What System Biologists can find under the SYCAMORE tree
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 (www.copasi.org) and databases such as BRENDA (www.brenda-enzymes.info) and SABIO-RK (sabio.villa-bosch.de/SABIORK) 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 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).
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