Infobiotics is a computational framework implementing a synergy between executable biology, multi-compartmental stochastic simulations, formal model analysis and structural/parameter model optimisation for computational systems and synthetic biology.
Infobiotics workbench provides a user-friendly front-end allowing the modeller to design in-silico experiments, analyse and visualise results using its four components:
- A modelling language based on P systems which allows modular and parsimonious multi-cellular model development including geometric information.
- A multi-compartmental stochastic simulator based on Gillespie’s Stochastic Simulation Algorithm for multi-cellular systems.
- Formal model analysis using the stochastic model checkers PRISM and MC2 for the study of temporal and spatial model properties.
- Structural and parameter model optimisation using evolutionary algorithms to automatically generate models whose dynamics match specified targets.
The Infobiotics workbench is available for download under the GNU GPL v3 license for different platforms. Click in the repository below for download:
Multiple models have been developed using the Infobiotics Workbench. Below we enumerate some of them.