[Bio-software] (no subject)

Rebecca Wade via bio-soft%40net.bio.net (by rebecca.wade from eml-r.villa-bosch.de)
Fri Jul 11 06:08:11 EST 2008

Please could you post this on BIOSCI newsgroup BIO-SOFTWARE / 


Rebecca Wade


SYCAMORE—a SYstems biology Computational Analysis and MOdeling Research 

EML Research and the University of Heidelberg would like to announce the 
availability of SYCAMORE at http://sycamore.eml.org/.

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 has been developed in order to support the user, particularly
the non-expert user, in setting up, simulating and analysing biochemical 

SYCAMORE is a web browser-based application that facilitates 
construction, simulation and analysis
of kinetic models in systems biology. Functions include database 
supported modelling,
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 (www.copasi.org)
  and databases such as  BRENDA (www.brenda-enzymes.info) 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 
Bioinformatics 2008 24(12):1463-1464; doi:10.1093/bioinformatics/btn207

SYCAMORE is freely available for academic use at 
http://sycamore.eml.org. 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)

The authors can be contacted at:
sycamore_support from eml-r.villa-bosch.de

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
Telephone: +49 (0)6221 - 533 - 247

Rebecca Wade

Tel: +49-6221-533 247
Fax: +49-6221-533 298
Email: rebecca.wade from eml-r.villa-bosch.de


EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter


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