Eyanosch Individual Reflection
Statement of work
Researched Shigella flexneri with Oregon Trail survivors and found a microarray paper suitable for the final project review. I was one of the GenMAPP users along with Kristin, we took the LogRatios from our mircroarray paper and compiled an indepth analysis of the effects of rifamycin on Shigella flexneri. A power point was made explaining the experimental method of the microarray. A journal presentation was created by along with the other GenMAPP user to identify and explain the methods and purpose of the microarray experiment. A final presentation was given in regards to our findings using PostgreSQL, GenMAPP, and other programs to create a succinct analysis of the microarray papers data. I created Gene MAPPS for the most induced or repressed pathways within our criterionGO files of RPRX at 0.5xMIC at 10 minutes and RPRX at1xMIC at 60 minutes for both drugs. Provide references or links to artifacts of your work, such as:
Wiki pages Eyanosch Week 15
Files Created:
- Flagellum Ribosomal Map 0pt5 10min
- Flagellum Ribosomal Mapp 1 60min
- RP Compiled Raw Data Final 12/10
- RP .txt format GenMAPP ready 12/6
- RP Exceptions file in Excel format (filtered)
- RP Exceptions (txt)
- RP .gex file
Files I contributed to:
- Microarray Journal Club Power Point
- Microarray Compiled Raw Data RP/RX IDLR
- Microarray Corresponding Files Table
- Compiled Raw Microarray Dataset (.xlsx)
- Data Used for Import into GenMAPP (.txt)
- GenMAPP Expression Dataset File (.gex)
- Exceptions file (.EX.txt)
- Raw MAPPFinder results files (-GO.txt)
- .gmf file
- Final PowerPoint Presentation
- ScalingCentering file 12/1 .xlsx
Assessment of Project
Give an objective assessment of the success of your project workflow and teamwork.
What worked and what didn't work?
The workload is divided into two basically, the biologist side and the computational computer science side. I found it difficult to help the QA and coder when it was just me and them working on the project. Although they are working on a completely different part of the project, it helps to be able to bounce questions off each other. I relied on Kristin and Dr. Dhalquist whenever an issue came up that I couldn't solve on my own. I felt like the in-class time dedicated to working on the project and asking questions helped.
What would you do differently if you could do it all over again?
Start the deliverables a weekend earlier and practice our presentations a few more times. Often times we found our group meeting Sunday or Monday night and trying to crank out the assignment due that midnight. Giving ourselves more time to complete these tasks may have lessened the level and stress and improved quality of work.
Evaluate the Gene Database Project and Group Report in the following areas:
Content: What is the quality of the work?
The quality of work is good, we have all of the deliverables completed. Every bullet point was taken care of and completed within a google doc that will be uploaded as the final culmination to a good semester.
Organization: Comment on the organization of the project and of your group's wiki pages.
Our group was fairly organized in terms of managing time even when we couldn't all meet together. Conversations were had about what needs to be done or what was done. Our Oregon trail survivors page is fairly easy to traverse and aesthetically pleasing.
Completeness: Did your team achieve all of the project objectives? Why or why not?
Our team completed all the project objectives. We made sure to check off everything when we finished it and have someone review our work. Kristin and I reviewed each others input into the final project to make sure it met the criteria we both deemed necessary for this project. There was a constant dialogue going back and forth among our team. Oregon Trail Survivors completed all of the project objectives because we kept each other accountable and planned ahead. During Finals time people's lives become hectic and its hard to find a time everyone can meet. We had a group messaging system going to make sure each section was being taken care of or if anyone had questions those were addressed.
Reflection on the Process
I liked how the process of the final project was constructed. For the last assignment in class we did a mock final genMAPP assignment with the vibrio cholera data. This laid the foundation for which the GenMAPP users would essentially use. The first time using GenMAPP I was completely and utterly lost, after a few times I gradually picked up on the format and the different files needed and how the database .gbd and .gex files relate to each other. The gradual build up to the final project definately helped with preparations. I did like how we gave a power point presentation before the deliverables were due, this allowed for us to obtain feedback that we used, I know I did personally, towards the deliverables. I found the constructive criticism very helpful.
What did you learn?
With your head (biological or computer science principles)
I learned new analytical techniques regarding both biological and computer science principles. Taking the best of both worlds and formulating it into one. Before this class I wasn't familiar with many of the concepts we discussed but over time and with many hours of practice I have built a framework for these ideas to stick to. This class has challenged me to being uncomfortable and working through that in order to meet the end result which has been so rewarding.
With your heart (personal qualities and teamwork qualities that make things work or not work)?
I have developed a soft spot for this class. The computer science students and biology students meshed well together in this class, especially when working out of ones comfort zone and in an area not of their expertise. The camaraderie within this class is unlike any other I've taken. This class has helped improve skills regarding teamwork and setting goals towards accomplishing a group effort final task.
With your hands (technical skills)?
I have become more resourceful when it comes to collecting data from outside sources and compiling that information together. This class has provided the tools to become better adapted to work involving online databases and bioinformatics. I pick up much easier on things now that I have been exposed to programming logic. I have become better at conceptualizing the computer science and biological aspect of the class.
What lesson will you take away from this project that you will still use a year from now?
I will take away this research experience and how it brought forth teamwork, technical skill, and a greater understanding of community standards within the scientific community and if I want to be a contributing factor what is required. Research in bioinformatics and genetics is an upcoming field and will only become more relevant. I will take with me the readings from the class of those who paved the way so that we can analyze and compare massive databases with the click of a button. The importance of making reproducible work has been ingrained into my being.
