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.
Bug reports or feature requests should be submitted to the bug tracker.
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: an integrated in silico modelling platform for Systems and Synthetic Biology.
Jonathan Blakes, Jamie Twycross, Francisco Jose Romero-Campero and Natalio Krasnogor
Bioinformatics (2011) doi: 10.1093/bioinformatics/btr571
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