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boolnet.html
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<!DOCTYPE html>
<html>
<head>
<title>biographer: Google Summer of Code 2012</title>
<link rel="stylesheet" href="main.css" type="text/css" />
</head>
<body>
<div>
<div>
<h1>Boolean network simulation</h1>
Our goal for this idea is to extend the biographer
to simulate and analyze Boolean networks.
In this summer, we will start with deterministic synchronous Boolean models.
(After that, we will go on to asynchronous and probabilistic Boolean networks,
as well as to simulating more complex kinds of kinetics.)
<h2>Motivation</h2>
<p>
Boolean networks are a simple approach to simulate regulatory
networks, analyze their behavior and predict possible outcomes.
Species in a Boolean network can only have two states, active or inactive.
In various approaches it has been shown, that Boolean
networks can reproduce the behavior of biological systems while still
being simple to handle.
</p>
<h2>Project goals during this summer</h2>
<h3>Model import</h3>
<p>
In order to graphically represent the evolution of activities in a reaction network over time,
possibilies to load Boolean models from existing
packages, like <a href="http://code.google.com/p/booleannet/">booleannet</a> or
<a href="http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/boolnet/">R's BoolNet</a>
shall at first be coded.
</p>
<h3>Automated model generation</h3>
<p>
In a second approach, which will be essential
for all cases, in which no curated Boolean model is available for a network,
a tool which creates a basic Boolean model from a network through automated model generation
shall be implemented.
For this approach <a href="http://code.google.com/p/libscopes/">libScopes</a> project will provide a good start.
</p>
<h3>Model export: SBML-LRG implementation</h3>
<p>
After the user has created a reasonable model for his network,
he will in most cases want to save it.
Therefore we want the currently supported <a href="http://sbml.org">SBML</a> import/export to be extended
by implementation of the
<a href="http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Qualitative_Models">SBML-LRG standard</a>, which allows
for implementation of models into SBML files.
</p>
<h3>Model visualization</h3>
<p>
For the visualization of networks,
<a href="http://code.google.com/p/biographer/source/browse?repo=visualization">biographer's existing UI</a>
will be used,
which already provides for <a href="http://www.sbgn.org/">SBGN</a> specification conformity.
The currently supported representation of networks
through <i>process description</i> (PD; see also SBGN specification)
must therefore be extended to support the <i>activity flow</i> standard (AF),
which additionally includes symbols for logical functions like <b>AND</b> and <b>OR</b>.
</p>
<h3>Interactive model simulation</h3>
<p>
A Boolean model's update rules shall be provided to the browser as JavaScript,
allowing for in-browser simulation of the time-dependent evolution
of node states.
The state (on/off) of each node shall be changeable by clicking it.
Appropriate functions have to be integrated into existing biographer UI
JavaScript code, to change e.g. the color of a node.
</p>
<h3>Model analysis</h3>
<p>
The user's Boolean model will also be
submitted to the server for analysis.
We want to provide a summary of "interesting" information about the network to the user:
trajectory lengths, cyclic attractors or steady states.
</p>
<h2>Necessary skills</h2>
The biographer consists at first of a server, which is written in Python (we are using the
Python web framework web2py, it's very easy to learn if you don't know it).
On the other hand, there is the browser UI: Therefore you need to know about HTML and
have a good experience with JavaScript.
You will not have to start from scratch, but advance existing code, which makes your work easier,
as soon as you are familiar with the code.
To estimate the complexity of the existing code, you may want to have a look at the
source repositories of <a href="http://code.google.com/p/biographer/source/browse?repo=server">server</a>
and <a href="http://code.google.com/p/biographer/source/browse?repo=simulator">simulator</a>
but don't worry, we are working as a team and you can always ask any questions.
<h2>Mentors:</h2>
<ul>
<li><a href="mailto:[email protected]">Till Scharp</a></li>
<li><a href="mailto:[email protected]">Matthias Bock</a></li>
</ul>
<br/>
Please feel free to ask all questions you may have on the students' discussion list:<br/>
<ul>
<li><a href="http://groups.google.com/group/biographer-gsocstud?pli=1">Mailing-List</a>
</li>
<li><a href="mailto:[email protected]">[email protected]</a>
</li>
</ul>
We, Till and Matthias, will also be there and answear everything you need to know for you application.
<br/>
<br/>
You may also want to check out our small <a href="http://code.google.com/p/biographer/wiki/index?tm=6">Wiki</a>,
which provides some basic information on how everything works so far.
</div>
</div>
</body>
</html>