ICSB 2014 Tutorial

Tutorial: Modelling and Simulation of Biological Models

Melbourne, Australia
Sunday, September 14th, 2014 (9:00 - 18:00)

This workshop is a satellite of the 15th International Conference on Systems Biology (ICSB).
Participants will learn how to set up quantitative computer models of biological networks using experimental kinetic data and simulate 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:

  • Model setup using different software tools and systems biology platforms
  • Using experimental data for setting up quantitative models
  • Parameter estimation, optimization and model fitting
  • Simulation, analysis and visualization of biochemical models
  • Database supported modelling: integrated data management and model databases
  • Community standards and formats for systems biology models

Target audience
Experimentalists and modellers with some basic experience in modelling and simulation of biological networks.


Melbourne, Australia
Ether Conference Centre
265 Little Bourke Street
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Registration fee: 60 AUD (to cover for catering)
Lunch and catering during coffee breaks will be provided and is included in the registration fee.

If you are not attending ICSB please register through the ICSB registration

In case you will not attend ICSB, you still can only register for the tutorial:


  • Akira Funahashi and Noriko Hiroi: Keio University (Yokohama, Japan)
  • Martin Golebiewski: Heidelberg Institute for Theoretical Studies (Germany)
  • Mike Hucka: California Institute of Technology (Pasadena, CA, USA)
  • Ursula Kummer and Jürgen Pahle: University of Heidelberg (Germany)
  • Nicolas Le Novère: Babraham Institute (Cambridge, UK)
  • Chris J. Myers: University of Utah (Salt Lake City, UT, USA)
  • Ion Moraru: University of Connecticut Health Center (Farmington, CT, USA)
  • David Nickerson: Auckland Bioengineering Institute (New Zealand)
  • Falk Schreiber and Tobias Czauderna: Monash University (Melbourne, Australia)
  • Jacky Snoep: Stellenbosch University (South Africa)
  • Natalie Stanford: University of Manchester (UK)


Full Agenda (Slides and recordings will be up soon at this page.)

PDF agenda: <html><a href="http://co.mbine.org/system/files/COMBINE ERASysAPP Tutorial_0.pdf"><img src="http://co.mbine.org/system/files/pdf-small.jpg" height="30" align="middle" /></a></html>

Covered tools, platforms, databases and standards


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, and 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 4.4


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 4.12 (Build 81) from the website www.copasi.org and install it on your computer.


iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. Recently, modeling and visualization support has been added for multi-cellular and spatial models as well. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). It can import all levels and versions of SBML and is able to export Level 3 Version 1. It supports all core SBML modeling constructs except some types of fast reactions, and also has support for the hierarchical modeling, arrays, layout, and flux balance constraints packages. It was the first tool to produce correct results for all examples in the SBML benchmark suite. It has also been tested successfully on the stochastic benchmark suite and the curated models in the BioModels database. Finally, it is one of the first tools to also support the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology. Version 3.0 of iBioSim will be available in September from our website http://www.async.ece.utah.edu/iBioSim/, and it will be the version that we demo. Please download it before the tutorial.


OpenCOR is a cross-platform modelling environment which can be used to organise, edit, simulate and analyse CellML files on Windows, Linux and OS X.
Download and Install OpenCOR


SBGN-ED is a tool which allows the creation of all three types of SBGN maps (Process Description, Entity Relationship, and Activity Flow) from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from the KEGG and MetaCrop databases or from SBML files into SBGN and the export of SBGN maps into several file and image formats. In addition it supports SBGN bricks to easily represent knowledge in SBGN maps.
Download and Install SBGN-ED

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 (5.2 or later) from the website http://vcell.org/ and install it on your computer.

You should 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.

Physiome Repository


The Physiome Repository is an extensible software system that provides a platform for collaborative development and sharing of models and data, along with facilities that can perform basic reasoning over the annotations of the stored information. Users of the repository are able to make use of versioned and embeddable workspaces to take advantage of modularity and reusability in model and data standards. Specific revisions of workspaces are able to be promoted and presented in a web-friendly manner through the use of extensible presentation plugins.



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 David Nickerson
Phone: +49-6221-533-281
Phone: +64-9-923-1994
FAX: +49-6221-533-298
FAX: +64-9-367-7157
Auckland Bioengineering Institute
Schloss-Wolfsbrunnenweg 35
70 Symonds Street
D-69118 Heidelberg
Auckland 1010
New Zealand