Simulation of systems biology models in Java: support for new features

<p>Systems biology studies the mechanisms underlying complex biological processes as integrated systems of many interacting components. Modeling biological systems has always been a difficult and often challenging task. A particular challenge is to make such models reproducible and thereby reusable by a broader community. Different languages and libraries have been developed to address the exchangeable encoding of computational models. Examples are formats such as the Systems Biology Markup Language (SBML) and Simulation Experiment Description Markup Language (SED-ML), which can represent complex biological models and libraries such as the Systems Biology Simulation Core Library (SBSCL) which can simulate them. But until now, SBSCL still lacks certain features that need to be implemented. Essential new features are</p> <p>i) Implementation of new features of <strong>SBML Level 3 Version 2</strong>.</p> <p>ii) Support for newer versions of existing SBML packages such as <strong>FBC Version 3</strong> in SBSCL.</p> <p>iii) Implementation of <strong>stochastic</strong> simulation in SBSCL.</p> <p>iv) Improvement of support for SBML models with <strong>comp</strong> extension.</p>