Overview

BioNessie Lite is the command-line version of the BioNessie simulator.  BioNessie Lite can simulate biochemical pathway models in SBML and can also perform parameter scans.  Simulation and parameter scan results are textual, keeping with the lightweight approach.  The command-line interaction allows for easy distribution across a computer cluster and integrates well with the MC2(PLTLc) model checker.  BioNessie Lite was developed at the Bioinformatics Research Centre in the University of Glasgow.

Features

The main features of BioNessie Lite are:

      * SBML:  Reads both SBML versions 1 and 2.

      * Simulation:  Fast ODE-based simulation of biochemical pathway models.

      * Parameter Scans:  Perform simulation with a range of values for a kinetic rate constant or initial concentration.

      * MC2(PLTLc) Integration:  Can be integrated with the MC2(PLTLc) model checker by reading output files or using Unix pipe.

      * Easily Parallelised:  The command-line approach of BioNessie Lite allows easy distribution across a computer cluster.

Download

The latest BioNessie Lite package released 15th May, 2008 can be downloaded:  BioNessie Lite v1.0.

Required Libraries

BioNessie Lite requires a compiled version of The SBML ODE Solver Library.  Pre-compiled versions are available below:

     * Mac OS X (Intel)

     * Windows

     * Linux (Intel)

     * Linux (AMD 64-bit)

Contact

For any comments, suggestions or technical problems, please e-mail:  radonald@brc.dcs.gla.ac.uk.  BioNessie Lite author:  Robin Donaldson.

Last updated:  15th May, 2008