Software

Over the years we have developed a variety of tools for simulating and analyzing biochemical networks. We are currently on our 2nd generation of development and are about to embark on the 3rd generation.

One of the things which characterizes us from other software groups is that we are users as well as developers. Moreover, at our Institute we have two full time courses on computational systems biology so that some of our software is specifically developed to address teaching needs as well as users who wish to use simulation software on a more causal basis.

Our goal is to develop software that has the widest appeal and also deliver the most sophisticated algorthisms and analysis techniques available to Computational Systems Biology.

The main software download is the Systems Biology Workbench. This includes a variety of tools and first time users are recommneded to download SBW first. Many of the tools that come with SBW are also available separately.

SBW - Systems Biology Workbench

Download SBW - release 3a

The Systems Biology Workbench is a software infrastructure that allows diverse tools to connect and share data and computational resources. The first version supports connections via Sockets and supports a variety of languages, including C/C++, Java, Delphi, Perl, Python, and Matlab.

SBW is available for download from SourceForge (or below) and includes the infrastructure software, Jarnac, JDesigner, SBML readers and writers (from libSBML), Matlab and FORTRAN translators, Metatool and the SBW Inspector.

For more details see SBW.

Jarnac

Jarnac is a script based biochemical network simulation tool. Supports deterministic as well as stochatic simulation, perform time course or steady state based simulations. Includes metabolic control analysis and extensive matrix operations.

Jarnac is a language for describing and manipulating cellular system models and can be used to describe metabolic, signal transduction and gene networks, or in fact any physical system which can be described in terms of a network and associated flows. Jarnac is basically version 2 of SCAMP.

For more details see Jarnac

NOTE: Jarnac is available with the SBW download given above.

Windows download: Jarnac - Version 2

JDesigner

JDesigner is a Win32 application which allows one to draw a biochemical network and export the network in the form of SBML (Level 1 or Level 2). JDesigner has an SBW interface that allows it to be called from other SBW compliant modules, for example Python. In addition, JDesigner has the ability to use Jarnac as a simulation servier (via SBW) thus allowing modules to be run from within JDesigner. In this mode, JDesigner is both a network design tool and a simulator. Simulations can be time course or steady state based. Under steady state access to the indices in metabolic control analysis is available together with basic stability information. Fill binaries and source code is available in the download.

For more details see JDesigner.

NOTE: JDesigner is available with the SBW download given above.

Windows download: JDesigner - Executable + source code, version 1.9c

SBW Matlab Interface

The SBW-Matlab Interface is exactly what it says it is, it permits Matlab to call out to SBW modules and allows users to write Matlab functions so that other SBW modules can call Matlab. The use of Matlab functions once packaged as SBW modules does not require Matlab to be installed on the client machine. Thus developers can write Matlab based modules and easily distribute them to other users even though the user may not have Matlab installed. This took kit was developed by Cameron Wellock as part of the DARPA funded BioSPICE program.

See CWELLOCK for more details.

Windows download: SBWMatin - SBW-Matlab Interface

WinSCAMP

SCAMP is a general purpose simulator of metabolic and chemical networks. It is based around a simple metabolic language. The version of SCAMP available here is the PC version. Other versions may be available at other sites. The PC executable is a full 32-bit application that can be run from Windows or the DOS command line. A manual in LaTex format is also available here.

For more details see WinSCAMP.

download: WinSCAMP - WinSCAMP, Version 1.2, to activate use the password: 'WZ11a'

SBW Inspector