Biochemical Networks Modeling Group
Software
Our group has produced a number of software applications for biochemical networks, others are currently being developed and will appear here later.
Following Gepasi, this is a simulator of biochemical networks.
COPASI is available for Windows, OS X, Linux, and Solaris.
COPASI models the dynamics of biochemical networks using ODEs or using stochastic methods, and is compatible with
SBML.
COPASI has many powerful analysis tools, such as optimization, sensitivity analysis, Lyapunov exponents, etc.
home page |
download
Gepasi
This is one of the most popular generic biochemical simulators, used in many
research and
education applications. Gepasi has many optimization algorithms to allow for data fitting and for optimization of model paramters. Gepasi runs on MS Windows, and on Macintosh (with windows emulators) and Linux (with
wine).
home page |
download
MEG
This is a helper application for transforming one Gepasi model into another one that corresponds to many replicates of the first. This is useful to construct multicellular models based on a single-cell model. MEG allows parameters of each cell to be based on the parameters of the original model but with some random variation; it also allows metabolites to be exchanged between cells.
home page and download
ParCorA
Software for partial correlation analysis for the purpose of biochemical network inference from large scale observations, such as obtained with microarrays and metabolic profiling. (see ometer, below, which also is able to carry out partial correlation analysis)
download Windows version
download Linux version
download Sun Solaris (sparc) version
ometer
ometer is software for multivariate analysis of functional genomics and systems biology data (it can be used for other types of data, too). Ometer is driven by a plain command line interface, which allows it to be called directly from scripts, including from web interfaces. Some of the analyses available are: PCA, Partial Correlation Analysis, Correlation Analysis, Discriminant Analysis, and Genetic Algorithm variable selection for discriminant analysis. Ometer is also used as part of the DOME system.
home page and download
Brome
Brome is a tool for data visualization on biochemical networks. Brome uses the KEGG metabolic pathway diagrams or metabolite neighborhood maps that we have constructed ourselves. Brome is also used as part of the DOME system.
home page and download
home page
