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

• cobra.flux_analysis.room implemented along with the respective test case.
• Documentation was also added to reflect the addition of the new method.
• PR: https://github.com/opencobra/cobrapy/pull/708
• Commit: 725c41c31901e334316db891e8f1f30d262022bf

Second task: Implementing Geometric FBA for COBRApy

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

• cobra.flux_analysis.geometric implemented along with the respective test case.
• Documentation was also added to reflect the addition of the new method.
• PR: https://github.com/opencobra/cobrapy/pull/710
• Commit: 67e692c2524d94dcf1e6c04e3334a97a3b95aadc

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

• The repository hierarchy was cleaned up by my mentor, Moritz, and made to follow modern conventions.
• Commit: 111f930fb6428794f59a7c99cc9acf25e49f4650
• driven.omics.gimme and driven.omics.imat were refactored to take advantage of improved cobrapy APIs. Tests were migrated from unittest to pytest.
• Commit: 0492655f69d7413d2dcb9d53a2405a294c291cb6
• driven.omics.gim3e was added but due to lack of reproducible experimental dataset, tests could not be implemented as of now, but will be implemented as soon as a working dataset is obtained.
• Commit: 17b8523bcd9cec52c9199e348d4b4f35ad712ff4
• Visualizations have been migrated from matplotlib to altair. It is planned to completely migrate visualizations to a different package which would include high-level APIs with backends of most used visualization toolboxes.
• Commit: 23d4b6b5718851bbf25441886e0c1d9b992796d6
• Example Jupyter notebooks were added to notebooks to be added to the documentation.
• Commit: ba3195928f2d04ce442691150be845369d311822
• driven.fluxomics and driven.metabolomics have been retained to be worked on in the future.
• Commit: bbddb7f84729546fc3dabe59625e8b7a8f680e56
• driven.data_sets.ExpressionProfile and driven.data_sets.FluxConstraints were refactored and docstrings and tests were added.
• Commit: b91dfde6fec333352ec0f3ef2f0439cecd25920b

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.