The process of constructing and testing models, particularly those that incorporate significant prior knowledge, involves multiple steps that are currently very poorly integrated. We have developed SB-Pipeline to create an effective workflow based on open-source code, public standards and modern sof...

A collection of bioinformatics subprograms targeted at parallel architectures.

TCGA2S3DB is an infrastructure that exposes data from The Cancer Genome Atlas (TCGA) using Semantic Web Formalisms, specifically, as a SPARQL endpoint. Experimental data, such as the one being generated by the TCGA project, is often intrinsically complex and very heterogeneous. For that reason, it ...

This project describes some python tools for that are (hopefully) useful in systems biology. == pysbml == Unfortunately due time constraints, I could no long maintain this package. So I've I separated out some the components as stand alone libraries (see below). == VisualiseSBML == Visua...

=== NEWS === 26/3/09: SBML L2v4 version of the DSMTS is released === Motivation === Stochastic simulation is a very important tool for Systems Biology modelling. However, it is difficult to check the correctness of a stochastic simulator, since any two realizations from a single model will ...

http://abhikshah.googlepages.com/pebl-logo.png Pebl is a python library and command line application for learning the structure of a Bayesian network given prior knowledge and observations. Pebl includes the following features: * Can learn with observational and interventional data * Handl...

Mechanism-based chemical kinetic models are increasingly used to describe biological signaling. Such models serve to encapsulate current understanding of pathways and to enable insight into complex biological processes. Currently, there is no standard formulation for these models, making it difficul...

PathwayAnalyser (PA) is a tool for systems biologists for analysis of metabolic pathways, particularly by Flux Balance Analysis and ODE simulation. PA interfaces with the GNU Linear Programming Toolkit (GLPK) for linear programming, as well as with Taylor for performing high precision simulations (e...

Here we present the Connection of Biological Lists Tool (COBALT), a Java application for interactively exploring and visualizing relationships between gene sets and biological concepts including diseases, pathways, and drugs targets. To estimate the significance of these connections, this tool impl...

Systems Biology Code Library