FunGals Deliverables

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Information and Links

FunGals Links
BIOL Databases Main Page FunGals: Project Overview Page Final Project Deliverables Requirements FunGals: Final Project Deliverables
Assignment Pages Week 11 Week 12/13 Week 15

User Pages

Knguye66 
Marmas
Icrespin
Eyoung20

Template Page

Template:FunGals

Checklist

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

Data and Files

Individual Assessment and Reflection

Michael Armas

Statement of Work

  • Describe exactly what you did on the project.
    • As a coder is was my responsibility to do the database work. I created the database in MS Access, the metadata sheets, and the read me. This included working with the database to organize and universalize the data with the other groups. For the final report, I wrote the Introduction for the paper as well as added methods concerning the creation of the database and a few concluding points about the facilitation of results through the database. The presentation was mostly formatted by some of the other group members, but I was able to help a lot with the explanation of data during the presentation. The whole group worked hard to help each other with what was to be said during the presentation as well! As the project manager, I organized meeting times and made sure the entire group was on top of milestones and deliverables. I feel as if my contribution, alongside the help of my fellow group members, helped the outcome of the final project.
  • Provide references or links to artifacts of your work, such as:

Assessment of Project

  • Give an objective assessment of the success of your project workflow and teamwork.
    • I felt as if my success during this project was very satisfying. Hearing from the DA's that the database worked successfully was great to hear that I was able to help out with the assessment of data. For the other components, I feel as if I held my weight very much so when writing for the paper or presenting to the class. I enjoyed being the project manager for this group and felt as if my organization of meetings and milestones helped keep the group on track!
  • What worked and what didn't work?
    • Meeting at certain times was great and it really helped to communicate in person rather than over text or call. This worked well with our team and I feel as if this was the most successful way to work. What I felt didn't work was sometimes leaving some assignments to the last minute. While we were able to get the work in on time always, it was stressful to be working sometimes until late into the night.
  • What would you do differently if you could do it all over again?
    • I would get started with things much earlier. I am a person that tries to avoid procrastination, but sometimes that doesn't go as planned. If I could encourage myself and others to get started early on this project, I would be much less stressed during finals week.
  • 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 the work was great, I think we are all happy with how the project turned out and with our discoveries. Going through and organizing some pages gave the final touches to the presentation of the project to make it look clean.
    2. Organization: Comment on the organization of the project and of your group's wiki pages.
      • The pages are organized and easy to follow. Headers are established and a table of contents allowed for things to be found easily. Most importantly, our deliverables are all organized into a page that has different sections to find files that will be graded.
    3. Completeness: Did your team achieve all of the project objectives? Why or why not?
      • Yes, we did achieve all of the project objectives. As I type this, we are just finishing the final touches on the final report, and will be ready to turn in the assignment before 4:00pm on Friday.

Reflection on the Process

  • What did you learn?
    • With your head (biological or computer science principles)
      • I learned a lot about bioinformatics, a field of study which I really knew nothing about. This field allows for the ability to do something that humans could never do. The efficiency of bioinformatics blows me away with how fast data can be analyzed.
    • With your heart (personal qualities and teamwork qualities that make things work or not work)?
      • I continue to develop interpersonal skills with people when doing group projects. Working with a group always comes with its set of challenges, but working through problems is what being human is all about! I really did enjoy working with this group!
    • With your hands (technical skills)?
      • Being able to work with MS Access and virtual machines is a skill I never thought I would need. However, I understand how the familiarity with MS Access and all of the bioinformatics software is valuable to employers in that field. These skills will absolutely be going on my CV!
  • What lesson will you take away from this project that you will still use a year from now?
    • I hope that my interpersonal skills with group members continues to develop. Working with groups will be something I absolutely do in the future. Additionally, maybe in the next year I will be working for a company that will need me to work with databases or bioinformatics.

Kaitlyn Nguyen

Statement of Work

Assessment of Project

  • Give an objective assessment of the success of your project workflow and teamwork.
  • What worked and what didn't work?
    • What worked was everyone's ability to understand each other's situations, final exams, and work patiently to help each other. What didn't work was waiting until the last minute to finish all the work (final presentation, wiki page, final paper) rather than slowly work on it throughout the weeks.
  • What would you do differently if you could do it all over again?
    • I would definitely start the paper much earlier to leave more space to help reformatting and editing.
  • 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? 9/10
    2. Organization: Comment on the organization of the project and of your group's wiki pages.
      • Our organization is quite good actually, we follow off the requirements and deliverables in order.
    1. Completeness: Did your team achieve all of the project objectives? Why or why not? Yes!

Reflection on the Process

  • What did you learn?
    • With your head (biological or computer science principles)
      • I learned that understanding an entirely new language, whether it be biological, computational, or both require a lot of existing knowledge and/or hours of practice to figure out the methods.
    • With your heart (personal qualities and teamwork qualities that make things work or not work)?
      • Personal qualities that work are communication skills and leadership. A teamwork quality that is always effective is patience. Sometimes a team member in the group may not understand something and rather than rushing through the work just to merely finish it, other team members would be patient and understanding in helping them understand the work.
    • With your hands (technical skills)?
      • I have funnily learned that I have a knack for typing fast, but hat I need to slow down to catch mistakes earlier on, rather than later due to typos that become much larger errors later on.
  • What lesson will you take away from this project that you will still use a year from now?
    • I definitely understand the use of running Queries now. I've also learned that there are so many other functions on Excel that I could use over and over again in the future.

Emma Young

Statement of Work

  • As a Data Analysis I worked with Kaitlyn Nguyen to analysis the data from the Kitagawa et al. 2002 journal article. Here is a break down of what I did out of the Data Analysis work we split.
    • Ran the Sanity Check on the ANOVA DATA
    • Created the STEM input sheet
    • Helped to Run STEM
    • Created the Combined Gene Lists
    • Ran The GENElist through YEASTRACT
    • Chose the Genes for the network and ran them Through YEATTRACT
    • Visualized the unweighted networks in GRNsighted
    • Created the Red profile GRNmap input worksheet
    • Ran the Red profile GRNmap input worksheet through GRNmap using MATLAb
    • Visualized the GRNmap weighted network results in GRNsight
    • worked on the shared individual journal pages to record the process
    • added milestones and reflections to group pages
    • worked on presentation
    • worked on final paper

Assessment of Project

  • Give an objective assessment of the success of your project workflow and teamwork.
  • What worked and what didn't work?
    • We worked well together when we could all work together at the same time. There was not a clear communication on when everyone was free to work. This lead to some tense moments were the work flow was not very consistent. It also left some people ahead and some people rushing to get work done.
  • What would you do differently if you could do it all over again?
    • I would work out meeting times that worked on everyones schedule and possibly divide up the workload a little more evenly.
  • 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 the work was reasonable for the time frame we had. I think each of us put as mush as we were able into the work. Is it the best we could do, no. But I think in order to achieve that best we would have at least need another week. So given the time frame and the stressful and busy time of the semester I am proud of the work we did.
    1. Organization: Comment on the organization of the project and of your group's wiki pages.
    • I found the formate of our team page a little hard to look through. Everything is present but I feel it could have been organized a bit better. I also found the project organization a little weird. I felt like we rewrote a lot of information between the presentation, the deliverables, the group page and the individual journals. I feel like the repletion although useful for remembering the steps and what we did a little unnecessary. Maybe in the future combining the delieverables with he paper would be a good idea since they both contain the same information.
    1. Completeness: Did your team achieve all of the project objectives? Why or why not?
    • Yes we achieved all the project objectives although on a time crunch. I think it has to do with the fact that we became flexible with each others needs especially when writing the paper. We helped each other out with each section. If someone was running behind or overwhelmed we helped each other. Illiana and Kaitlyn especially had my back when the methods section overwhelmed me a bit.

Reflection on the Process

  • What did you learn?
    • With your head (biological or computer science principles)
      • I learned a lot about data anaylsis and how to tell if a paper has good data or if its contents should be looked at more critically.
    • With your heart (personal qualities and teamwork qualities that make things work or not work)?
      • I learned that team work can need a lot of compassion. A lot of the times our team worked best when we helped each other out.
    • With your hands (technical skills)?
      • I learned a lot of new tricks for excel, as well as how to use an access database something I have never used before.
  • What lesson will you take away from this project that you will still use a year from now?\
    • I think the lesson on how to critically look at a research article is one I will most definitely use for the rest of my scientific career.

Eyoung20 (talk) 16:23, 13 December 2019 (PST)

Iliana Crespin

Individual Assessment and Reflection

Acknowledgments

This section is in acknowledgement to partners Michael Armas, Iliana Crespin, Emma Young, and Kaitlyn Nguyen.

Thank you Dr. Dahlquist for helping us on this project and being able to answer our questions. It was great having you as our professor this semester.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Icrespin (talk) 21:34, 12 December 2019 (PST) Marmas (talk) 10:52, 13 December 2019 (PST) Eyoung20 (talk) 16:23, 13 December 2019 (PST)

References

Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8

Final Project. (2019). Deliverables. Retrieved December 10, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables

FunGals. (2019). Home Page. Retrieved December 12, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/FunGals

Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v

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