Yeast Beasts

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

Final version of presentation

Yeast Beasts Deliverables

Week Reflections

Week 13

Hailey's Reflection [Quality Assurance]

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

Hivanson (talk) 23:35, 17 April 2024 (PDT)

Andrew's Reflection [Coder/Designer]

To find my electronic notebook for this week please click on Andrew Sandler's Week 13 Lab Notebook Executive Summary

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

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

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

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

Dean's Reflection [Coder/Designer]

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

Msymond1 (talk) 13:33, 18 April 2024 (PDT)

Katie's Reflection

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

Kmill104 (talk) 23:09, 17 April 2024 (PDT)

Charlotte's Reflection:

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

Ckapla12 (talk) 14:00, 18 April 2024 (PDT)

Weeks 14 and 15

Hailey's Reflection [Quality Assurance]

• During weeks 14 and 15, Charlotte, Katie, and I completed milestones 3-5. I oversaw what they did and helped complete all tasks on the shared Excel file, and communicated with the coder/designers about what was needed from them to finish the database. From there, the whole team worked to complete all of the deliverables.
• I thought it was still working well to split up, with Natalija going with the coder/designers and me going with data analysis. It felt easier to split up the work for the final project deliverables this way as well. It also worked well to use the online shared Excel file.
• It did not work to not assign people exact things that they were doing for the final project deliverables. It is also difficult to enforce deadlines and quality standards for work.

Hivanson (talk) 10:43, 3 May 2024 (PDT)

Dean's Reflection

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

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

Charlotte's Reflection Week 14/15:

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

Ckapla12 (talk) 19:21, 2 May 2024 (PDT)

Katie's Reflection Weeks 14/15

Due to the wiki being down during Week 14, we had to combine our reflections for Week 14/15 into one. During Week 14, Charlotte, Hailey, and I worked on completing milestone 3 on the Data Analysts page, which contained instructions on how to complete the ANOVA analysis on our new Log2 transformed data. After determining our suitable cut-off p-value, we filtered our data to fit that value. We then worked on completing Milestone 4, which involved clustering with stem and then putting that data into YEASTRACT. More detailed instructions can be seen on our Data Analysts Week 14 journal entry. We had a better experience of working together this week. With the ANOVA data, we were able to use Microsoft Excel online and work at the same time to compute our ANOVA values. We still had some trouble with divvying up the steps for obtaining our stem and YEASTRACT data, as only one person could use their computer to run the data through these programs. During Week 15, we worked with Dean to complete Milestone 5, who helped design queries to obtain our GRNmap input data. Again, a more detailed description of what was done can be seen on our Data Analysts Week 15 and the Coder's individual journal pages. After the input data was sent to Dr. Dahlquist, she was able to run GRNmap and upload the output data. Once this was done, we analyzed our results and worked as a group to complete our presentation, the group report, and uploaded all of the deliverables that were outlined by Dr. Dahlquist. We had some trouble coordinating a time that would work for everybody to meet, but we were able to work both in person and virtually to complete everything for the project. If I were to do this project again, I would try to have organized our time just a little bit better, as we were completing this during finals week and had limited opportunities.

Andrew's Section

1. What worked?

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

2. What didn't work?

The class website did not work.


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

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