Lights, Camera, InterACTION!

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Team Members

File Roundup

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 		22
Thanksgiving Break 		23
Thanksgiving Break 		24
Thanksgiving Break 		25
26 27 28
C: First Integration projected completion
PM:
DA: 		29 30
C: Check in with other groups about progress
PM:
DA: 		1 2
3 4 5
C: Check in with groups, and further integrate as needed.
DA: 		6 7
C: Check in with other groups about progress
PM:
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
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 - Data Analysis

Blair - Coder

  1. 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.
  2. 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.
  3. 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.
  4. 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.

  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.

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.
  2. We utilized the Calendar outline from the JASPAR the Friendly Ghost page, but changed the milestone/tasks due.

References

  1. Meyer, R. (2015, July 09). The Secret Startup That Saved the Worst Website in America. Retrieved November 7, 2017, from https://www.theatlantic.com/technology/archive/2015/07/the-secret-startup- saved-healthcare-gov-the-worst-website-in-america/397784/

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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