />
<br />
====Assessment of Project====<br />
#'''Objective Assessment'''<br />
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.<br />
#'''What worked and didn't work?'''<br />
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.<br />
#'''What would you do differently?'''<br />
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.<br />
#'''Team Evaluation'''<br />
#*'''Content'''<br />
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.<br />
#*'''Organization'''<br />
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.<br />
#*'''Completedness'''<br />
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.<br />
<br />
====Reflection on the Process====<br />
#'''What did you learn?'''<br />
#*'''With your Head'''<br />
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.<br />
#*'''With your Heart'''<br />
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules. <br />
#*'''With your Hands'''<br />
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data. <br />
#'''What lessons did you take away from this project that you will still use a year from now?'''<br />
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.<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)<br />
<br />
===Ivy Macaraeg's Final Reflection===<br />
==== Statement of Work ====<br />
<br />
* Describe exactly what you did on the project.<br />
:-For this project, I worked with Marcus to organize and analyze the data. We worked together during and outside of class time to figure out what we needed to do so that the other members of our team could complete their jobs. I also worked with the other groups to better understand my role and the project in general. I helped do the ANOVA, STEM, GO, GRNsight, and GRNmap analyses. I also helped put together the final project and the final report. <br />
* Provide references or links to artifacts of my work:<br />
:-[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
:-[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
:-[[Media:Thorsendata_sulfiknights_pvalueslide.pptx|PowerPoint of ANOVA table and Screenshots of STEM Profile Results]]<br />
:-[[Media:Profile923_GRNsight_network.xlsx| Profiles 9 and 23 input network (Excel)]], [[Media:Profil923_GRNsight_matrix.PNG]]<br />
:-[[Media:Colored_GRNsight_923.PNG]]<br />
:-[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
:-[[Media:Profile4048_GRNsight_matrix.PNG]], [[Media:Colored GRNsight 4048.PNG]]<br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_genelist.zip|Zipped Gene Lists for Significant Profiles]] <br />
:-[[Media:SwtVnwt_1mM_ALLprofiles_GOlist.zip|Zipped GOLists for Significant Profiles]]<br />
:-[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
:-[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
:-[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
:-[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
:-[[Sulfiknights DA Week 12/13]]<br />
:-[[Sulfiknights DA Week 14]]<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 />
==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 />
[[Dmadere Week 12|Dmadere Week 12/13]]<br />
<br />
[[Dmadere Week 15]]<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:DM_Metadata_Sheet.xlsx|Metadata Sheet]]<br />
<br />
[[Image:Access_Database_Schema_Screenshot.PNG|1000px|Access_Database_Schema_Screenshot.PNG]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7827Sulfiknights Deliverables2019-12-13T22:05:19Z<p>Imacarae: /* Ivy Macaraeg's Final Reflection */ added links</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 />
===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 />
===DeLisa Madere's Final Reflection===<br />
====Statement of Work====<br />
#'''Role as Designer'''<br />
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.<br />
#'''Links to Artifacts'''<br />
#*[[Sulfiknights]]<br />
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip]]<br />
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]<br />
<br />
====Assessment of Project====<br />
#'''Objective Assessment'''<br />
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.<br />
#'''What worked and didn't work?'''<br />
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.<br />
#'''What would you do differently?'''<br />
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.<br />
#'''Team Evaluation'''<br />
#*'''Content'''<br />
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.<br />
#*'''Organization'''<br />
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.<br />
#*'''Completedness'''<br />
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.<br />
<br />
====Reflection on the Process====<br />
#'''What did you learn?'''<br />
#*'''With your Head'''<br />
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.<br />
#*'''With your Heart'''<br />
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules. <br />
#*'''With your Hands'''<br />
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data. <br />
#'''What lessons did you take away from this project that you will still use a year from now?'''<br />
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.<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)<br />
<br />
===Ivy Macaraeg's Final Reflection===<br />
==== Statement of Work ====<br />
<br />
* Describe exactly what you did on the project.<br />
:-For this project, I worked with Marcus to organize and analyze the data. We worked together during and outside of class time to figure out what we needed to do so that the other members of our team could complete their jobs. I also worked with the other groups to better understand my role and the project in general. I helped do the ANOVA, STEM, GO, GRNsight, and GRNmap analyses. I also helped put together the final project and the final report. <br />
* Provide references or links to artifacts of my work:<br />
[[Media:Sulfiknights_Final_Presentation.pptx| Sulfiknights Final Presentation]]<br />
<br />
[[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data (Updated 12/2/19)]]<br />
<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)]], [[Media:Profil923_GRNsight_matrix.PNG]]<br />
<br />
[[Media:Colored_GRNsight_923.PNG]]<br />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Media:Profile4048_GRNsight_matrix.PNG]], [[Media:Colored GRNsight 4048.PNG]]<br />
<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 />
[[Media:Profile923_rankedbytf.xlsx|Profiles 9 and 23]]<br />
<br />
[[Media:Profile4048_rankedbytf.xlsx|Profiles 40 and 48]]<br />
<br />
[[Media:GRNmap923_input_worksheet.xlsx|GRNmap Input Worksheet: Profiles 9 and 23]]<br />
<br />
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
<br />
[[Sulfiknights DA Week 12/13]]<br />
<br />
[[Sulfiknights DA Week 14]]<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 />
==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 />
[[Dmadere Week 12|Dmadere Week 12/13]]<br />
<br />
[[Dmadere Week 15]]<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7825Sulfiknights Deliverables2019-12-13T21:54:08Z<p>Imacarae: /* Naomi Tesfaiohannes's Final Reflection */ added my header</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 />
===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 />
===DeLisa Madere's Final Reflection===<br />
====Statement of Work====<br />
#'''Role as Designer'''<br />
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.<br />
#'''Links to Artifacts'''<br />
#*[[Sulfiknights]]<br />
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip]]<br />
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]<br />
<br />
====Assessment of Project====<br />
#'''Objective Assessment'''<br />
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.<br />
#'''What worked and didn't work?'''<br />
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.<br />
#'''What would you do differently?'''<br />
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.<br />
#'''Team Evaluation'''<br />
#*'''Content'''<br />
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.<br />
#*'''Organization'''<br />
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.<br />
#*'''Completedness'''<br />
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.<br />
<br />
====Reflection on the Process====<br />
#'''What did you learn?'''<br />
#*'''With your Head'''<br />
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.<br />
#*'''With your Heart'''<br />
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules. <br />
#*'''With your Hands'''<br />
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data. <br />
#'''What lessons did you take away from this project that you will still use a year from now?'''<br />
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.<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)<br />
<br />
===Ivy Macaraeg's Final Reflection===<br />
<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 />
[[Dmadere Week 12|Dmadere Week 12/13]]<br />
<br />
[[Dmadere Week 15]]<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7824Sulfiknights Deliverables2019-12-13T21:53:11Z<p>Imacarae: edited header</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 />
===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 />
===DeLisa Madere's Final Reflection===<br />
====Statement of Work====<br />
#'''Role as Designer'''<br />
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.<br />
#'''Links to Artifacts'''<br />
#*[[Sulfiknights]]<br />
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip]]<br />
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]<br />
<br />
====Assessment of Project====<br />
#'''Objective Assessment'''<br />
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.<br />
#'''What worked and didn't work?'''<br />
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.<br />
#'''What would you do differently?'''<br />
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.<br />
#'''Team Evaluation'''<br />
#*'''Content'''<br />
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.<br />
#*'''Organization'''<br />
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.<br />
#*'''Completedness'''<br />
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.<br />
<br />
====Reflection on the Process====<br />
#'''What did you learn?'''<br />
#*'''With your Head'''<br />
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.<br />
#*'''With your Heart'''<br />
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules. <br />
#*'''With your Hands'''<br />
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data. <br />
#'''What lessons did you take away from this project that you will still use a year from now?'''<br />
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.<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)<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 />
[[Dmadere Week 12|Dmadere Week 12/13]]<br />
<br />
[[Dmadere Week 15]]<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7823Sulfiknights Deliverables2019-12-13T21:52:37Z<p>Imacarae: moved reflections</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 />
==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 />
===DeLisa Madere's Final Reflection===<br />
====Statement of Work====<br />
#'''Role as Designer'''<br />
#*My role in this project was a Designer. As a designer, I collaborated with the other coders to come up with a metadata sheet incorporating information regarding the citations of the paper as well as the sample-to-data sheet including the different treatments, yeast strains, timepoints, concentrations, and replicates. After creating the metadata sheet, I worked with the QAs to create the database compiling the datasets from our microarray data for the Data Analysts to analyze further. Once all the data was analyzed, I then worked with the QAs and the other coders to create a database compiling our data, the degradation rates, production rates, metadata table, as well as the other datasets from the other groups (FunGals, Skinny Genes, Dahlquist Lab) to visualize the relationships in a database schema. Each dataset was standardized under common headers such as author_publicationyear_log2_expression, and each dataset had common headers as well representing each replicate such as yeaststrain_treatment_concentration_LogFC_time-replicate. The final database is linked together through a standardized ID that each of the datasets contained.<br />
#'''Links to Artifacts'''<br />
#*[[Sulfiknights]]<br />
#*[[Media:Access_Database_Schema_Screenshot.PNG|Access_Database_Schema_Screenshot.PNG]]<br />
#*[[Media:BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip |BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip]]<br />
#*[[Media:DM_Metadata_Sheet.xlsx|Sulfiknights Meta Data Sheet]]<br />
<br />
====Assessment of Project====<br />
#'''Objective Assessment'''<br />
#*Overall, our team did a great job with staying on task. With the responsibilities that we were given for this project, our team carried them out in a timely manner, and we all worked together to get it done. We consistently met up to talk about our project and asked each other for help along the way, creating a strong group dynamic.<br />
#'''What worked and didn't work?'''<br />
#*What worked really well was that we each focused on our specific responsibilities and asked each other if we needed assistance. From focusing on our own tasks, we were able to understand our roles more. The only difficulty with this project was the workload that we each had outside of this, so maintaining a balance between our Database coursework and our other coursework.<br />
#'''What would you do differently?'''<br />
#*Since my responsibility came a little later on in the milestones, I would have liked to understand more what the other members of my group were doing, specifically the data analysts. I would have had a better understanding early on what actions were being carried out in the project. I would like to also have taken more initiative in helping the other members.<br />
#'''Team Evaluation'''<br />
#*'''Content'''<br />
#::-I think the quality of work was good. I feel very proud of our team in the way that we presented our data to the class and was happy with the outcome.<br />
#*'''Organization'''<br />
#::-The organization of our project was good. Since the project itself was very step-by-step, that helped us with coming up with a timeline of each of our milestones. Regarding the wiki page, our deliverables page is very well organized with each assignment that needs to be on it and whether or not the task is complete. There is always room for improvement with organization in general, so there could have been a better flow with navigating certain links, but overall our organization turned out good.<br />
#*'''Completedness'''<br />
#::-Our team completed all of the project objectives. There was not one moment where we forgot to do something or neglected to include something. We were able to complete everything and in a timely manner.<br />
<br />
====Reflection on the Process====<br />
#'''What did you learn?'''<br />
#*'''With your Head'''<br />
#::-From this project as well as this whole semester, I have learned how to analyze data in a microarray with understanding gene expression as well as why databases are important in these specific experiments. I have also learned more about what Microsoft Access is (I have always had it on my computer just sitting there) and how it is important in storing data and creating databases.<br />
#*'''With your Heart'''<br />
#::-From my team, I was able to learn that it is okay to ask for help. I constantly asked my team to explain certain things to me especially since I had to miss half of class the first day, we were assigned these tasks. I have also learned that being understanding of each other really helps when working in a team. Our team was very understanding of other coursework that needed to be done and was able to work around all of our schedules. <br />
#*'''With your Hands'''<br />
#::-I have learned more about technology in general and how computer technology can be incorporated into Biology. I was always interested in seeing how these two relate and through this have learned the importance of having comprehensible reproducible data. <br />
#'''What lessons did you take away from this project that you will still use a year from now?'''<br />
#*From this project, I have learned that it is important to always be consistent and comprehensible when producing different experiments for others to understand and take away. It is important to lay out everything and to not neglect to include different methods or vital information when explaining data.<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)<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 />
[[Dmadere Week 12|Dmadere Week 12/13]]<br />
<br />
[[Dmadere Week 15]]<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7670Sulfiknights Deliverables2019-12-08T01:29:16Z<p>Imacarae: /* Electronic notebook corresponding to the microarray results files */ added links</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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_DA_Week_14&diff=7668Sulfiknights DA Week 142019-12-08T00:55:11Z<p>Imacarae: /* Methods and Results */ added steps</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Purpose==<br />
* To analyze data collected by [https://doi.org/10.1152/physiolgenomics.00236.2006 Thorsen et al.] regarding gene expression changes in response to sulfate exposure through using an ANOVA, running [http://www.cs.cmu.edu/~jernst/stem/ STEM], [http://www.yeastract.com/ YEASTRACT], [https://dondi.github.io/GRNsight/ GRNsight], [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap], and Microsoft Access<br />
* To check the efficacy of the work done by [https://doi.org/10.1152/physiolgenomics.00236.2006 Thorsen et al.]<br />
<br />
==Methods and Results==<br />
===Loading Data into STEM===<br />
#Downloaded all STEM software needed found on [[Week 9]].<br />
#Deleted the "1080" data column from the "swtVnwt_1mM_stem" sheet found in the [[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data Excel File]].<br />
#*This was done so that the profile graphs were clearer<br />
#Converted this file into a .txt file<br />
#Ran STEM with this file under these parameters:<br />
#*No normalization/add 0<br />
#*Spot IDs included in the data file<br />
#*Browse: gene_association.sgd.gz<br />
#Selected "X-axis scale should be: Based on real time" in the Interface Options on the All STEM Profiles (1) pop-up window.<br />
#All genelists and GOlists for the significant profiles (9,23,40, and 48) were downloaded and saved as .txt files. <br />
#*Profiles 9 and 23 were colored red to show clusters that were involved in down-regulation.<br />
#*Profiles 40 and 48 were colored green to show clusters that were involved in up-regulation.<br />
===Creating regulatory networks with YEASTRACT===<br />
#Copied the gene lists from Profile 9 and 23. <br />
#Inputted this list into the [http://www.yeastract.com/ YEASTRACT database] and under the "Rank by TF".<br />
#Took the first 17 significant transciption factors and put them into both boxes of the [http://www.yeastract.com/formregmatrix.php Generate Regulation Matrix page].<br />
#*CSV file that was generated was converted into an Excel file. <br />
#File was delimited and organized so that "p"s were deleted, everything was captalized, and the regulatees and regulators were alphabetized and in the same order. <br />
#Position A1 was changed to the text: "rows genes affect/cols genes controlling".<br />
#We deleted transcription factors that were not connected to others and/or only connected to itself.<br />
#Sheet was named "network", saved, and inputted into the [http://dondi.github.io/GRNsight/ GRNsight] home page.<br />
#*Resulting matrices were organized into Grid Layout and saved.<br />
'''''Steps 1-7 were repeated with the genes from Profiles 40 and 48. In the end, we had two networks and two GRNsight matrices (black and white).'''''<br />
===Creating GRNmap Input Workbook===<br />
#Downloaded MS Access database created by Designer<br />
#Imported network for Profiles 9 and 23<br />
#Created production_rates, degradation_rates, and Thorsen_2007_log2_expression sheets by following steps:<br />
#*Clicked "Create", then "Query Design", and selected "network" and desired sheet<br />
#*Arranged arrow so that id was correlated to Standard name and joined properties<br />
#*Dragged id and desired sheets (production rates, degradation rates, and Thorsen data at each time point, 3 replicates each)<br />
#*Right clicked in grey space, Make Table Query<br />
#*Ran query and saved query<br />
#Each sheet was copied and pasted into the GRNmap Input Worksheet<br />
#The original network sheet was pasted into Input Worksheet <br />
#The Network_weights sheet also contained the original network<br />
#The optimization_parameters sheet was copied from sample worksheet and mutants were deleted in row 15 to only show "wt"<br />
#*Row 14 only contains time points 15, 30, and 60<br />
#the threshold_b sheet contained "0"s for each transcription factor<br />
#Input workbook was saved<br />
'''''Steps 1-9 were repeated with network for Profiles 40 and 48. In the end, we had two input workbooks (one for 9 and 23, and one for 40 and 48).'''''<br />
===Running Input Files with MATLAB===<br />
#Opened MATLAB R2014b, opened GRNmodel.m<br />
#Ran MATLAB with Input Workbook for Profiles 9 and 23<br />
#Once it was done running, we saved the files (.jpgs, output .xlsx file, and .mat file) and zipped them together<br />
#We submitted the output .xlsx file into the [http://dondi.github.io/GRNsight/ GRNsight page] to visualize results as a colored Grid matrix.<br />
'''''These steps were repeated with the Input Workbook for Profiles 40 and 48. In the end, we have two separate, zipped output files for Profiles 9 and 23 and for Profiles 40 and 48. We also have two colored GRNsight matrices.'''''<br />
<br />
==Data and Files==<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 />
===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 />
===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 />
==Conclusion==<br />
The data analysis performed produced various graphs showing expression trends and networks that depicted regulation between genes. After running STEM, four profiles were produced (profiles 9, 23, 40, 48) and profiles 9 and 23 were combined for further analysis because both illustrating gene repression, while profiles 40 and 48 were also combined because they both illustrated gene expression. The network illustrating gene regulation for profiles 9 and 23 suggests RAP1 was highly regulated during exposure to sulfate and the network illustrating gene regulation for profiles 40 and 48 suggest both MSN2 and MSN4 were highly regulated during exposure to sulfate.<br />
<br />
==References==<br />
*GRNsight. Retrieved December 3, 2019, from https://dondi.github.io/GRNsight/ .<br />
<br />
*Short Time-series Expression Miner (STEM). Retrieved November 26, 2019, from http://www.cs.cmu.edu/~jernst/stem/ .<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 />
*Week 9. Retrieved November 26, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9 .<br />
<br />
*YEASTRACT. Retrieved December 3, 2019, from http://www.yeastract.com/formregmatrix.php .<br />
<br />
==Acknowledgements==<br />
We would like to thank [[User:Kdahlquist]] for helping with this investigation. Except for what is noted above, this individual journal entry was completed by the member of team [[Sulfiknights]] and not copied from another source.</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_DA_Week_14&diff=7664Sulfiknights DA Week 142019-12-08T00:48:44Z<p>Imacarae: /* Methods and Results */ added steps</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Purpose==<br />
* To analyze data collected by [https://doi.org/10.1152/physiolgenomics.00236.2006 Thorsen et al.] regarding gene expression changes in response to sulfate exposure through using an ANOVA, running [http://www.cs.cmu.edu/~jernst/stem/ STEM], [http://www.yeastract.com/ YEASTRACT], [https://dondi.github.io/GRNsight/ GRNsight], [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap], and Microsoft Access<br />
* To check the efficacy of the work done by [https://doi.org/10.1152/physiolgenomics.00236.2006 Thorsen et al.]<br />
<br />
==Methods and Results==<br />
===Loading Data into STEM===<br />
#Downloaded all STEM software needed found on [[Week 9]].<br />
#Deleted the "1080" data column from the "swtVnwt_1mM_stem" sheet found in the [[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data Excel File]].<br />
#*This was done so that the profile graphs were clearer<br />
#Converted this file into a .txt file<br />
#Ran STEM with this file under these parameters:<br />
#*No normalization/add 0<br />
#*Spot IDs included in the data file<br />
#*Browse: gene_association.sgd.gz<br />
#Selected "X-axis scale should be: Based on real time" in the Interface Options on the All STEM Profiles (1) pop-up window.<br />
#All genelists and GOlists for the significant profiles (9,23,40, and 48) were downloaded and saved as .txt files. <br />
#*Profiles 9 and 23 were colored red to show clusters that were involved in down-regulation.<br />
#*Profiles 40 and 48 were colored green to show clusters that were involved in up-regulation.<br />
===Creating regulatory networks with YEASTRACT===<br />
#Copied the gene lists from Profile 9 and 23. <br />
#Inputted this list into the [http://www.yeastract.com/ YEASTRACT database] and under the "Rank by TF".<br />
#Took the first 17 significant transciption factors and put them into both boxes of the [http://www.yeastract.com/formregmatrix.php Generate Regulation Matrix page].<br />
#*CSV file that was generated was converted into an Excel file. <br />
#File was delimited and organized so that "p"s were deleted, everything was captalized, and the regulatees and regulators were alphabetized and in the same order. <br />
#Position A1 was changed to the text: "rows genes affect/cols genes controlling".<br />
#We deleted transcription factors that were not connected to others and/or only connected to itself.<br />
#Sheet was named "network", saved, and inputted into the [http://dondi.github.io/GRNsight/ GRNsight] home page.<br />
#*Resulting matrices were organized into Grid Layout and saved.<br />
'''''Steps 1-7 were repeated with the genes from Profiles 40 and 48. In the end, we had two networks and two GRNsight matrices (black and white).'''''<br />
===Creating GRNmap Input Workbook===<br />
#Downloaded MS Access database created by Designer<br />
#Imported network for Profiles 9 and 23<br />
#Created production_rates, degradation_rates, and Thorsen_2007_log2_expression sheets by following steps:<br />
#*Clicked "Create", then "Query Design", and selected "network" and desired sheet<br />
#*Arranged arrow so that id was correlated to Standard name and joined properties<br />
#*Dragged id and desired sheets (production rates, degradation rates, and Thorsen data at each time point, 3 replicates each)<br />
#*Right clicked in grey space, Make Table Query<br />
#*Ran query and saved query<br />
#Each sheet was copied and pasted into the GRNmap Input Worksheet<br />
#The original network sheet was pasted into Input Worksheet <br />
#The Network_weights sheet also contained the original network<br />
#The optimization_parameters sheet was copied from sample worksheet and mutants were deleted in row 15 to only show "wt"<br />
#*Row 14 only contains time points 15, 30, and 60<br />
#the threshold_b sheet contained "0"s for each transcription factor<br />
#Input workbook was saved<br />
'''''Steps 1-9 were repeated with network for Profiles 40 and 48. In the end, we had two input workbooks (one for 9 and 23, and one for 40 and 48).'''''<br />
<br />
==Data and Files==<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 />
[[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 />
===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 />
===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 />
==Conclusion==<br />
The data analysis performed produced various graphs showing expression trends and networks that depicted regulation between genes. The network illustrating gene regulation for profiles 9 and 23 suggests RAP1 was highly regulated during exposure to sulfate and the network illustrating gene regulation for profiles 40 and 48 suggest both MSN2 and MSN4 were highly regulated during exposure to sulfate.<br />
<br />
==References==<br />
*GRNsight. Retrieved December 3, 2019, from https://dondi.github.io/GRNsight/ .<br />
<br />
*Short Time-series Expression Miner (STEM). Retrieved November 26, 2019, from http://www.cs.cmu.edu/~jernst/stem/ .<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 />
*Week 9. Retrieved November 26, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_9 .<br />
<br />
*YEASTRACT. Retrieved December 3, 2019, from http://www.yeastract.com/formregmatrix.php .<br />
<br />
==Acknowledgements==<br />
We would like to thank [[User:Kdahlquist]] for helping with this investigation. Except for what is noted above, this individual journal entry was completed by the member of team [[Sulfiknights]] and not copied from another source.</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_DA_Week_14&diff=7657Sulfiknights DA Week 142019-12-08T00:34:12Z<p>Imacarae: /* Methods and Results */ added steps</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Purpose==<br />
* To analyze data collected by [https://doi.org/10.1152/physiolgenomics.00236.2006 Thorsen et al.] regarding gene expression changes in response to sulfate exposure through using an ANOVA, running [http://www.cs.cmu.edu/~jernst/stem/ STEM], [http://www.yeastract.com/ YEASTRACT], [https://dondi.github.io/GRNsight/ GRNsight], [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap], and Microsoft Access<br />
* To check the efficacy of the work done by [https://doi.org/10.1152/physiolgenomics.00236.2006 Thorsen et al.]<br />
<br />
==Methods and Results==<br />
===Loading Data into STEM===<br />
#Downloaded all STEM software needed found on [[Week 9]].<br />
#Deleted the "1080" data column from the "swtVnwt_1mM_stem" sheet found in the [[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data Excel File]].<br />
#*This was done so that the profile graphs were clearer<br />
#Converted this file into a .txt file<br />
#Ran STEM with this file under these parameters:<br />
#*No normalization/add 0<br />
#*Spot IDs included in the data file<br />
#*Browse: gene_association.sgd.gz<br />
#Selected "X-axis scale should be: Based on real time" in the Interface Options on the All STEM Profiles (1) pop-up window.<br />
#All genelists and GOlists for the significant profiles (9,23,40, and 48) were downloaded and saved as .txt files. <br />
#*Profiles 9 and 23 were colored red to show clusters that were involved in down-regulation.<br />
#*Profiles 40 and 48 were colored green to show clusters that were involved in up-regulation.<br />
===Creating regulatory networks with YEASTRACT===<br />
#Copied the gene lists from Profile 9 and 23. <br />
#Inputted this list into the [http://www.yeastract.com/ YEASTRACT database] and under the "Rank by TF".<br />
#Took the first 17 significant transciption factors and put them into both boxes of the [http://www.yeastract.com/formregmatrix.php Generate Regulation Matrix page].<br />
#*CSV file that was generated was converted into an Excel file. <br />
#File was delimited and organized so that "p"s were deleted, everything was captalized, and the regulatees and regulators were alphabetized and in the same order. <br />
#Position A1 was changed to the text: "rows genes affect/cols genes controlling".<br />
#We deleted transcription factors that were not connected to others and/or only connected to itself.<br />
#Sheet was named "network", saved, and inputted into the [http://dondi.github.io/GRNsight/ GRNsight] home page.<br />
'''''Steps 1-7 were repeated with the genes from Profiles 40 and 48. In the end, we had two networks and two GRNsight matrices (black and white).'''''<br />
<br />
==Data and Files==<br />
==Conclusion==<br />
The data analysis performed produced various graphs showing expression trends and networks that depicted regulation between genes.<br />
<br />
==References==<br />
<br />
==Acknowledgements==<br />
We would like to thank [[User:Kdahlquist]] for helping with this investigation. Except for what is noted above, this individual journal entry was completed by the member of team [[Sulfiknights]] and not copied from another source.</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_DA_Week_14&diff=7649Sulfiknights DA Week 142019-12-08T00:18:49Z<p>Imacarae: /* Methods and Results */ wrote section</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Purpose==<br />
This section of the investigation focused on analyzing data collected by [https://doi.org/10.1152/physiolgenomics.00236.2006 Thorsen et al.] regarding gene expression changes in response to sulfate exposure through using an ANOVA, running [http://www.cs.cmu.edu/~jernst/stem/ STEM], [http://www.yeastract.com/ YEASTRACT], [https://dondi.github.io/GRNsight/ GRNsight], [http://kdahlquist.github.io/GRNmap/downloads/ GRNmap], and Microsoft Access.<br />
<br />
==Methods and Results==<br />
===Loading Data into STEM===<br />
#Downloaded all STEM software needed found on [[Week 9]].<br />
#Deleted the "1080" data column from the "swtVnwt_1mM_stem" sheet found in the [[Media:Thorsendata_sulfiknights.xlsx|Thorsen Data Excel File]].<br />
#*This was done so that the profile graphs were clearer<br />
#Converted this file into a .txt file<br />
#Ran STEM with this file under these parameters:<br />
#*No normalization/add 0<br />
#*Spot IDs included in the data file<br />
#*Browse: gene_association.sgd.gz<br />
#Selected "X-axis scale should be: Based on real time" in the Interface Options on the All STEM Profiles (1) pop-up window.<br />
#All genelists and GOlists for the significant profiles (9,23,40, and 48) were downloaded and saved. <br />
#*Profiles 9 and 23 were colored red to show clusters that were involved in down-regulation.<br />
#*Profiles 40 and 48 were colored green to show clusters that were involved in up-regulation.<br />
<br />
<br />
#Copied the gene lists from Profile 9 and 23 and inputted them into<br />
<br />
==Data and Files==<br />
==Conclusion==<br />
==Acknowledgements==<br />
==References==</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7644Sulfiknights Deliverables2019-12-08T00:03:48Z<p>Imacarae: /* Checklist: */ edited</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 />
[[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 />
<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Thorsen_2007_log2_expression_923_querydesign.PNG&diff=7642File:Thorsen 2007 log2 expression 923 querydesign.PNG2019-12-08T00:02:41Z<p>Imacarae: Imacarae uploaded a new version of File:Thorsen 2007 log2 expression 923 querydesign.PNG</p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7638Sulfiknights Deliverables2019-12-07T23:57:11Z<p>Imacarae: /* Checklist: */ marked items complete</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 />
==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 />
==Electronic notebook corresponding to the microarray results files==<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7635Sulfiknights Deliverables2019-12-07T23:50:27Z<p>Imacarae: added header</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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
==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 />
==Electronic notebook corresponding to the microarray results files==<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7634Sulfiknights Deliverables2019-12-07T23:49:25Z<p>Imacarae: /* Query design for populating a GRNmap input workbook from the database */ added screenshots</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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
==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 />
==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 />
==Electronic notebook corresponding to the microarray results files==<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Thorsen_2007_log2_expression_923_querydesign.PNG&diff=7633File:Thorsen 2007 log2 expression 923 querydesign.PNG2019-12-07T23:47:20Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Degradationrates_923_querydesign.PNG&diff=7632File:Degradationrates 923 querydesign.PNG2019-12-07T23:46:48Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Productionrates_923_querydesign.PNG&diff=7631File:Productionrates 923 querydesign.PNG2019-12-07T23:44:50Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7630Sulfiknights Deliverables2019-12-07T23:38:56Z<p>Imacarae: /* PowerPoint of ANOVA Table... */ edited pictures</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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
==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 />
==Query design for populating a GRNmap input workbook from the database==<br />
<br />
==Electronic notebook corresponding to the microarray results files==<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7629Sulfiknights Deliverables2019-12-07T23:33:16Z<p>Imacarae: /* Checklist: */ marked as complete</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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
<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 />
<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 />
==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 />
==Query design for populating a GRNmap input workbook from the database==<br />
<br />
==Electronic notebook corresponding to the microarray results files==<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7627Sulfiknights Deliverables2019-12-07T23:32:16Z<p>Imacarae: /* PowerPoint of ANOVA Table... */ added picture</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 '''INCOMPLETE'''<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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
<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 />
<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 />
==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 />
==Query design for populating a GRNmap input workbook from the database==<br />
<br />
==Electronic notebook corresponding to the microarray results files==<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Colored_GRNsight_923.PNG&diff=7625File:Colored GRNsight 923.PNG2019-12-07T23:31:26Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7578Sulfiknights Deliverables2019-12-06T00:26:14Z<p>Imacarae: /* GRNmap output workbook and output plots */ added link</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 '''INCOMPLETE'''<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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Image:Profile4048_GRNsight_matrix.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 />
==GRNmap output workbook and output plots==<br />
[[Media:GRNmap923_output_files.zip|GRNmap Output Files: Profiles 9 and 23]]<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
<br />
==Electronic notebook corresponding to the microarray results files==<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:GRNmap923_output_files.zip&diff=7576File:GRNmap923 output files.zip2019-12-06T00:25:35Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7571Sulfiknights Deliverables2019-12-06T00:22:18Z<p>Imacarae: /* GRNmap input workbook */ added link</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 '''INCOMPLETE'''<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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Image:Profile4048_GRNsight_matrix.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 />
==GRNmap output workbook and output plots==<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
<br />
==Electronic notebook corresponding to the microarray results files==<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]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:GRNmap923_input_worksheet.xlsx&diff=7570File:GRNmap923 input worksheet.xlsx2019-12-06T00:21:33Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7516Sulfiknights Deliverables2019-12-03T23:45:49Z<p>Imacarae: /* PowerPoint of ANOVA Table... */ added pics</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 '''INCOMPLETE'''<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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network (Excel)]]<br />
<br />
[[Image:Profile4048_GRNsight_matrix.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 />
<br />
==GRNmap output workbook and output plots==<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
<br />
==Electronic notebook corresponding to the microarray results files==</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Profile4048_GRNsight_matrix.PNG&diff=7509File:Profile4048 GRNsight matrix.PNG2019-12-03T23:44:22Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Profil923_GRNsight_matrix.PNG&diff=7506File:Profil923 GRNsight matrix.PNG2019-12-03T23:43:54Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7499Sulfiknights Deliverables2019-12-03T23:42:06Z<p>Imacarae: /* GRNmap input workbook */ edited</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 '''INCOMPLETE'''<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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
==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 />
<br />
==GRNmap output workbook and output plots==<br />
<br />
==MS Access database==<br />
[[Media: SK_Expression-and-Degradation-rate-database_2019.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
<br />
==Electronic notebook corresponding to the microarray results files==</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7495Sulfiknights Deliverables2019-12-03T23:41:04Z<p>Imacarae: /* GRNmap input workbook */ added 2 links</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 '''INCOMPLETE'''<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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
==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:Profile923_GRNsight_network.xlsx|Profile 9 and 23 input network]]<br />
<br />
[[Media:Profile4048_GRNsight_network.xlsx|Profile 40 and 48 input network]]<br />
<br />
==GRNmap output workbook and output plots==<br />
<br />
==MS Access database==<br />
[[Media: Expression-and-Degradation-rate-database_12_3.zip | MS Access Database of Thorsen & Dahlquist data]]<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
<br />
==Electronic notebook corresponding to the microarray results files==</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Profile4048_GRNsight_network.xlsx&diff=7492File:Profile4048 GRNsight network.xlsx2019-12-03T23:40:28Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Profile923_GRNsight_network.xlsx&diff=7491File:Profile923 GRNsight network.xlsx2019-12-03T23:38:54Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Template:Imacarae&diff=7444Template:Imacarae2019-12-03T22:47:22Z<p>Imacarae: edited</p>
<hr />
<div>[[User:Imacarae|Imacarae's User Page]]<br />
<br />
{| class="wikitable"<br />
|-<br />
! Assignment<br />
! Shared Entries<br />
! Individual Entries<br />
|-<br />
| [[Week 1]]<br />
| [[Class Journal Week 1]]<br />
| ----<br />
|-<br />
| [[Week 2]]<br />
| [[Class Journal Week 2]]<br />
| [[Imacarae Week 2]]<br />
|-<br />
| [[Week 3]]<br />
| [[Class Journal Week 3]]<br />
| [[HSF1/YGL073W Week 3]]<br />
|-<br />
| [[Week 4]]<br />
| [[Class Journal Week 4]]<br />
| [[Imacarae Week 4]]<br />
|-<br />
| [[Week 5]]<br />
| [[Class Journal Week 5]]<br />
| [[CancerSEA Week 5]]<br />
|-<br />
| [[Week 6]]<br />
| [[Class Journal Week 6]]<br />
| [[Imacarae Week 6]]<br />
|-<br />
| [[Week 7]]<br />
| [[Class Journal Week 7]]<br />
| [[Imacarae Week 7]]<br />
|-<br />
| [[Week 8]]<br />
| [[Class Journal Week 8]]<br />
| [[Imacarae Week 8]]<br />
|-<br />
| [[Week 9]]<br />
| [[Class Journal Week 9]]<br />
| [[Imacarae Week 9]]<br />
|-<br />
| [[Week 10]]<br />
| [[Class Journal Week 10]]<br />
| [[Imacarae Week 10]]<br />
|-<br />
| [[Week 11]]<br />
| [[Sulfiknights]]<br />
| [[Imacarae Week 11]]<br />
|-<br />
| [[Week 12/13]]<br />
| [[Sulfiknights]]<br />
| [[Sulfiknights DA Week 12/13]]<br />
|-<br />
| ----<br />
| [[Sulfiknights]]<br />
| [[Sulfiknights DA Week 14]]<br />
|}<br />
<br />
[[Category:Journal Entry]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_DA_Week_14&diff=7440Sulfiknights DA Week 142019-12-03T22:46:16Z<p>Imacarae: added headers</p>
<hr />
<div>{{Sulfiknights}}<br />
<br />
==Purpose==<br />
==Methods and Results==<br />
==Data and Files==<br />
==Conclusion==<br />
==Acknowledgements==<br />
==References==</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Template:Imacarae&diff=7438Template:Imacarae2019-12-03T22:44:21Z<p>Imacarae: added week 14 links</p>
<hr />
<div>[[User:Imacarae|Imacarae's User Page]]<br />
<br />
{| class="wikitable"<br />
|-<br />
! Assignment<br />
! Shared Entries<br />
! Individual Entries<br />
|-<br />
| [[Week 1]]<br />
| [[Class Journal Week 1]]<br />
| ----<br />
|-<br />
| [[Week 2]]<br />
| [[Class Journal Week 2]]<br />
| [[Imacarae Week 2]]<br />
|-<br />
| [[Week 3]]<br />
| [[Class Journal Week 3]]<br />
| [[HSF1/YGL073W Week 3]]<br />
|-<br />
| [[Week 4]]<br />
| [[Class Journal Week 4]]<br />
| [[Imacarae Week 4]]<br />
|-<br />
| [[Week 5]]<br />
| [[Class Journal Week 5]]<br />
| [[CancerSEA Week 5]]<br />
|-<br />
| [[Week 6]]<br />
| [[Class Journal Week 6]]<br />
| [[Imacarae Week 6]]<br />
|-<br />
| [[Week 7]]<br />
| [[Class Journal Week 7]]<br />
| [[Imacarae Week 7]]<br />
|-<br />
| [[Week 8]]<br />
| [[Class Journal Week 8]]<br />
| [[Imacarae Week 8]]<br />
|-<br />
| [[Week 9]]<br />
| [[Class Journal Week 9]]<br />
| [[Imacarae Week 9]]<br />
|-<br />
| [[Week 10]]<br />
| [[Class Journal Week 10]]<br />
| [[Imacarae Week 10]]<br />
|-<br />
| [[Week 11]]<br />
| [[Sulfiknights]]<br />
| [[Imacarae Week 11]]<br />
|-<br />
| [[Week 12/13]]<br />
| [[Sulfiknights]]<br />
| [[Sulfiknights DA Week 12/13]]<br />
|-<br />
| [[Week 14]]<br />
| [[Sulfiknights]]<br />
| [[Sulfiknights DA Week 14]]<br />
|}<br />
<br />
[[Category:Journal Entry]]</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7437Sulfiknights Deliverables2019-12-02T23:50:39Z<p>Imacarae: added headers</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 '''INCOMPLETE'''<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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
==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 />
<br />
==GRNmap output workbook and output plots==<br />
<br />
==MS Access database==<br />
<br />
==Query design for populating a GRNmap input workbook from the database==<br />
<br />
==Electronic notebook corresponding to the microarray results files==</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7436Sulfiknights Deliverables2019-12-02T23:49:00Z<p>Imacarae: /* Excel Spreadsheet with ANOVA Results */ edited header</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 '''INCOMPLETE'''<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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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 />
==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 />
<br />
==GRNmap output workbook and output plots==<br />
<br />
==MS Access database==</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7435Sulfiknights Deliverables2019-12-02T23:48:18Z<p>Imacarae: /* Checklist: */ changed status to complete</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 '''INCOMPLETE'''<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) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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==<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 />
==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 />
<br />
==GRNmap output workbook and output plots==<br />
<br />
==MS Access database==</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7434Sulfiknights Deliverables2019-12-02T23:48:02Z<p>Imacarae: /* YEASTRACT "Rank by TF" Results */ added 2 links</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 '''INCOMPLETE'''<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) '''INCOMPLETE'''<br />
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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==<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 />
==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 />
<br />
==GRNmap output workbook and output plots==<br />
<br />
==MS Access database==</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Profile4048_rankedbytf.xlsx&diff=7433File:Profile4048 rankedbytf.xlsx2019-12-02T23:47:41Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=File:Profile923_rankedbytf.xlsx&diff=7432File:Profile923 rankedbytf.xlsx2019-12-02T23:47:09Z<p>Imacarae: </p>
<hr />
<div></div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7431Sulfiknights Deliverables2019-12-02T23:36:29Z<p>Imacarae: /* Checklist: */ changed status to complete</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 '''INCOMPLETE'''<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) '''INCOMPLETE'''<br />
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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==<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 />
==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 />
<br />
==GRNmap input workbook==<br />
<br />
==GRNmap output workbook and output plots==<br />
<br />
==MS Access database==</div>Imacaraehttps://xmlpipedb2024.lmucs.io/biodb/fall2019/index.php?title=Sulfiknights_Deliverables&diff=7430Sulfiknights Deliverables2019-12-02T23:35:58Z<p>Imacarae: added headers</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 '''INCOMPLETE'''<br />
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) '''INCOMPLETE'''<br />
#YEASTRACT "rank by TF" results (.xlsx) '''INCOMPLETE'''<br />
#GRNmap input workbook (with network adjacency matrix, .xlsx) '''INCOMPLETE'''<br />
#GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together '''INCOMPLETE'''<br />
#MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) '''INCOMPLETE'''<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) '''INCOMPLETE'''<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==<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 />
==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 />
<br />
==GRNmap input workbook==<br />
<br />
==GRNmap output workbook and output plots==<br />
<br />
==MS Access database==</div>Imacarae