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Bioinformatics Advance Access published online on May 7, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn207
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SYCAMORE - A SYstems biology Computational Analysis and MOdeling Research Environment

Andreas Weidemann 1,2,*, Stefan Richter 3,*, Matthias Stein 3, Sven Sahle 2, Ralph Gauges 2, Razif Gabdoulline 3, Irina Surovtsova 2, Nils Semmelrock 3, Bruno Besson 3, Isabel Rojas 1, Rebecca Wade 3 and Ursula Kummer 2,{dagger}

1Scientific Databases and Visualization Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany. 2Department for Modeling of Biological Processes, Institute for Zoology, BIOQUANT, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany. 3Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.

{dagger}To whom correspondence should be addressed. Dr. Ursula Kummer, E-mail: ursula.kummer{at}bioquant.uni-heidelberg.de


  Abstract

Summary: SYCAMORE is a browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Thus, it allows e.g. database supported modelling, basic model checking and the estimation of unknown kinetic parameters based on protein structures. In addition, it offers some guidance in order to allow non-expert users to perform basic computational modelling tasks.

Availability: SYCAMORE is freely available for academic use at http://sycamore.eml.org. Commercial users may acquire a license.

Contact: ursula.kummer{at}bioquant.uni-heidelberg.de

Associate Editor: Dr. Trey Ideker

*to whom correspondence should be addressed

Received on October 16, 2007; revised on January 3, 2008; accepted on April 23, 2008

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