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SBI Australia Workshop – CellDesigner - Melbourne, May 2013

"CellDesigner: A process diagram editor for gene-regulatory and biochemical networks"


Workshop overview


CellDesigner is software for modeling and simulation of biochemical and gene regulatory networks, originally developed by the Systems Biology Institute in Japan. While CellDesigner itself is a sophisticated structured diagram editor, it also enables users to directly integrate various tools, such as built-in SBML ODE Solver and SBW-powered simulation/analysis modules. CellDesigner runs on various platforms such as Windows, MacOS X and Linux, and is freely available from

This course will explain how CellDesigner can be used from both modeling and software development perspectives. The first topic will feature network modeling using CellDesigner, and will show how to build a model from scratch, and examine simulations. This topic also includes an explanation of how we build a biochemical network as a "map" which includes links to several existing databases, and how we build a mathematical model by the aspect of process-diagram based modeling.

Once a model is described with appropriate mathematical equations and parameters, running a simulation on CellDesigner is quite straight forward. The second session will demonstrate how to easily tweak your model from CellDesigner's user-interface and observe some changes in the dynamics. Not just building a model from scratch, this course also introduces how it is possible to "import" an existing model from several third-party databases (e.g., PANTHER database). This will be particularly useful for users who have obtained a published model, but do not have enough experience in building a mathematical model by hand.
The final topic will feature plugin development of CellDesigner, which allows users to manipulate network diagrams in many ways (for example changing the color/size of node, reflecting experimental data, etc.). This session will cover both modeling and software development topics, but mainly focuses on the modeling aspects.
CellDesigner users and software developers are encouraged to join this 2-day workshop.

Presenters: Associate Professor Akira Funahashi and Assistant Professor Noriko Hiroi, Systems Biology Laboratory, Department of Biosciences and Informatics, Keio University, Japan

Associate Professor Akira Funahashi received his BE, ME, and PhD degrees in Computer Science from Keio University, Japan, in 1995, 1997, and 2000 respectively. He was a Research Associate in the Department of Information Technology, Mie University, Japan, from 2000 to 2002. He joined Kitano Symbiotic Systems Project, JST and The Systems Biology Institute as a researcher before moving to Keio University in 2007. His research interests include the area of systems biology, computational biology, interconnection network and parallel processing. He has been involved in the development of CellDesigner for 11 years.

[1] Novere, N. L., et al. "The systems biology graphical notation", Nature Biotechnology, 27(8), pp.735-41, 2009.
[2] Funahashi, A., et al. "CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks", Proceedings of the IEEE, Special Issue: Computational Systems Biology. 96 (8). pp.1254-1265, 2008

Assistant Professor Noriko Hiroi started her career in Molecular Biology and Biochemistry, and currently works in Systems Biology and Quantitative Biology area. Her research interest includes in vivo crowding; molecular mechanisms of higher-functions of central nerve systems, microfluidics technology and image informatics. She was the first CellDesigner user, and has participated in the test-and-feedback work for pre-release versions of CellDesigner for 10 years, and is also involved in the development of Plugin software.

[1] Takizawa H, Hiroi N and Funahashi A. Mathematical Modeling of Sustainable Synaptogenesis by Repetitive Stimuli Suggests Signaling Mechanisms.  PLoS One, 7(12): e51000. doi: 10.1371/journal.pone.0051000
[2] Hiroi N, Okuhara T, Kubojima T, Iba K, Tabira A, Yamashita S, Okada Y, Kobayashi TJ and Funahashi A. Physiological intracellular crowdedness is defined by perimeter to area ratio of subcellular compartments. Front Physiol. 2012; 3:293. doi: 10.3389/fphys.2012.00293.

Workshop details

When:  9:00am - 5:00pm, Tuesday 7 and Wednesday 8 May, 2013

Where: Engineering computer laboratories, Building 60, Monash University, Clayton campus (see here for map).

Registration Cost: $280

Please note that all course material, software and hardware will be provided.

What’s Included: Lunch, morning / afternoon teas

Places are limited, please register here

For further information on the workshop contact:

If the workshop is full or the closing date has arrived, please contact