Lights, Camera, InterACTION!

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Team Members

File Roundup

Lights, Camera, InterACTION! Deliverables

Team Schedule

November & December
Sunday Monday Tuesday Wednesday Thursday Friday Saturday
1 2 3 4
5 6 7 8 9 10 11
12 13 14
C: PPT Presentation
PM/DA: Journal Articles 		15 16 17 18
19 20 21
C: Complete setup steps (Milestones 0-4)
PM/DA: Journal Club Presentations
DA: Week 8 and Week 10 edits 		22
Thanksgiving Break 		23
Thanksgiving Break 		24
Thanksgiving Break 		25
26 27 28
C: First Integration projected completion
PM: Check in with team
DA: 		29 30
C: Check in with other groups about progress
PM: Check in with team
DA: 		1 2
3 4 5
C: Check in with groups, and further integrate as needed.
PM: Check in with team
DA: complete week 10 data analysis 		6 7
C: Check in with other groups about progress
PM: Check in with team
DA: 		8 9
10 11
Final group Presentation 2:00-4:00PM 		12 13 14 15
All deliverables due 4:30PM 		16

Executive Summaries

Week 11

Katie - PM/QA

For this week, I worked with Emma to find papers to use as reference in our final research paper. Emma and I both found papers that are related to yeast cold shock reactions and most of them use microarray data. I am excited to read these articles more in depth as we develop our research project and paper. Further information can be found on my Week 11 journal page.

  1. What worked? Using the three different sources was really helpful because I had never used "Web of Science" before. It was good to learn about how different these results can be, especially with tweaking the search terms a little bit.
  2. What didn't work? I had poor time management this week. I waited until Monday to do the majority of the work and definitely should not have done so. The rest of the project went well, however.
  3. What will I do next to fix what didn't work? I will plan to meet up with Emma early on in the week so we can work together on our presentation. This way I will be held accountable to get my work done earlier.

Emma - Data Analysis

This week Katie and I worked on the annotated bibliography (below). We chose papers that provided more information on yeast gene regulation in response to cold shock. Pub Med, Google Scholar, and Web of Science were utilized to perform basic searches using key words as well as advanced searches which helped to narrow the results. More detailed information can be found on my individual journal entry page: Emmatyrnauer Week 11. Meanwhile, Blair and Zach worked on coder journal club presentation. Construction of the group page was completed during class.

  1. Overall, this week went pretty smoothly; Katie and I communicated over text to determine which papers we were going to write the bibliographies for and were available to each other for any questions we had.
  2. There wasn't really anything that didn't work.
  3. Since we will be working this next week on our journal club presentation, it might be beneficial to meet in person.

Emmatyrnauer (talk) 20:26, 13 November 2017 (PST)

Blair - Coder

This week Zach and I created the Powerpoint presentation about The secret startup that saved the worst website in America article. We created individual outlines of the article on our respective pages, mine is as follows: Bhamilton18 Week 11. Our presentation is linked here: Zach and Blair's Powerpoint

  1. Overall, our communication and diving up of tasks went well and smoothly. Meanwhile, Katie and Emma worked on the annotate bibliography. While I primarily worked with Zach our communication amongst group members went well and we hope to continue to do so for the future.
  2. Something that didn't work as well was our time management. Next time we hope to have more class time and start working earlier on our portion of the assignment.
  3. For the future, we will continue to communicate in person and through messaging and will work on time management by starting earlier.

Bhamilton18 (talk) 23:35, 13 November 2017 (PST)

Zach - Coder

Zach and Blair's Powerpoint
Zvanysse Week 11
This week, Blair and I created a Powerpoint about the "Secret Startup that saved the worst website in America." We read through the article and picked out the relevant themes and main messages to put on the PowerPoint. We wrote these themes and summaries out on our individual Journals. Then, we collaborated and made our PowerPoint.

  1. Things that went well: Blair and I's communication was very strong and we knew exactly what was going on with one another. We knew when we were going to meet up and what was expected for each of us.
  2. Things that didn't go well: Blair and I missed the mark on our time management. We did not expect this assignment to take this long. Next time, we will make sure to start on assignments earlier.
  3. Like I said above, we will plan out exact times earlier on in the week that we can meet up

Zvanysse (talk) 23:44, 13 November 2017 (PST)

Week 12

Katie - PM/QA

Emma and I worked on our presentation on "Genome-wide expression analysis of yeast response during exposure to 4 degrees C," details of which can be found on my Week 12 page. The presentation can be found in the "file roundup" section of this page.

  1. What worked?Emma and I met up outside of class to work on the assignment, which was really helpful.
  2. What didn't work?I underestimated to the time it would take to find 10 terms that I didn't know before reading the paper. It was hard to find 10, so I resorted to picking terms that I knew but wanted to know more about. It was also difficult to find definitions for some of these words, because some of them weren't in biological dictionaries.
  3. What will I do next to fix what didn't work?I should start work on the assignment before the weekend begins. That way, I don't have to spend the majority of my Monday afternoon/evening on the project. It is better to be able to come back to a project several times, and each time have "fresh" eyes.

Emma - Data Analysis

This week I made all the corrections listed on the talk page of my user page for both Emmatyrnauer Week 8 and Emmatyrnauer Week 10. This included corrections to the excel files, stem analysis, electronic notebooks, analysis of log fold changes and p values, and the acknowledgements section. Following the completion of fixing the errors in the excel file, I emailed Dr. Dahlquist to ascertain that I completed the analysis correctly. For the individual assignment this week, Katie and I met up to work on our journal club presentation of the paper that we were assigned (can be accessed on my individual journal page, Emmatyrnauer Week 12. We divided up what portions we would be responsible for and have planned to meet up before class tomorrow to practice. The paper we were assigned is: Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. The powerpoint presentation and updated excel file can be accessed above under "File Roundup."

  1. What worked well: It was very helpful to meet up in person with Katie to begin working on the powerpoint before separating everything out.
  2. What didn't worked well: This week I had so much to do including fixing both week 8 and week 10 individual pages and redoing stem because of the mistake I made in excel. I could have asked for an extension on the excel files to allow for more time to work on the presentation. I could have also been in better communication with Blair and Zach this week.
  3. What will we do to fix what didn't work? I will communicate more with the professors. Sitting down together with my group will also help to get us all on the same page for the future weeks.

Emmatyrnauer (talk) 20:03, 20 November 2017 (PST)

Blair - Coder

As mentioned on my electronic notebook, Bhamilton18 Week 12, this week's assignment Zachary Van Ysseldyk and I worked on the Coder Milestones 0-4. Zach and I will be working on the integration of the website bringing together the other groups work to function on the GRNsight website. Katie and Emma worked on their respective journal club presentation, but we communicated to check base on how everyone is doing in the progression of the project. Zach and I met in person to collaborate on formatting of the team page, individual journal pages and project progress.

  1. What worked well: Zach and I worked on better time management as well as expectations for the assignment. We were able to communicate without any hiccups, and meeting up in person was ideal for clarifying issues.
  2. What didn't worked well: We were unsure of our progress in the project as our understanding of milestone 4 meant we needed to wait this week on others.
  3. What will we do to fix what didn't work? Checking in with our project teams/coders will help us understand how they are doing, as well as how our own progression is lining up.

Bhamilton18 (talk) 19:15, 20 November 2017 (PST)

Zach - Coder

This week, Blair and I worked on the coder milestones. We will work on integrating the actual other team's parts as they start to finish. We also collaborated with Emma and Katie to make sure that we were on the same page.
Zvanysse Week 12

  1. Things that went well: we were better about our time management as well as we communicated well. We met up together periodically to make sure that we were on the same page.
  2. Things that didn't go well: We were a little confused on how to go about the project for our milestone considering that it was more of a waiting game this week rather than actual integration. So, we didn't really know how to quantify our progress.
  3. What we will do to fix it: We maybe should have collaborated with the other teams a little bit more to be able and gauge how their projects are coming along.

Week 14

Katie - PM/QA

Emma - Data Analysis

This week I worked on completing the week 10 analysis and visualized a gene regulatory network for the wild type strain with GRNsight. All of the steps I took and files used can be found on my individual page: Emmatyrnauer Week 14.

  1. Things that went well: It was nice that I had already completed the week 8 and week 10 corrections so that I could just focus on completing the data analysis. I went in to talk to Dr. Dahlquist with issues that I was having during analysis of the microarray data. This allowed for faster and accurate completion of the analysis. I was also able to contact the data analysis guild with any questions that I had.
  2. Things that didn't go well: Everything went pretty smoothly this week; it was very helpful having work time in class to complete my last milestone.
  3. What we will do to fix it: For next week, I will continue to work with the data analyst guild to complete final individual tasks for the project. I will also be collaborating more with my group members to pull together the final deliverables, paper, and presentation.

Emmatyrnauer (talk) 19:31, 4 December 2017 (PST)

Blair - Coder

This week Zach and I worked on the first integration of the website and added a right click feature to each gene. We met in person and text messaged each other. As mentioned in my electronic notebook, Bhamilton18 Week 14, we found online resources to add this right click feature as well as collaborate with Dr. Dionisio for syntax problems. This week Emma focused on progressing with data analysis for the gene wild type and then Katie made sure all groups were giving us their deliverables.

  1. Things that went well: Collaboration with other groups was productive and went smoothly. Having Dr. Dionisio as a resource has been very helpful and quickened the process.
  2. Things that didn't go well: Working in D3 syntax has been difficult to progress in certain deliverables.
  3. What we will do to fix it: In order to fix this problem, Zach and I hope to work closely with Dr. Dionisio finding external resources and fixing small errors.

Bhamilton18 (talk) 21:25, 4 December 2017 (PST)

Zach - Coder

This week Blair and I worked on the first integration by merging through github as well as working on the right click function. This function enabled us to right click and automatically link the gene that was clicked on to that particular gene page. We connected by texting as well as meeting up in person before committing our week's work to make sure that we were on the same page. We mentioned this on my electronic notebook, Zvanysse Week 14. We collaborated with Dr. Dionisio to work out some of the D3 technical syntax problems that came about. Emma worked on progressing on the data analysis for the gene wild type and Katie make sure that everyone was on task.

  1. What went well: Our communication and procrastination was overall much better. Collaborating with other teams went smoothly and connecting with Dr. Dionisio for syntax went well as the problem was diagnosed soon after it became about.
  2. What Didn't go well: Working with D3 was a little difficult because the syntax ultimately changed for the API. This was unforeseen so it was a little frustrating.
  3. How will we fix this: When it comes to syntax problems, we will be more in communication with Dr. Dionisio

Zvanysse (talk) 21:36, 4 December 2017 (PST)

Week 15

Katie - PM/QA

Emma - Data Analysis

This week I completed last steps for data analysis including the visualization of my gene network in GRNsight. Specifics of steps performed and associated files can be accessed on Emmatyrnauer Week 15. I also met up with my teammates prior to the presentation to complete the powerpoint as well as practice a few times. Once the presentation was complete, our entire group communicated over text to finish the final deliverables for this project (i.e. the group report, individual statements, etc.) I was really happy with how things turned out!

Emmatyrnauer (talk) 18:01, 14 December 2017 (PST)

Blair - Coder

For the final week of the project Zach and I worked heavy on the integration portion of the coding. We inputed the data into the overall info.html page, referenced the gene ids of the following databases: NCBI, SGD, UniProt, JASPAR and Ensembl, and finally met with each coding groups to finalize the final pull of code from everyone. More details on the code and final project can be read on my electronic lab notebook: Bhamilton18 Week 15. For the final project deliverables, Katie, Emma, Zach and I met twice to collaborate on the presentation, read over our slides and add in details/pictures. Lastly, we communicated through text message and google slides/docs to complete the powerpoint and final paper.

Bhamilton18 (talk) 22:04, 13 December 2017 (PST)

Zach - Coder

This week was mainly focused on pulling together all the coder's code for major integrations. Blair and I inputed all the data pulled from the API team to integrate into the HTML file so the page designers could see their final product. The integration team all worked on the presentation together in person. We communicated through texting, calling, and meeting up in person. More information can be found on our electronic notebooks, but overall the project was completed. If any other teams make major changes which mess with the integration teams website, I will be on call until the deadline on Friday at 4:30.

Zvanysse (talk) 21:26, 14 December 2017 (PST)


Bibliography

Paper 1

Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.

Paper 2

Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., ... & Fujita, K. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128.

Paper 3

Becerra, M., Lombardia, L. J., González‐Siso, M. I., Rodríguez‐Belmonte, E., Hauser, N. C., & Cerdán, M. E. (2003). Genome‐wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and functional genomics, 4(4), 366-375.

PubMed Abstract: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/

PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/pdf/CFG-04-366.pdf

Publisher Full Text (HTML): unavailable

Publisher Full Text (PDF): http://downloads.hindawi.com/journals/ijg/2003/175356.pdf

Copyright: Copyright © 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Publisher: Hindawi Publishing Corporation

Availability: Open access

Did LMU pay a fee for this article: no

Paper 4

Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Comprehensive+expression+analysis+of+time-dependent+genetic+responses+in+yeast+cells+to+low+temperature

PubMed Central: not available

Publisher Full Text (HTML): http://www.jbc.org/content/277/51/50015.long

Publisher Full Text (PDF): http://www.jbc.org/content/277/51/50015.full.pdf

Copyright: "Other parties are welcome to copy, distribute, transmit and adapt the work — at no cost and without permission — for noncommercial use as long as they attribute the work to the original source using the citation above." from http://www.jbc.org/site/misc/Copyright_Permission.xhtml

Publisher: American Society for Biochemistry and Molecular Biology

Availability: All articles from this journal are free 1 year after publishing.

Did LMU pay a fee for this article: No.


Acknowledgments

  1. Our group collaborates on this page each week filling out our respective team journal assignments and project updates.
    • WE have a group chat to communicate problems, questions and ideas for our weekly assignments/milestones.
  2. We utilized the Calendar outline from the JASPAR the Friendly Ghost page, but changed the milestone/tasks due.

References

Navigational Links

Category Links
Interwiki Main Page   Course schedule   Lights, Camera, InterACTION!   LCI! Deliverables
Team Members Blair Hamilton   Emma Tyrnauer   Katie Wright   Zach Van Ysseldyk
GRNsight Gene Page
Project Instructions 		Main Instructions   Project Deliverables   Week 11   Week 12   Week 14   Week 15
Guilds Project Manager   Quality Assurance   Data Analysis   Coder
GitHub GRNsight Link https://github.com/bhamilton18/GRNsight
GRNsight Gene Page Project Links
Overview Deliverables Reference Format Guilds Project Manager Quality Assurance Data Analysis Coder
Teams Page Desiigner Lights, Camera, InterACTION! Gene hAPI JASPAR the Friendly Ghost
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