SBSCL wiki page for GSoC 2018

Shalin Shah edited this page Aug 7, 2018 · 4 revisions

Introduction

The Systems Biology Simulation Core Library 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.

In future, Shalin will continue to contribute to SBSCL, however, this and all other work will happen on Draeger lab GitHub repository. This repository will only serve as a demonstration of Shalin's summer work for GSoC'18.

Important links

A short summary of GSoC summer work:

Proposed work finished:

  • Added support for repeatedTasks, post-processing repeated tasks
  • Added support for simulation graph plots
  • Added support for simulating hierarchical SBML models
  • Replaced proprietary IBM cplex dependency with open-source library SCPsolver
  • Support for reading OMEX files

Additional work finished:

  • Reorganized simulation-core code as per maven standards
  • Added JUnit tests to check features in the current build
  • Added support for Travis continuous integration for build check
  • Auto download test files such as SBMLTestSuite using Travis at compile time
  • Added simplified support for OneStep and SteadyState simulations
  • Added support for finding the nearest match simulation algorithm
  • Added support for plotting sedml outputs
  • Created a project website using maven
  • Updated javadoc and license files using maven
  • Several other bug-fixes and updated README

Conclusion

All the work mentioned above has been extensively discussed and merged with Draeger lab GitHub repository using a pull-request. Additionally, all the issues created on this forked repository have been transferred to the original repository using Issue mover for GitHub

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