SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
+49 381 498-7571
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.
Experimentalists and modellers with basic experience in modelling and simulation. No previous knowledge about the used standards and tools is required.
|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
Please register for this tutorial through the ECCB 2016 web page.