Skip to content

Instantly share code, notes, and snippets.

@hemilpanchiwala

hemilpanchiwala/GSoC2020-report.md

Last active August 28, 2020 16:40
Show Gist options
  • Save hemilpanchiwala/b52d7b285028566c35eb085d8a405aa2 to your computer and use it in GitHub Desktop.
Save hemilpanchiwala/b52d7b285028566c35eb085d8a405aa2 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
GSoC2020-report.md

GSoC 2020 - Hemil Panchiwala

Project - Simulation of systems biology models in Java: support for new features
Organization - National Resource for Network Biology (NRNB)
Mentors

Introduction

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java™ implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution. This library is based on the JSBML project and can be used on every operating system for which a Java Virtual Machine is available.

For the information about my project, please visit the my GSoC project page.

Important Links

Summary of the GSoC work

  • Added support for SBML Level 3 Version 2
  • Added support for all models from the SBML Test Suite and passing most of them successfully.
  • Added support for stochastic simulations
  • Added support for all models from the Stochastic Test Suite and passing most of them successfully on comparing using the distance metrics specified in Stochastic Test Suite.
  • Update the complete documentation of the library with the README.
  • Fixed the Travis CI build.
  • Updated to the newer JSBML v1.5
  • Added a wrapper for the SBML Test Runner for comparing the result plots and also visualizing the distances with the reference results. Also, added a script to write the results to output files for the SBML Test Runner
  • Added new distance metrics for comparison of results - Maximum Absolute Distance, Maximum Relative Distance, Maximum Divergence Tolerance. Also, tests are added for all the distance metrics.
  • CobraSolver now updates to FluxBalanceAnalysis with newer updates
  • Merged the FERN repository (with stochastic simulation features) to SBSCL
  • The interpreter class SBMLinterpreter is now breaked into two smaller classes with initializations in EquationSystem and processing in SBMLinterpreter.
  • Complete formatting of the library with newer code styles from Google Style Guides.
  • Added user guidelines with the sequence diagrams for the better understanding of workflow of the library
  • Refactored support for the test of models from BiGG models database with successfully passing all of them.
  • Updated the project website using maven.
  • Added feature of getting simulation results at every update instead of waiting for the simulation to complete.
  • Several other minor bug-fixes and completely updated the structure of library.
  • Released version 2.0 of the library with all new updates.

The complete info about each of the updates in the library is present in my weekly blogposts at https://gsoc20hemil.blogspot.com/.

Conclusion

All the work mentioned above has been properly discussed and merged in the Draeger lab's SBSCL GitHub repository using the pull requests linked above. Also, all the issues opened are present under the issue tracker at the main repository.

Personal Note

Google Summer of Code has been a super comfortable and fun experience for me. I’ve learnt much about the systems biology and how it works tuning with computer science. My mentors - Andreas Dräger, Matthias König, Mykola Zakharchuk, and Shalin Shah have been immensely helpful and have guided me throughout the project.

I would surely contribute to this project in future to make it one of the best simulator supporting all features for the systems biology models.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment