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A Web-based Repository of Reproducible Simulation Experiments for Systems Biology

M.A. Guravage, R.M.H. Merks. A Web-based Repository of Reproducible Simulation Experiments for Systems Biology. Proceedings of SIMULTECH 2011 2011, 134–141, 2011.

A Web-based Repository of Reproducible Simulation Experiments for Systems Biology

Systems Biology requires increasingly complex simulation  models. Effectively interpreting and building upon previous  simulation results is both difficult and time consuming. Thus,  simulation results often cannot be reproduced exactly; making it  difficult for other modellers to validate results and take the  next step in a simulation study.

The Simulation Experiment Description Mark-up Language (SEDML), a subset of the Minimum Information About a Simulation Experiment (MIASE) guidelines, promises to solve this problem by prescribing the form and content of the information required to reproduce simulation experiments. SEDML is detailed enough to enable automatic rerunning of simulation experiments.

Here, we present a web-based simulation-experiment repository lets modellers develop SEDML compliant simulation-experiment descriptions The system encourages modellers to annotate their experiments with text and images, experimental data and domain meta-information. These informal annotations aid organisation and classification of the simulations and provide rich search criteria. They complement SEDML's formal precision to produce simulation-experiment descriptions that can be understood by both men and machines. The system combines both human-readable and formal machine-readable content, thus ensuring exact reproducibility of the simulation results of a modelling study.