Revision as of 23:38, 15 December 2017

Statement of Work

Filling both the roles of a project manager and quality assurance member for the JASPAR the Friendly Ghost team, I contributed in a number of ways to the success of our team. The initial contribution I added to our team was in the form of the literature review on the effects of cold shock on yeast, which I conducted alongside our teams [Data_Analysis|data analyst], Antonio Porras. The first step of this process was an in-depth literature search which was conducted with the use of three credible online resources (Google Scholar, Pubmed, and Web of Science). The results of these searches can be seen in my week 11 electronic notebook. After having found a number of articles on the topic, we honed in on one article in particular, namely 'Genome-Wide Analysis of the Yeast Transcriptome Upon Heat and Cold Shock', and created and presented a journal club presentation to the class. [Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|This presentation]], and our work which went into creating this presentation, can be viewed on my week 12 electronic lab notebook.

After the journal club presentation had been completed, I primarily functioned as the coordinator for all of the team milestones and deadlines. To better facilitate this task, I met with each member of my team and came up with a number of checkpoints. These checkpoints were then formatted into a calendar which can be seen on the team page. In addition to this initial planning, I also performed a secondary planning for the final group deliverables, as I outlined what I forecasted as being each team members primary responsibilities in my week 15 electronic notebook. Along with these more explicitly visible examples of managing, I also spearheaded the efforts of collaboration outside of class, working to text in our team group chat to coordinate best times to meet and ensure that each individual member of the team was performing their assignments.

While coordinating the team's efforts was a primary role, I also served in a number of other areas. Another major task that I completed was to identify the fields we wished to retrieve from each of the five databases (JASPAR, NCBI, Ensembl, UniProt, and SGD) we would be utilizing. I worked closely with the other project managers (Emma Tyrnauer, Katie Wright, and Hayden Hinsch) to visit each of the five databases and determine which database was best suited for which information. I outlined all of the fields we identified for each database on my week 14 electronic journal page. after having compiled an initial list, I ran these fields past Dr. Dahlquist to determine if there were any other fields which she wished to be included. And after having added all of these fields that Dr. Dahlquist requested, I shared this information with both our JASPAR API team and the Gene hAPI team so that they could develop the appropriate code. Along with just providing a list for each of the desired fields, I also included the answer to each field for a sample gene 'hsf1', which was done to assist the coders in recognizing which parts of each database to pull. Furthermore, I also followed up with the coders continuously (namely my two team members, Eddie A, and John) to help them with any issues they had and ensure that their code was working. I also noted which fields they were unable to retrieve for any reason, and documented these fields in my week 15 electronic notebook so that they could be identified as potential fields to retrieve in the future.

In regards to the final project, I created and kept our team deliverable page, along with working on a number of parts of the final deliverables. Specifically, I created google docs/slides for both the final paper and ppt, and invited my team members to each of them. In the ppt, I worked on crafting the entire introduction section along with the conclusion and outline (which the help of my team members of course). Along with focusing primarily on my portion of the ppt, I also assisted my team members in their parts, providing feedback and checking for format/grammar issues. The final group presentation can be found on our team page. For the paper, I focused on primarily the same sections that I did for the ppt, writing the introduction and the bulk of the conclusion. I also wrote my own methods portion.

Overall, as both project manager and quality assurance member, I played a number of roles on the team.

Qlanners (talk) 20:52, 14 December 2017 (PST)

Assessment of Project

• What worked and what didn't work?
  • As a team there were a number of things that worked, but also a couple things that did not work so well. Focusing first on the positive stuff, we worked very well as a team and communicated well. All team members were willing and able to meet on multiple occasions, which made for very good work sessions and allowed for us as a team to stay on task. Furthermore, everyone in the team was very willing to take on their responsibilities. Additionally, all team members were very respectful of each other, providing constructive criticism on presentation slides, areas of the paper, or other areas of our work. These forms of constructive criticism allowed for our deliverables to be improved without creating any tension between the team members. However, while overall we worked very well, there were a few difficulties we ran into. The first difficulty was with our coders, who initially had troubles with the execution of their code. They had to work with Dr. Dondi to overcome this difficulty, and although it eventually worked in the end, it cut into the time that they were able t help on the group presentation and paper in class and thus put a bit more stress on the project manager and data analyst. Furthermore, there was definitely some difficulty communicating the importance of the two aspects of the project to all of the team members. What I mean by this is that the data analyst had little idea what the coders were doing and vice versa. While our collaborative work on the presentation definitely helped clear this issue up a bit, there was never full understanding for all teammates on the purpose and methods of the two facets of the project.
• What would you do differently if you could do it all over again?
  • If I could do it all over again, I would definitely begin the project by establishing what the purpose of our research was with all of the team members. In this way, we all would have known exactly what we are striving for as a team and would have better been able to understand how the two parts of the project were going to fit together. This would have made the creating of our final presentation and paper much easier, as I wouldn't have had to spend so much time explaining the connection to my teammates. And although there was more general understanding towards the end, the project still felt very separated throughout the whole process. Another idea would have been to have small group meetings between our group at the beginning or end of each class to update each person in the team on your status so that we were always on track. This also would have helped me as project manager to ensure everyone was on pace with their deadlines.
• Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
  • Content: What is the quality of the work?
    • I felt that we as a team delivered very high qualities of work, especially given the time constraints on this project (and the fact that we all had to coordinate our work around a very busy time of year). Our coders successfully retrieved all of the desired fields from JASPAR that I as quality assurance identified. In that sense, we completed our goal as a team in regards to the GRNsight feature. In regards to the group presentation and paper, I felt we did a very good job al circumstances considered. It was incredibly difficult to coordinate the work for these projects, as everyone was very busy with finals, but we still managed to meet as a team on multiple occasions. Furthermore, I felt that we as a team paid very good attention to the details, not only handing in all the deliverables but also ensuring that the deliverables met all of the requirements.
  • Organization: Comment on the organization of the project and of your group's wiki pages.
    • While at the beginning of the project our wiki page was definitely lacking a bit, after I was given some time to work on the page, I felt our team page became very easy to navigate and held all of the necessary information in a very logical manner. Additionally, all of us completed every weekly journal and were sure to link all of these to our team page, further enhancing our level of organization. If there were any deficits in the organization, it probably came in regards to our work on the final paper. As everyone was busy towards the end of the week, our organization was a bit tough to maintain at times, however, I feel we did a good job of finishing strong and ensuring to clean everything up before finalizing it.
  • Completeness: Did your team achieve all of the project objectives? Why or why not?
    • Yes we completed all deliverables. There was a bit of a time crunch at the end, but thanks to good communication and teamwork we managed to get everything turned in on time.

Qlanners (talk) 20:52, 14 December 2017 (PST)

Reflection of the Process

• What did you learn?
  • With your head (biological or computer science principles)
    • There was a variety of information that I learned a lot more about in this course. Speaking first to the biological portion of the course, while I have taken a number of biology and chemistry classes before, I have not taken a genetics course before. So this course was a bit of a crash course on how genetics works. Being that I am very interested in data analysis, I was particularly interested in all of the data that is collected in genomics, and the unique ways that this data is analyzed. While I loved learning about the background and different techniques that go into genomics (such as microarrays, STEM, etc.), I would like to gain a deeper understanding of exactly what each of the statistical steps we took in the class did. I felt at times like I was just blindly following a list of steps and would have appreciated a deeper sense of understanding.In regards to the computer science principles, I learned a decent amount about how API calls work, and how you can use navigation features to easily work through the code of a website. I also enjoyed getting a short little intro the basics of how HTML works.
  • With your heart (personal qualities and teamwork qualities that make things work or not work)?
    • Having a number of partner and group projects throughout the semester, I learned a lot about the importance of starting things early. Especially early on in the class, there were several occasions were I was cramming to get things done on the night before things were due. Furthermore, as project manager of my team, I gained invaluable experience about the importance of ensuring constant communication between team members. I found that the more we stayed in touch the more productive we were as a team. These are skills that I will certainly take with me into whatever I end up pursuing as a career.
  • With your hands (technical skills)?
    • While I did practice a few technical skills in this class, in all honesty, this is the part of the course I was a bit disappointed in. I was hoping to have much more exposure to writing code and doing data analysis. While there was a decent amount of code writing, since I was not a coder for the final project, I felt like I really did not gain any meaningful technical skills in regards to programming. However, I did at least gain knowledge about how to use developer tools to easily navigate a website which I'm sure will come in handy down the road. And in regards to the data analysis, while there was a week with quite a bit of Excel work, as I explained earlier, the Excel worked felt like I was just mindlessly following a script. This kind of technical skills will not stick with me, as I honestly was not sure what the meaning behind each manipulation was.
• What lesson will you take away from this project that you will still use a year from now?
  • Overall, it is not the technical skills but rather the experience I gained as a team member and project manager that I will be using a year from now. I definitely learned a lot about the importance of planning ahead, setting milestones, and identifying deadlines. Furthermore, I learned a lot about the importance of constant communication to ensure that these deadlines are met and that the work is done right. While I do wish that I would have gained a bit more technical skills from the class, I cannot take for granted the amount that these managerial skills will aid me going forward.

Qlanners (talk) 20:52, 14 December 2017 (PST)

Acknowledgements

• The members of the JASPAR the Friendly Ghost team for all their hard work.
• The template on the GRNsight Gene Page Project Deliverables for the format of this page.
  

While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
Qlanners (talk) 15:38, 15 December 2017 (PST)

Resources

LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 14, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables

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