Difference between revisions of "FunGals Deliverables"
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* Describe exactly what you did on the project. | * 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: | * Provide references or links to artifacts of your work, such as: | ||
** Wiki pages | ** Wiki pages | ||
| + | ***[[Marmas Week 11|Individual Journal Week 11]] | ||
| + | ***[[Marmas Week 12/13|Individual Journal Week 12/13]] | ||
| + | ***[[Marmas Week 15|Individual Journal Week 15]] | ||
** Other files or documents | ** Other files or documents | ||
| + | ***Significant Files I produced or helped produce: | ||
| + | ****[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]] | ||
| + | ****[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]] | ||
| + | ****[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]] | ||
** Code or scripts | ** Code or scripts | ||
| + | *** Not very applicable, but the database is outlined in the files above. | ||
==== Assessment of Project ==== | ==== Assessment of Project ==== | ||
| − | * Give an objective assessment of the success of your project workflow and teamwork. | + | * Give an objective assessment of the success of your project workflow and teamwork. |
| − | * What worked and what didn't work? | + | **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? | * 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: | * Evaluate your team’s portion of the Final Project and Group Report in the following areas: | ||
| − | *# Content: What is the quality of the work? | + | *# 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. | ||
*# Organization: Comment on the organization of the project and of your group's wiki pages. | *# 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. | ||
*# Completeness: Did your team achieve all of the project objectives? Why or why not? | *# 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 ==== | ==== Reflection on the Process ==== | ||
| Line 108: | Line 123: | ||
* What did you learn? | * What did you learn? | ||
** With your head (biological or computer science principles) | ** 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)? | ** 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)? | ** 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? | * 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=== | ===Kaitlyn Nguyen=== | ||
Revision as of 00:28, 13 December 2019
Contents
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) | Incomplete |
| 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
- Group Report
- Group PowerPoint presentation
- Metadata Workbook
- ANOVA results/STEM formatting
- Figure Slides
- Gene List and GO List
- YEASTRACT "rank by TF" results
- GRNmap Input Workbooks
- GRNmap Output Workbooks
- MS Access Database
- ReadMe
- Query Design Screenshot
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:
- Wiki pages
- Other files or documents
- Significant Files I produced or helped produce:
- Code or scripts
- Not very applicable, but the database is outlined in the files above.
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:
- 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.
- 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.
- 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.
- Content: What is the quality of the work?
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!
- With your head (biological or computer science principles)
- 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
- Describe exactly what you did on the project.
- Provide references or links to artifacts of your work, such as:
- Wiki pages
- Other files or documents
- Code or scripts
Assessment of Project
- Give an objective assessment of the success of your project workflow and teamwork.
- What worked and what didn't work?
- What would you do differently if you could do it all over again?
- Evaluate your team’s portion of the Final Project and Group Report in the following areas:
- Content: What is the quality of the work?
- Organization: Comment on the organization of the project and of your group's wiki pages.
- Completeness: Did your team achieve all of the project objectives? Why or why not?
Reflection on the Process
- What did you learn?
- With your head (biological or computer science principles)
- With your heart (personal qualities and teamwork qualities that make things work or not work)?
- With your hands (technical skills)?
- What lesson will you take away from this project that you will still use a year from now?
Emma Young
Statement of Work
- Describe exactly what you did on the project.
- Provide references or links to artifacts of your work, such as:
- Wiki pages
- Other files or documents
- Code or scripts
Assessment of Project
- Give an objective assessment of the success of your project workflow and teamwork.
- What worked and what didn't work?
- What would you do differently if you could do it all over again?
- Evaluate your team’s portion of the Final Project and Group Report in the following areas:
- Content: What is the quality of the work?
- Organization: Comment on the organization of the project and of your group's wiki pages.
- Completeness: Did your team achieve all of the project objectives? Why or why not?
Reflection on the Process
- What did you learn?
- With your head (biological or computer science principles)
- With your heart (personal qualities and teamwork qualities that make things work or not work)?
- With your hands (technical skills)?
- What lesson will you take away from this project that you will still use a year from now?
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)
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
