SYCAMORE

Category Cross-Omics>Agent-Based Modeling/Simulation/Tools

Abstract SYCAMORE (SYstems biology Computational Analysis and MOdeling Research Environment) is a web-based system that provides you with a facilitated access to a number of tools and methods in order to 'build models' of biochemical systems, view, analyze and refine them, as well as perform quick simulations.

SYCAMORE integrates different online applications as well as locally installed software.

It provides user guidance for the sequence of steps associated with model building (especially based on database knowledge), model checking, simulation and analysis of results.

Moreover, it offers some unique features, e.g. access to protein structure-based parameter estimation.

Thus, it does Not compete with web-based applications like WebCell (see G6G Abstract Number 20457), VCell (see G6G Abstract Number 20440) or JSim which are online simulation and analysis tools, but rather should serve as a kind of 'expert system' facilitating the setting up of the models.

To really analyze a final model in detail SYCAMORE interfaces with locally installed tools like COPASI (see G6G Abstract Number 20296) and does Not intend to substitute or compete with this class of tools.

SYCAMORE aids the user in ensuring that their files are compatible with the Systems Biology Markup Language (SBML) file standard for biochemical models.

This facilitates the exchange and re-useability of kinetic models in systems biology.

SYCAMORE also facilitates the searching of enzymatic reaction kinetics databases such as BRENDA and SABIO-RK which contain kinetic parameters and kinetic equations that are required for setting up a kinetic model.

SYCAMORE Use Case --

Suppose the user is interested in simulating the first two (2) steps of glycolysis in human hepatocytes.

First a model has to be set-up.

For this, SYCAMORE provides an interface to the SABIO-RK database to permit the user to locate and select the relevant kinetic data for these two (2) reaction steps.

Once the data have been selected and sent to SYCAMORE, the parameters can be adjusted in the SYCAMORE editor, e.g. to make the units used consistent.

SYCAMORE also allows the user to add further reactions, e.g. to make the system open and define an influx of glucose and an efflux of fructose-6-phosphate.

SYCAMORE will then enable the user to check the model for completeness as regards the kinetic equations and their parameters.

If parameters are missing, SYCAMORE provides search tools to locate relevant data for parameter estimation and the ability to estimate parameters using protein structural data or perform a classical parameter estimation using experimental data and locally installed software.

In the case of the protein structural data, electrostatic distances between related proteins are computed and the kinetic parameters for the electrostatically most similar protein can be chosen.

A parameter sensitivity analysis can also be performed.

Once the model is complete, a simulation can be carried out on the SYCAMORE server using COPASI with SYCAMORE displaying a plot of the resulting time course or by launching locally installed software, e.g. COPASI or ProMoT (see G6G Abstract Number 20332).

System Requirements

SYCAMORE is a web-browser-based application running on Tomcat and currently supporting the Internet Explorer, Firefox, Mozilla web browsers running on Linux, Mac and Windows operating systems.

It is mainly based on Java Server Pages (JSP) technology.

Manufacturer

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.

Manufacturer Web Site SYCAMORE

Price Contact manufacturer.

G6G Abstract Number 20456

G6G Manufacturer Number 104083