.. 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`