.. Infobiotics documentation master file Welcome to 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'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. #################################### Availability #################################### Binaries are available for `Windows XP, Vista and 7 `_, `Mac OS X 10.6 `_ and Linux (`deb `_ / `rpm `_). `Source code `_ is also available to download under the `GNU GPL v3 license `_. ################### Getting Started ################### A quick start, tutorials and the complete documentation are available from the links below: .. toctree:: :maxdepth: 1 quickStart/quickStart tutorial/tutorial completeDocumentation/completeDocumentation ################### Model Repository ################### Multiple models have been developed using the Infobiotics Workbench. Click on the link below to access them: .. toctree:: :maxdepth: 1 models/repressilator/repressilator models/pulseGenerator/pulseGenerator models/IFFL/FFLpulse models/auxinTransport/auxinTransport ###################### How To Acknowledge ###################### If you intend to use results produced with the Infobiotics Workbench, please consider citing the following publications: .. toctree:: :maxdepth: 1 publications/publications.rst ________________________________________________________________ The Infobiotics Workbench is funded by the following grants: .. figure:: epsrc.png :scale: 100 :alt: alternate text :align: left *(Semi)Formal Artificial Life Through P-Systems and Learning Classifier Systems: An Investigation into InfoBiotics (EP/E017215/1)* .. figure:: bbsrc.png :scale: 100 :alt: alternate text :align: left *BB/D0196131 Centre for Plant Integrative Biology* .. Indices and tables .. ================== .. * :ref:`genindex` .. * :ref:`modindex` .. * :ref:`search`