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
Second task: Implementing Geometric FBA for COBRApy
Third task: Implementing Dynamic FBA
- In progress:
dynamicfba.dynamic_fbacould 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
- The repository hierarchy was cleaned up by my mentor, Moritz, and made to follow modern conventions.
- Commit: 111f930fb6428794f59a7c99cc9acf25e49f4650
driven.omics.imatwere refactored to take advantage of improved
cobrapyAPIs. Tests were migrated from
- Commit: 0492655f69d7413d2dcb9d53a2405a294c291cb6
driven.omics.gim3ewas 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
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
notebooksto be added to the documentation.
- Commit: ba3195928f2d04ce442691150be845369d311822
driven.metabolomicshave been retained to be worked on in the future.
- Commit: bbddb7f84729546fc3dabe59625e8b7a8f680e56
driven.data_sets.FluxConstraintswere refactored and docstrings and tests were added.
- Commit: b91dfde6fec333352ec0f3ef2f0439cecd25920b
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.