ICSB 2013 workshop

Modelling and Simulation of Quantitative Biological Models

Wednesday, September 4th, 2013 (9:30 - 18:00)
Copenhagen, Denmark

This workshop is a satellite of the 14th International Conference on Systems Biology (ICSB). You can sign in for the tutorial (free of charge) when registering for the conference at http://www.icsb2013.dk.

Participants will learn setting-up quantitative computer models of biological networks using experimental kinetic data and simulating them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included providing attendees with the necessary skills to enable them to access experimental kinetics data from available resources, assembling computer models with these data and finally simulating the models within different tools.

The topics will include:

  • Using experimental data for setting up quantitative models
  • Parameter estimation, optimization and model fitting
  • Simulation, analysis and visualization of biochemical models
  • Integrated data management and model databases
  • Community standards and formats for systems biology models

Target audience
Modellers and experimentalists with some basic experience in modelling and simulation of biological networks.


Copenhagen, Denmark
Technical University of Denmark (DTU)
DTU meeting center, room 1

Directions how to get to DTU can be found here
Download a map of DTU

Lunch (self-pay) can be obtained at the DTU cafeteria on-site.


09:30 – 09:45 Introduction – Martin Golebiewski (HITS Heidelberg, Germany) <html><a href="http://co.mbine.org/system/files/Intro Tutorial 2013.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>

09:45 – 11:15 Community standards and formats for models

09:45 – 10:00 COMBINE – Nicolas Le Novère (Babraham Institute, Cambridge, UK) <html><a href="http://co.mbine.org/system/files/COMBINE-LeNovere.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>
10:00 – 10:30 SBGN – Tobias Czauderna (IPK Gatersleben, Germany) <html><a href="http://co.mbine.org/system/files/ICSB_Introduction_to_SBGN.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>
10:30 – 11:15 SBML – Mike Hucka (California Institute of Technology, Pasadena, CA, USA) <html><a href="http://co.mbine.org/system/files/mhucka-icsb-2013-tutorial-final.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>

11:15 – 11:30 Coffee

11:30 – 13:15 Setting up models using experimental data

11:30 – 12:10 SABIO-RK – Martin Golebiewski & Andreas Weidemann (HITS Heidelberg, Germany) <html><a href="http://co.mbine.org/system/files/SABIO-RK ICSB2013 tutorial.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>
12:10 – 13:15 CellDesigner – Akira Funahashi & Noriko Hiroi (Keio University, Yokohama, Japan) <html><a href="http://co.mbine.org/system/files/CellDesignerTutorial.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>

13:10 – 14:00 Lunch Break (self-pay)

14:05 – 16:15 Setting up and simulating models

14:05 – 15:10 COPASI – Sven Sahle, Frank Bergmann, Ursula Kummer (University of Heidelberg, Germany) & Pedro Mendes (University of Manchester, UK) <html><a href="http://co.mbine.org/system/files/COPASI-CPH.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>
15:10 – 16:15 Virtual Cell – Ion Moraru (University of Connecticut Health Center, Farmington, CT, USA)

16:15 – 16:25 Coffee

16:25 – 18:00 Online tools, model databases and data management

16:25 – 16:40 SysMO-DB and Virtual Liver SEEK – Katy Wolstencroft (University of Manchester, UK) & Martin Golebiewski <html><a href="http://co.mbine.org/system/files/ICSBWorkshopSEEK2.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>
16:40 – 17:00 SYCAMORE – Andreas Weidemann (University of Heidelberg & HITS Heidelberg, Germany) <html><a href="http://co.mbine.org/system/files/Sycamore_ICSB_2013_Tutorial.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>
17:00 – 17:30 BioModels – Nick Juty (EMBL-EBI, Hinxton, UK) & Nicolas Le Novère (Babraham Institute, Cambridge, UK) <html><a href="http://co.mbine.org/system/files/biomodels-tutorial_20130904.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>
17:30 – 18:00 JWS Online & OneStop – Jacky Snoep & Dawie van Niekerk (University of Stellenbosch, South Africa) <html><a href="http://co.mbine.org/system/files/dawie_jacky_icsb.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>


This survey aims to identify which repositories and standards are commonly used in the Systems Biology community and where there are issues and problems.

ISBE survey: https://www.surveymonkey.com/s/SFRN7V9
This survey was developed within the project Infrastructure for Systems Biology in Europe (ISBE): http://isbe.eu/

Covered tools, platforms, databases and standards

BioModels database: http://www.ebi.ac.uk/biomodels-main/
CellDesigner: http://www.celldesigner.org/
COMBINE: http://co.mbine.org/
COPASI: http://www.copasi.org
JWS Online/OneStop: http://jjj.biochem.sun.ac.za/
SABIO-RK: http://sabio.h-its.org/
SBGN: http://www.sbgn.org
SBML: http://sbml.org
SYCAMORE: http://sycamore.eml.org
SysMO-DB: http://www.sysmo-db.org/
Virtual Cell (VCell): http://vcell.org/
Virtual Liver SEEK: http://seek.virtual-liver.de/


Attendees are expected to bring their own computer for hands-on training.
In order to profit best from the offered training you should pre-install the following software:


CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. By using CellDesigner, you can browse and modify existing SBML models with references to existing databases, simulate and view the dynamics through an intuitive graphical interface. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver, SBML Simulation Core and Copasi.
Download and Install CellDesigner 4.3


COPASI is a software tool for handling, simulating, and analysing kinetic models of biochemical reaction networks. It is intended for biologists who are not experts in numerical algorithms or programming languages. The tutorial will give an overview over the features of COPASI, such as deterministic and stochastic simulation, parameter scans, sensitivities and control analysis. It will then focus on parameter estimation. We will provide model files for download in this space, so if you want to follow along the presentation on your own computer, please download the latest COPASI version 4.10 (Build 55) from the website www.copasi.org and install it on your computer.

Virtual Cell (VCell)

The Virtual Cell is a computational environment for modeling and simulation of cell biology. It has been specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. The creation of biological or mathematical models can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multi-layered models used to probe the predicted behavior of complex, highly non-linear systems. The Virtual Cell is deployed as a distributed application that is used over the Internet. Users can build complex models with a web-based interface to specify compartmental topology and geometry, molecular characteristics, and relevant interaction parameters.
Please download the latest VCell version 5.1 (Build 10) from the website http://vcell.org/ and install it on your computer.

You can also have a look at these online tools, databases and data management systems that will be introduced in detail during the tutorial workshop:

BioModels database


BioModels Database serves as a reliable repository of computational models of biological processes. It hosts models described in peer-reviewed scientific literature and models generated automatically from pathway resources (Path2Models). A large number of models collected from literature are manually curated and semantically enriched with cross-references from external data resources. The resource allows scientific community to store, search and retrieve mathematical models of their interest. In addition, features such as generation of sub-models, online simulation, conversion of models into different representational formats, and programmatic access via web services, are provided.

JWS Online


JWS Online is both a repository of curated biochemical pathway models and a simulation tool for these models. Users are able to view the models in the database, select a particular model, alter its parameters and perform a simulation on it. JWS Online is based on a client-server architecture, with the calculations performed on the server side. All that is required on the client side is a browser which is able to run Java applets.



SABIO-RK is a curated database that contains information about biochemical reactions, their kinetic rate equations with parameters and experimental conditions. The data is either manually extracted from published literature or directly submitted by experimenters. The system offers standardized data by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. SABIO-RK enables the access to kinetic data for experimentalists and modellers, supporting the setup of quantitative computer models.



SEEK is a web-based platform, with associated tools, for finding, sharing and exchanging data, models and processes in Systems Biology. It is designed as data management platform to support systems biology consortia and distributed research networks. It is used, among others, in the European SysMO (Systems Biology of Microorganisms) consortium (http://www.sysmo-db.org/), as well as in the German Virtual Liver Network (http://seek.virtual-liver.de/)



SYCAMORE is a system that provides you with a faciliated access to a number of tools and methods in order to build models of biochemical systems, view, analyse and refine them, as well as perform quick simulations. SYCAMORE is not intended to substitute for expert simulation and modeling software packages, but might interact with those. It is rather intended to support and guide system biologists when doing computational research.


Martin Golebiewski

Phone: +49-6221-533-281
FAX: +49-6221-533-298
Email: martin.golebiewski@h-its.org

Schloss-Wolfsbrunnenweg 35
D-69118 Heidelberg