GSoC 2018 with Open Bioinformatics Foundation

This post is intended to work as the final report for my project with Open Bioinformatics Foundation as part of the Google Summer of Code 2018. I already have a blog series which aims to go in-depth about the work and also my experience being a part of it. I have linked all the PRs, commit hashes and the blog posts of individual tasks. The basic idea of this post is to have a general overview of the tasks and the metadata associated with it as part of the evaluation process for GSoC.


First task: Implementing ROOM for COBRApy

Blog post: https://medium.com/@synchon_mandal/gsoc-18-first-task-463ff57de5bd

Second task: Implementing Geometric FBA for COBRApy

Blog post: https://medium.com/@synchon_mandal/gsoc-18-second-task-163898b3eea7

Third task: Implementing Dynamic FBA

Blog post: https://medium.com/@synchon_mandal/gsoc-18-third-task-3fe31c56e27d
  • Complete: dynamicfba.lexicographic implemented.
  • In progress: dynamicfba.dynamic_fba could not be implemented properly due to the increasing complexity of the approach which would have ultimately slowed down the other implementations. The current code will be able to model a basic kinetic equation.
  • Repository: https://github.com/synchon/dynamic-fba

Fourth task: Updating driven

Blog post: https://medium.com/@synchon_mandal/gsoc-18-updating-driven-9520683c70be

Final thoughts

GSoC ’18 was the first of its kind for me and I quite thoroughly enjoyed it. It gave me an opportunity to know and work with talented people who embrace open-source. I am happy about the fact that the community I contributed to, is filled with awesome and helpful people. I am also excited about the fact that I will continue to contribute to the projects and will help in their future developments.