Welcome to the NCSB SEDML Repository

The NCSB's Simulation & Experiment Description Repository

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Why A Repository

The value of an experiment, whether simple or complex, is that under certain conditions, with familiar apparatus and the necessary skill, it can be at any time reproduced as long as we re-create the same situation.

-- Johann von Goethe

Modelers are producing more and more complex models. Unless these models are sufficiently characterized and made available to the research community their reuse will be minimal, and reproducing simulation experiments incorporating them will prove problematic. Consensus on the content and form of experiment recipes that combine models and simulations will encourage model sharing and facilitate reuse.

A set of guidelines specifying the Minimum Information About a Simulation Experiment (MIASE) proposes a common set of information necessary to reproduce simulation experiments that incorporate quantitative models. We have instantiated these guidelines in a web-based content management system. With RepoSE you can create Simulation and Experiment Descriptions, enrich them with experimental data and annotate them with domain meta-information to facilitate classification, searching and cross referencing.

 

SED-ML

One instantiation of the MIASE guidelines is SED-ML - an XML schema, instances of which are recipes describing the combination of models and simulations into reproducible experiments. In particular, SED-ML describes five components essential to compose a simulation experiment description, i.e.:

 

Insuring Reproducable Results

The Simulation & Experiment Description Meta Language (SED-ML) is a means - like a recipe - to describe the combination of simulations and models in reproducible experiments.  We have built a web-based simulation and experiment description repository based on SED-ML. Implemented as a Plone add-on product, our repository allows researchers to:

 

In contrast to EBI's existing BioModels database, which hosts only biochemical models written in SBML, our repository will uniquely record any simulation experiment, including those written in \Cpp, thus making the tool generally applicable to the types of simulation models used within the NCSB.

We have extended the SED-ML standard to accommodate source-code models, and enriched the output types with descriptive text, images and animations - which makes the repository useful as a laboratory notebook.

 

Results

 
 

Getting Started

Watch a video showing how to compose a SED.
 
Send us an email and we will add you as a modeller in our public sandbox repository.