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.
A detailed documentation of the workbench is presented below. Alternatively you can download the entire documentation in pdf format in this link.
A quick start, tutorials and the complete documentation are available from the links below:
Multiple models have been developed using the Infobiotics Workbench. Click on the link below to access them:
If you intend to use results produced with the Infobiotics Workbench, please consider citing the following publications:
The Infobiotics Workbench is funded by the following grants:
(Semi)Formal Artificial Life Through P-Systems and Learning Classifier Systems: An Investigation into InfoBiotics (EP/E017215/1)
BB/D0196131 Centre for Plant Integrative Biology