Sulfiknights Deliverables

Sulfiknight Links
BIOL Databases Main Page	Sulfiknights: Project Overview Page	Final Project Deliverables Requirements	Sulfiknights: Final Project Deliverables	Members	Project Manager & Quality Assurance: Naomi Tesfaiohannes	Quality Assurance: Joey Nimmers-Minor	Data Analysis: Ivy-Quynh Macaraeg & Marcus Avila	Designer: DeLisa Madere
				Assignment Pages	Week 11	Week 12/13	Week 15

Template:Sulfiknights

Checklist:

1. Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents) COMPLETE
2. Group Report (.doc, .docx or .pdf file) COMPLETE
3. Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to Dr. Dahlquist)COMPLETE
4. Group PowerPoint presentation (given on Tuesday, December 10, .ppt, .pptx or .pdf file) COMPLETE
5. Excel spreadsheet with ANOVA results/stem formatting (.xlsx) COMPLETE
6. PowerPoint of ANOVA table, screenshots of stem results (.pptx), screenshot of black and white GRNsight input network and colored GRNsight output networks COMPLETE
7. Gene List and GO List files from each significant profile (.txt compressed together in a .zip file) COMPLETE
8. YEASTRACT "rank by TF" results (.xlsx) COMPLETE
9. GRNmap input workbook (with network adjacency matrix, .xlsx) COMPLETE
10. GRNmap output workbook (.xlsx) and output plots (.jpg) zipped together COMPLETE
11. MS Access database, unified by the three teams with expression tables and metadata table(s) created (.accdb) COMPLETE
12. 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
13. Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, .txt) COMPLETE
14. 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

Group Report

File:Biological Databases Group Report sulfiknights.docx

Individual Statements of Work, Assessments, Reflections

Joey Nimmers-Minor's Final Reflection

Individual Assessment and Reflection

Statement of Work

• Describe exactly what you did on the project.
  • 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.
• Provide references or links to artifacts of your work
  • Expression and Degradation Sheet of Thorsen & Dahlquist Data
  • Sulfiknights Final Presentation

Assessment of Project

1. Give an objective assessment of the success of your project workflow and teamwork.
   • I feel that our workflow always lead to productive sessions in the lab in preparation for our project. I truly enjoyed working together with this team of people, out communication and overall chemistry as a team led to great productivity and made the difficulty of this project much more bearable.
2. What worked and what didn't work?
   • In the beginning, we had a hard time splitting up assignments optimally, so we would have 2 people working on the same assignment at the same time when it would be a better usage of our limited time to have people working on separate tasks in tandem. As we realized this problem, however, we immediately worked to fix it and the standard of work that we began to produce in a short amount of time improved greatly because we didn't feel rushed and we were able to reach out to each other for assistance/review which allowed for a fresh pair of eyes to look at the assignment being done and judge it correctly and without bias.
3. What would you do differently if you could do it all over again?
   • Simply put, I would make sure that we fixed out mistakes slightly earlier and used more of our time over Thanksgiving break to work so we had more time to practice and relax once the project deadline began to come closer.

• Evaluate your team’s portion of the Final Project and Group Report in the following areas:

1. Content: What is the quality of the work?
   • The quality of work that came out of my team was tremendously high! I appreciate all that they did to make sure we never settled for less and we always found ways to improve on our work as we went into the finals leg of the project.
2. Organization: Comment on the organization of the project and of your group's wiki pages.
   • I thought it was pretty good! I feel that in the beginning, we were only slightly unorganized in the very beginning of the project, but once we got over the hump, we worked very efficiently and maintained organization of our project and presentation throughout the rest of the allotted time.
3. Completeness: Did your team achieve all of the project objectives? Why or why not?
   • Yes, the team reached all of the projects objectives thanks to our communication, teamwork, work-ethic, and cohesiveness as a unit. With everyone doing their own work simultaneously and a purpose, I feel that we produced a quality product that completed all of the objectives in what seemed like a very short span of time.

Reflection on the Process

• What did you learn?

1. With your head (biological or computer science principles)
   • I learned so much about how to operate seemingly complex database systems in order to present data in a new and informed way. Computer science seemed so complex when I came into this semester, but I feel that I've created a good starting point for myself if I decide to move further down the road of computer science.
2. With your heart (personal qualities and teamwork qualities that make things work or not work)?
   • I learned that a key component of efficiency in a group project setting is chemistry. I was lucky to be put with a group of genuinely kind and fun people, and I feel that knowing that they were partially depending on me made me want to work much harder to produce a good product.
3. With your hands (technical skills)?
   • I learned how specific and knit-picky the coding aspect of computer science is. From a simple task such as wiki syntax, I found out how much detail must go into anything that has to do with computer science. This is a lesson that will help me later if I decide to work more with computer science in the future. Detail and observation is key.
4. What lesson will you take away from this project that you will still use a year from now?
   • I learned the importance of time management in a class with stringent deadlines and requirements. I get away with procrastinating often as a student and a worker, but this class and it's unusual schedule of assignment times and dates forced me to learn new methods of time managements that made my approcah to other classes different and I can see myself using this method of time management for a very long time outside of this classroom.

Jnimmers (talk) 15:13, 13 December 2019 (PST)

Marcus Avila's Final Reflection

Individual Assessment and Reflection

Statement of Work

• Describe exactly what you did on the project.
  • For the project I worked with Ivy to decide how to organize the Thorsen data to run an ANOVA. After doing the ANOVA and running STEM, I then downloaded the Gene Lists for Profiles 40 & 48 and combined them to 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 Profile 40 and 48 network excel sheet. I then used GRNsight to create the weighted and unweighted network maps.
  • 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 sample workbook provided. Finally, I input the GRNmap input workbook from the GRNmap Input Worksheet Profiles 40 and 48 into MATLAB for analysis.

Assessment of Project

1. Give an objective assessment of the success of your project workflow and teamwork.
   • 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.
2. What worked and what didn't work?
   • 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.
3. What would you do differently if you could do it all over again?
   • I would ensure that each job had defined tasks or were assigned to help other members in their tasks.
4. Evaluate your team’s portion of the Final Project and Group Report in the following areas:
   • Content: What is the quality of the work?
     • 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.
   • Organization: Comment on the organization of the project and of your group's wiki pages.
     • Our wiki page was very organized because each section included a header and files were broken up into categories/steps.
   • Completeness: Did your team achieve all of the project objectives? Why or why not?
     • Yes, the Microsoft Access database was successfully made after analyzing the publish microarray data.

Reflection on the Process

• What did you learn?

1. With your head (biological or computer science principles)
   • I learned about how microarray experiments can be used to study gene expression changes in response to stress.
2. With your heart (personal qualities and teamwork qualities that make things work or not work)?
   • 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.
3. With your hands (technical skills)?
   • I learned how to input microarray data into MS Access, how to use GRNsight, YEASTRACT, and MATLAB.

• What lesson will you take away from this project that you will still use a year from now?

1. 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.

Mavila9 (talk) 15:18, 13 December 2019 (PST)

DeLisa Madere's Final Reflection

Statement of Work

1. Role as Designer
   • 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.
2. Links to Artifacts
   • Sulfiknights
   • Access_Database_Schema_Screenshot.PNG
   • BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip‎
   • Sulfiknights Meta Data Sheet

Assessment of Project

1. Objective Assessment
   • 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.
2. What worked and didn't work?
   • 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.
3. What would you do differently?
   • 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.
4. Team Evaluation
   • Content

   -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.

   • Organization

   -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.

   • Completedness

   -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.

Reflection on the Process

1. What did you learn?
   • With your Head

   -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.

   • With your Heart

   -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.

   • With your Hands

   -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.

2. What lessons did you take away from this project that you will still use a year from now?
   • 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.

Naomi Tesfaiohannes's Final Reflection

Statement of Work

Describe exactly what you did on the project.

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.

Provide references or links to artifacts of your work, such as:

Sulfiknights

Access_Database_Schema_Screenshot.PNG

Give an objective assessment of the success of your project workflow and teamwork.

What worked and what didn't work?

What worked was meeting outside of class and keeping in touch with progress by using the group chat What didn't work was sometimes not being able to answer each other's questions. Leaving us all confused.

What would you do differently if you could do it all over again?

Ask more questions about analyzing new data instead of trying to figure it out on my own.

Evaluate your team’s portion of the Final Project and Group Report in the following areas:

Content: What is the quality of the work?

Our work is a reflection of the collaborative effort from all of the team members in trying to understand the new data we reanalyzed.

Organization: Comment on the organization of the project and of your group's wiki pages.

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.

Completeness: Did your team achieve all of the project objectives? Why or why not?

Yes, but at our own pace. The objectives were completed by going through the deliverables for each members.

Reflection on the Process

What did you learn?

With your head (biological or computer science principles)

Connecting the affects of arsenic to budding yeast

With your heart (personal qualities and teamwork qualities that make things work or not work)?

Teamwork and collaborating with others by contributing my own section of work with theirs to form an overall analysis of the data.

With your hands (technical skills)?

Formatting the database column titles

What lesson will you take away from this project that you will still use a year from now?

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.

Ntesfaio (talk) 18:02, 9 December 2019 (PST)

Ivy Macaraeg's Final Reflection

Statement of Work

• Describe exactly what you did on the project.

-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.

• Provide references or links to artifacts of my work:

- Sulfiknights Final Presentation

-Thorsen Data (Updated 12/2/19)

-PowerPoint of ANOVA table and Screenshots of STEM Profile Results

- Profiles 9 and 23 input network (Excel)

-Profile 40 and 48 input network (Excel)

-Zipped Gene Lists for Significant Profiles

-Zipped GOLists for Significant Profiles

-Profiles 9 and 23

-Profiles 40 and 48

-GRNmap Input Worksheet: Profiles 9 and 23

-GRNmap Output Files: Profiles 9 and 23

-Sulfiknights DA Week 12/13

-Sulfiknights DA Week 14

Assessment of Project

• Give an objective assessment of the success of your project workflow and teamwork.

-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.

• What worked and what didn't work?

-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.

• What would you do differently if you could do it all over again?

-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.

• Evaluate your team’s portion of the Final Project and Group Report in the following areas:
  1. Content: What is the quality of the work?

     -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.

  2. Organization: Comment on the organization of the project and of your group's wiki pages.

     - 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.

  3. Completeness: Did your team achieve all of the project objectives? Why or why not?

     -Yes, we did achieve all of the project objectives because we were able to work efficiently together.

Reflection on the Process

• What did you learn?
  • With your head (biological or computer science principles)

    -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.

  • With your heart (personal qualities and teamwork qualities that make things work or not work)?

    - 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.

  • With your hands (technical skills)?

    - 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.

• What lesson will you take away from this project that you will still use a year from now?

  • - 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.

Imacarae (talk) 15:04, 13 December 2019 (PST)

Group Powerpoint Presentation

Sulfiknights Final Presentation

Excel Spreadsheet with ANOVA Results/STEM Formatting

Thorsen Data (Updated 12/2/19)

PowerPoint of ANOVA Table...

PowerPoint of ANOVA table and Screenshots of STEM Profile Results

Profiles 9 and 23 input network (Excel)

Profile 40 and 48 input network (Excel)

Gene List and GO List files

Zipped Gene Lists for Significant Profiles

Zipped GOLists for Significant Profiles

YEASTRACT "Rank by TF" Results

Profiles 9 and 23

Profiles 40 and 48

GRNmap input workbook

GRNmap Input Worksheet: Profiles 9 and 23

GRNmap Input Worksheet: Profiles 40 and 48

GRNmap output workbook and output plots

GRNmap Output Files: Profiles 9 and 23

GRNmap Output Files: Profiles 40 and 48

MS Access database

MS Access Database of Thorsen & Dahlquist data

ReadMe

Metadata Sheet

Design of Database

Query design for populating a GRNmap input workbook from the database

Profiles 9 and 23:

Profiles 40 and 48:

Electronic notebook corresponding to the microarray results files

Electronic notebook for Data Analysts:

Sulfiknights DA Week 12/13

Sulfiknights DA Week 14

Electronic notebook for Quality Assurance

Ntesfaio Week 12/13

Ntesfaio Week 15

Electronic notebook for Designer

Dmadere Week 12/13

Dmadere Week 15

Merge completed databases into a single database

BIOL_478_-_Sulfiknights_BioDB_CombinedDatabase.zip ‎