Modern software tools and standards for modeling biological systems


In this one-day tutorial, we will give an overview of current standards and standards-compliant tools for modeling and simulation in biology. The tutorial begins with an introduction to the COMBINE initiative, including the core standards (e.g., CellML, SBML, SED-ML and SBGN), and tools implementing these standards. We will also discuss current trends in model reproducibility and model management.

This will be followed by hands-on exercises. We introduce you to a variety of mostly web-based software tools to create, visualize, simulate and modify simulation models. You will work through two specific workflows (Creating your own mathematical model, Reusing existing models from open repositories) using several different modeling and analysis tools and online resources. At the end of the hands-on sessions, you will have created a standards-compliant, semantically annotated and reproducible simulation study.

Finally, we will give an outlook of future COMBINE developments, discuss the issues observed throughout the tutorial, hold open discussion and answer any remaining questions.


Dr. Frank Bergmann, Modeling of biological Processes, BioQUANT/COS, University of Heidelberg, Germany
Dr. Dagmar Waltemath, Dept. of Systems Biology and Bioinformatics, University of Rostock, Germany

Target audience

Experimentalists and modellers with basic experience in modelling and simulation. No previous knowledge about the used standards and tools is required.


time slot Topic
09:00 - 10:15 Welcome
09:15 - 10:15 Introductory lecture I: The landscape of systems biology standards and supporting software tools ( Frank Bergmann)
  Introductory lecture II: How standards and management strategies lead to reproducible modeling results. (Dagmar Waltemath)
10:15 - 10:45 break
10:45 - 12:30 Hands-on/Workflow I: Creating your own mathematical model. Tools: COPASI, CellDesigner (Frank Bergmann)
12:30 - 13:30 lunch
13:30 - 15:30 Hands-on/Workflow II: Reusing simulation models & reproducing results. Tools: BioModels, PMR2, SEEK, SED-ML Web tools, WebCAT, BiVeS (Dagmar Waltemath)
15:30 - 16:00 break
16:00 - 17:00 Summary & Outlook

Further information, registration & contact

Attendees must bring laptops for hands-on sessions in the afternoon. They should install the following software: latest version of COPASI and CellDesigner. All other tools are web-based.

Please register for this tutorial through the ECCB 2016 web page.

Should you have further questions, suggestions, or requirements for the tutorial, please do not hesitate to contact Dagmar Waltemath (

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