Simulating systems biology models in Java

<p>Computational models of biological systems play an important role in advancing science as they give insights about the biology without the need for performing real experiments. A significant challenge in the systems biology field is the reproducibility and reusability of such models and making these accessible to the broader biology community. To address this issue, computer-readable formats and tools for modeling complex biological systems have been developed. Standards such as Simulation Experiment Description Markup Language (SED-ML) and tools like Systems Biology Simulation Core Library (SBSCL) can represent such complex biological models and numerically simulate them. But until now only a subset of these standards have been implemented in SBSCL. Essential features that will catalyze reproducibility, exchangeability, and reusability are lacking so far. Namely, i) implementation of full support for simulation experiments; ii) plots and visualization of simulation studies; iii) support for standard archive formats; iv) support for Open Source solvers, and v) support for hierarchical models.</p>