Difference between revisions of "Lights, Camera, InterACTION!"

Revision as of 08:16, 21 November 2017

Pugs Not Drugs Logo

Team Members

• Blair Hamilton -Coder
• Emma Tyrnauer -Data Analyst
• Katie Wright -Project Manager/Quality Assurance
• Zach Van Ysseldyke -Coder

File Roundup

• Week 11 presentation by Blair and Zach: The Secret Startup that Saved the Worst Website in America
• Week 12 presentation by Emma and Katie: Genome-wide expression analysis of yeast response during exposure to 4 degrees C
• Microarray data excel spreadsheet (corrected) : Media:Wt_Microarraydata_ET.zip

Team Schedule

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? Sitting down together as a group will 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.

Bibliography

Paper 1

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

• PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/12818212
• PubMed Central: not available
• Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=12818212
• Publisher Full Text (PDF): https://electra.lmu.edu:3555/S0011224003000282/1-s2.0-S0011224003000282-main.pdf?_tid=4c9b7cc0-c775-11e7-af71-00000aab0f26&acdnat=1510469407_3e02bee4266fd6a211ea3f6e27b460cf
• Copyright: 2003 by Science Direct; article is not Open Access
• Publisher: Elsevier Science
• Availability: online at www.sciencedirect.com
• Did LMU pay a fee for this article: yes

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.

• PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Genome-wide+expression+analysis+of+yeast+response+during+exposure+to+4+degrees+C
• PubMed Central: not available
• Publisher Full Text (HTML): https://electra.lmu.edu:2529/article/10.1007/s00792-005-0480-1
• Publisher Full Text (PDF): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=16254683
• Copyright: 2005 by Springer-Verlag; article is not Open Access
• Publisher: Springer-Verlag
• Availability: online
• Did LMU pay a fee for this article: yes

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

• 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/
• Murata, Y., Homma, T., Kitagawa, E., Momose, Y., Sato, M. S., Odani, M., Shimizu, H., Hasegawa-Mizusawa, M., Matsumoto, R., Mizukami, S., Fujita, K., Parveen, M., Komatsu, Y., Iwahashi, H. (2006). Genome-wide expression analysis of yeast response during exposure to 4 C. Extremophiles, 10(2), 117-128. Retrieved from https://electra.lmu.edu:2529/content/pdf/10.1007%2Fs00792-005-0480-1.pdf

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