EPISIM Modeling and Simulation Platform
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EPISIM Multi-Scale Modeling and Simulation Platform

Graphical Multi-Scale Tissue Modeling and Agent-Based Simulation Platform

The EPISIM Platform provides the two ready-to-use and easy-to-install software systems EPISIM Modeller and EPISIM Simulator. EPISIM Modeller enables graphical multi-scale modeling of cellular behaviour in a multicellular context using process diagrams. The graphical cell behavioral models are automatically translated into executable code. This code can be loaded with EPISIM Simulator to conduct either a 2D or a 3D tissue simulation.

EPISIM Modeling and Simulation Platform

Cellular behavior is modeled with process diagrams using deterministic and / or stochastic model elements. SBML based quantiative subcellular models can be automatically imported and semantically integrated in a cell behavioral model. The EPISIM platform enables users to build their own cell behavioral model and tissue simulation in a purely graphical way. No dedicated programming skills are needed.

Get EPISIM

How to cite EPISIM:

Sütterlin T, Kolb C, Dickhaus H, Jäger D, Grabe N (2013). Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI. Bioinformatics. 2013 Jan 15;29(2):223-9. Epub 2012 Nov 18. PubMed PMID: 23162085.

EPISIM Movies

EPISIM Simulation
Demo Movies
EPISIM Introductory
Video Tutorials
EPISIM Semantic SBML
Model Integration Tutorials
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Selected EPISIM Publications

Sütterlin T and Grabe N (2014). Graphical Multi-Scale Modeling of Epidermal Homeostasis with EPISIM. In, Querleux,B. (Ed.), Computational Biophysics of the Skin. Pan Stanford Publishing, Singapore, p. 421–460.

Sütterlin T, Kolb C, Dickhaus H, Jäger D, Grabe N (2013). Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI. Bioinformatics. 2013 Jan 15;29(2):223-9. Epub 2012 Nov 18. PubMed
PMID: 23162085.
electronic version  supplements

Safferling K, Sütterlin T, Westphal K, Ernst C, Breuhahn K, James M, Jäger D, Halama N und Grabe N (2013). Wound healing revised: A novel reepithelialization mechanism revealed by in vitro and in silico models. Journal of Cell Biology, 203 (4), pp. 691–709.
electronic version

Sütterlin T, Huber S, Dickhaus H and Grabe N. (2009) Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems, Bioinformatics, 25, 2057-2063.
PMID: 19535533
electronic version  supplements

Complete list of publications

Acknowlegements

EPISIM would not exist if there were no freely available software libraries and frameworks. EPISIM is based on the following software being maintained and developed at university institutions:

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Moreover, EPISIM utilizes amongst others the following freely available platforms and libraries:

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hamamatsu, tiga center, tiga centre, tiga, epithelial, tissue, tissue analysis, tissue modelling, tissue imaging, hautsimulation, episim, imaging, analysis, model, modelling, Heidelberg, Universität Heidelberg, Bioquant, epithel, medizinische informatik, pathology, modeller, medical informatics