What System Biologists can find under the SYCAMORE tree

6 10 2008
EML Research and the University of Heidelberg announce the availability of SYCAMORE –a user-friendly, web-based Software Package for Systems Biology –
Finding answers to the complexity of questions emerging in modern biology requires the use of quantitative, computational approaches. Mathematical modelling is a critical component of systems biology studies of biochemical networks. However, the use and applicability of computational methods in systems biology is often hampered by the complexity of the software tools available for the modelling and simulation tasks. SYCAMORE stands for a SYstems biology Computational Analysis and MOdeling Research Environment. It has been developed in order to support the user, particularly the non-expert user, in setting up, simulating and analysing biochemical models.

SYCAMORE is a web browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Functions include database supported modeling, basic model checking, model simulation and the estimation of unknown kinetic parameters based on protein structures.
It interfaces with other tools such as the COPASI Complex Pathway Simulator ( and databases such as  BRENDA ( and SABIO-RK ( which contain enzymatic kinetic data. In addition, it offers guidance in order to allow non-expert users to perform basic computational modelling tasks.

SYCAMORE is described in the following article:
Andreas Weidemann, Stefan Richter, Matthias Stein, Sven Sahle, Ralph
Gauges, Razif Gabdoulline, Irina Surovtsova, Nils Semmelrock, Bruno
Besson, Isabel Rojas, Rebecca Wade and Ursula Kummer:
SYCAMORE—a systems biology computational analysis and modeling research environment. Bioinformatics 2008 24(12):1463-1464; doi:10.1093/bioinformatics/btn207

SYCAMORE is freely available for academic use at
Commercial users may acquire a license.

SYCAMORE is a joint project of the Molecular and Cellular Modeling Group
(MCM) and Scientific Databases and Visualization Group (SDBV) at EML
Research, as well as the department for Modeling of Biological Processes
at the University of Heidelberg. The development of SYCAMORE is
supported by the Klaus Tschira Foundation and the German Ministry of
Research and Education (BMBF) (HepatoSys Grant 0313078C).

Press Contact:
Dr. Peter Saueressig
EML Research gGmbH
Presse- und Öffentlichkeitsarbeit
Tel: +49-6221-533-245
Fax: +49-6221-533-198

Scientific Contact:
Prof. Dr. Ursula Kummer
Dept. Modeling of Biological Processes
Institute of Zoology/BIOQUANT BQ18
Im Neuenheimer Feld 267
Ruprecht-Karls-Universität Heidelberg
D-69120 Heidelberg
Phone: +49 (0)6221 - 5451 - 375

Dr. Rebecca Wade
Molecular and Cellular Modeling Group
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Phone: +49 (0)6221 - 533 – 247

More general questions also to
Dr. Michael Schwarz
Pressesprecher der Universität Heidelberg
Tel. 06221 542310, Fax 542317

Irene Thewalt
Tel. 06221 542310, Fax 542317

Editor: Email
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