Introduction
BioNessie is a free, state-of-the-art platform-independent biochemical networks simulation
and analysis software environment software.
It is developed using Java technology and can run on many platforms that support JRE (Java Runtime Environment 1.5 or higher).
It provides a full user-friendly Graphical User Interface (GUI) which allows the user to import, create, edit and export the biochemical models with the SBML (Systems Biology Markup Language) standard. The unique Concurrent Versions System (CVS) design helps users to keep track of the version history of their SBML models during construction and subsequent modification. The core of BioNessie comprises the SOSlib (SBML ODE Solver library), which provides a programming library for symbolic and numerical analysis of a system of ODEs (Ordinary Differential Equations) derived from a chemical reaction network encoded in SBML format. BioNessie can generate the changes of species amounts and parameter values over time by simulating the SBML model numerically with SOSlib. The simulation results can be generated in many ways: raw data files, plots, xml files and report text files.
BioNessie is not only an editor and simulator, but also an analyser. It supports
- multi-thread / core enabled parameter scans
- sensitivity analysis
- parameter estimation (model fitting)
Cooperating with National e-Science Centre (NeSC) at Glasgow on the project - BioNessieG, we extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale biochemical simulations in BioNessie.
The following analytical functions will be gradually added into BioNessie soon:
- linear temporal logic checking for biochemical networks
- SBML model composing
- cellML intergration
- stochastic simulator