RepoSE: An On-Line Repository for Simulation Experiment Descriptions

Presented RepoSE at Plone 2012 in Arnhem. System biologists are scientists who use mathematics to describe biological processes. They call their experiments ‘simulations’, and perform them not in a laboratory but on a computer. Simulations have grown so complex that scientists find it difficult to keep track of all the details necessary to rerun them. To manage this complexity they are using a recipe metaphor to describe simulation experiments. A simulation experiment recipe is composed of many small pieces that must fit together just so. The rules for what the recipe pieces look like and how they fit together are very strict. So strict in fact that a simulation recipe can be run automatically by software that knows the rules. This formal description is embodied in a schema called the Simulation Experiment Description Modelling Language (SED-ML). In my presentation I will describe how we instantiated the SED-ML schema as a set of more than thirty cooperating custom content types in Plone. These content types are the building blocks used to build reproducible simulation experiments that are readable by both men and machines.