Team:Sevilla/Modelling

Infobiotics is the synergy of executable biology, evolutionary and machine learning methods, mesoscopic simulation techniques and experimental data for a more principled practice of origins of life, bioinformatics, computational systems and synthetic biology research.

These activities are complemented by other groups in the SynBioNT Synthetic Biology Network for Modelling and Programming Cell-Chell Interactions.

Infobiotics Workbench 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. It 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.