Individual Assessment and Reflection

Mitchell Petredis

[[Team Name]]

Reference page for this assignment: Gene Database Project Report Guidelines

Statement of Work

• As coder of [[Team Name]], I was responsible for creating and tweaking versions of gmbuilder under the provision of Dr. Dionisio to help create a proper analysis tool for our species Sinorhizobium Meliloti (Strain 1021). Additionally, I imported the unique UniProt XML, GO OBO-XML, and GOA files into the PostgreSQL database for our species using my custom versions of gmbuilder and exported the .gdb files necessary for the quality assurance and GenMAPP users to do their respective roles.
• In total, 3 versions of gmbuilder were created and produced the following .gdb files (in order of oldest to newest):
  • gmbuilder-2.0b71.zip
    • Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_2013117.gdb
  • GenMAPP_Builder_2.0b72 S. meliloti.zip
    • Sinorhizobium_meliloti_1021_GenMAPP_database_mpetredi_20131121.gdb
  • Media: SmelilotiGenMAPP_Builder_2.0b73.zip
    • Media:Sinorhizobium_meliloti_1021_mpetredi_2013123-2.gdb

• My lab progression is listed below:
• mpetredi Week 12
• mpetredi Week 13
• mpetredi Week 14

NOTE: "Important Files 3" does not have a .gdb file because of accidentally importing duplicate data into PostgreSQL; I decided it would be a hindrance to use that .gdb file for analysis and therefore discarded it. A new database and .gdb file were created under "Important Files 4" to resolve this issue.

Assessment of Project

• Our project was somewhat successful, but it is still a work in progress. I believe my team displayed dedication to the quality of the project, and while we were not able to create an error-free database this semester, our work-ethic significantly contributed to the further completion of the gene database. If my team's schedule outside of this class weren't as complex, I believe we could have delivered a finished product.
• If I could do it all over again, I'd start the project earlier. Additionally, having a laptop with all the lab software would have made it more convenient to organize the project and work on it away from the lab.
• Gene Database Project and Group Report Evaluation
  1. Content: We described our methods with as much detail as we could and provided explanations for our results and discussion.
  2. Organization: We followed the prompt given to us, and reading the report over again it seems like it's structured well.
  3. Completeness: Considering the challenges we had with this project, I'd say our report feels as complete as it can be.

Reflection on the Process

• I learned the following
  • With my head: Biology and Computer Science can drastically benefit from each other. As technology improves, scientists can discover new things that previously could not be comprehended or understood.
  • With my heart: Close communication and flexibility in scheduling with team members is critical to achieving project goals.
  • With your hands: I gained a better understanding of how database management and organization works, and even learned some coding.
• A year from now, I'll remember the various SQL queries and how to utilize filtering mechanisms in large datasets.