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Authors: Michael A. Guravage and Roeland M. H. Merks

Affiliation: Netherlands Consortium for Systems Biology & Netherlands Institute for Systems Biology (NCSB-NISB), Netherlands

ISBN: 978-989-8425-78-2

Keyword(s): SED-ML, SBML, MIASE, Simulation, Modeling, Plone, CMS.

Related Ontology Subjects/Areas/Topics: Application Domains ; Collaboration and e-Services ; Collaborative Systems ; Complex Systems Modeling and Simulation ; e-Business ; Enterprise Information Systems ; Formal Methods ; Life Science Modeling and Simulation ; Mathematical Simulation ; Simulation and Modeling

Abstract: 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 SED-ML, 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. SED-ML enable automatic rerunning of simulation experiments. Here, we present a web-based simulation-experiment repository that lets modellers develop SED-ML 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 organisatio n and classification of the simulations and provide rich search criteria. They complement SED-ML'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. (More)

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Paper citation in several formats:
A. Guravage, M. and M. H. Merks, R. (2011). A WEB-BASED REPOSITORY OF REPRODUCIBLE SIMULATION EXPERIMENTS FOR SYSTEMS BIOLOGY.In Proceedings of 1st International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH, ISBN 978-989-8425-78-2, pages 134-141. DOI: 10.5220/0003598001340141

@conference{simultech11,
author={Michael A. Guravage. and Roeland M. H. Merks.},
title={A WEB-BASED REPOSITORY OF REPRODUCIBLE SIMULATION EXPERIMENTS FOR SYSTEMS BIOLOGY},
booktitle={Proceedings of 1st International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH,},
year={2011},
pages={134-141},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003598001340141},
isbn={978-989-8425-78-2},
}

TY - CONF

JO - Proceedings of 1st International Conference on Simulation and Modeling Methodologies, Technologies and Applications - Volume 1: SIMULTECH,
TI - A WEB-BASED REPOSITORY OF REPRODUCIBLE SIMULATION EXPERIMENTS FOR SYSTEMS BIOLOGY
SN - 978-989-8425-78-2
AU - A. Guravage, M.
AU - M. H. Merks, R.
PY - 2011
SP - 134
EP - 141
DO - 10.5220/0003598001340141

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