Project - Implementation of SBML-JSON converter and SBML-JSON scheme
Organization - National Resource for Network Biology (NRNB)
Mentors
- Dr. Matthias König
- Dr. Andreas Dräger
- Dr. Sarah M. Keating
- Dr. Lucian Paul Smith
So we've now officially come to an end to the amazing 12 weeks of Google Summer of Code 2020! This page summarize my entire work over the past 12 weeks.
- GSoC proposal
- Weekly GSoC blogs
- Forked repository for GSoC work
- COBRApy main repository
- List of Pull requests
- Final Summary in brief
- Fixed issue of infinity bounds in COBRApy and JSON.
- Fixed issue of annotation present in the form of list of list inside JSON.
- Fixed issue of consistently storing annotation resources in form of list.
- Modified JSON schema version 1 to fix up broken things.
- Added JSON schema version 2 defining new implemented features.
- Enabled support of Group package to JSON and other formats.
- Added the CVTerm class for storing external resources linked with a component.
- Added History class for storing component's provenence.
- Added KeyValuePair class for for storing any type of key-value pairs for that component.
- Added complete support of Notes for COBRA components and extended its support to JSON and other formats too.
- Added UserDefinedConstraint class which allows users to add their own constraints and extended its support to JSON and other formats.
- Added method for validating JSON models against JSON schemas.
- added the model's basic SBML information to JSON and other formats.
- Added tests for all implemented functionalities.
- Separating complete metadata classes in a separate package.
- Adding parser for fbc-v3 features when libsbml adds support for it.
The complete info about my weekly updates in last 12 weeks can be found here(https://hemant-gsoc2020.blogspot.com/).
Two pull requests during GSoC period and two prior to GSoC period have got merged, which fixed various issues. One pull request for metadata classes is under review and will be merged soon. The remaining one pull request may take some time because the interfacing library (libsbml) has still not added support for the functionalities implemented in this pull request.
This GSoC period has been an amazing experience for me. I learned to write code on a professional front. We started enthuciastically and completed most of the part in initial two months. But the members of COBRApy organisation were responding slowly, which stretched it till the last date. But overall, I enjoyed the complete GSoC period to fullest.
The mentors have been very supportive throughout the journey and they helped me more than I could have asked for. I would definitely love to keep up my involvement with COBRApy community and my mentors.