Team:Sevilla/Software/GPSE

From 2011.igem.org

Infobiotics



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-Cell Interactions.

Infobiotics Workbench



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‚Äôs 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.

Our software



GPSE (Graphical P-System Editor)

Our software is a CAD to design biological P-Systems. The main goal of our program is to make the preparation of the files needed for the P-Systems simulators easier, more intuitive. The main features of the software are as follow:

  • Projects organized in several levels: a level for description and documentation about the project, a level for DNA, cell level and a multicellular level.
  • Analysis: check for possible errors in the input and compatibility with BioBricks.
  • New modules available for download from repositories.
  • Drag&drop elements in the graphical interface.
  • You can export the project both as GPSE or CBML a format compatible with multiple biological simulators.

We've been using Google Code to keep our code online, with GNU GPL v3 license. Check it here! In several days you will see a stable version, which will be published in the Google Code web. Stay tunned!

The future of our software



For the next version of our software we will include:

  • Exports in more formats.
  • CBML and othe formats to import.
  • Other interesting features.


FAQ (Frequently Asked Questions)



Are we going to implement an instance of a P-system biochemically?

Our project is not intended to be an implementation of a P-system but it can be used to design implementations of a restricted version of P-system without membrane polarization, division or creation, among other things. It was conceived as a new level of abstraction that will allow us to design complex biological circuits. It's true that there are some similarities between our project and the definiton of a P-system; both are compartimentalized, paralell and maximal.

As you can see above, we are using infobiotics WB to do the simulation, so we are adapting our project into a P-system. We are also developing a software to make the tedious task of creating the configuration file for the IWB much easier.