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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>
<img src="images/title.png" usemap="#titlemap">
<map name="titlemap">
<area shape="rect" alt="TBP Homepage"
href="http://code.google.com/p/biographer/" coords="242,102,598,128" />
<area shape="rect" alt="Google Summer of Code"
href="http://code.google.com/soc" coords="206,70,627,94" />
<area shape="rect" alt="TBP Homepage"
href="http://www2.hu-berlin.de/biologie/theorybp/" coords="61,55,154,149" />
</map>
<div>
<p>
This site gives you an overview about the project opportunities at the
biographer project. We offer projects in the field of network
layout, web interface design, biological databases and boolean network simulation. The main code
languages used are JavaScript, Python and C++.
</p>
<h1>About biographer</h1>
<p>
<a href="http://code.google.com/p/biographer/">biographer</a> aims at providing a standard library for in-browser visualization
of biological reaction networks. This type of network is of particular importance in the field of systems biology and plays an important role
in understanding the function or dysfunction of cells. More details on these networks can be found at the end of this page.
</p>
<p>
biographer was started during last year's Google Summer of Code in the
<a href="http://www2.hu-berlin.de/biologie/theorybp/">Theoretical Biophysics Group</a> at <a href="http://www.hu-berlin.de/">Humboldt University</a>.
It matured into a JavaScript library generating SVG representations of such
networks. It features an automatic layout which is optimized for
reaction networks, an editor for network modifications and
a server component which
allows the import from various sources of biological networks, including the
<a href="http://www.reactome.org/">Reactome</a> database and <a href="http://sbml.org/">SBML</a> files.
</p>
<p>
Visualizations follow the <a href="http://www.sbgn.org/">SBGN</a> Process Description standard which defines how reaction networks
should be graphically represented.
This includes structured nodes which visualize the composition of protein
complexes, different edge types for
the various participant roles in biochemical reactions and various node types
representing the different biochemical entities
which can interact in a cellular environment.
</p>
<h1> About the group</h1>
<p>
The <a href="http://www2.hu-berlin.de/biologie/theorybp/">Theoretical Biophysics group</a> pursues scientific research in the field of
Systems Biology by the means of mathematical and computational models. We aim to
develop new techniques, software, incorporate new and well established knowledge
to get a better understanding of the fundamentals of life. In particular, we
focus on biological processes in Yeast, Bacillus subtilis and mammalian cells.
</p>
<p>
As vivid users of open source software we are also eagerly committed to feeding
back to the community by conceiving and implementing new <a href="http://www2.hu-berlin.de/biologie/theorybp/index.php?goto=tools">software tools</a> or
participating in existing projects. These tools are used by a large community of biologists of
different specializations, including metabolism, signaling and dynamical
modeling.
</p>
<p>
Since we are a university research group, we do teaching on a daily bases. In
addition to lecturing this also includes the mentoring of graduate students
during thesis preparation. Our GSoC students will strongly profit from this
experience when working on one of our project proposals.
</p>
<h1>Proposed Ideas</h1>
<p>
This year we propose a number of extensions to the functionality of biographer. The focus will be
on widening the audience by implementing interfaces to public database resources, creating a tablet version and extending to
further dialects of the SBGN standard. We propose the following projects but remain open to variants suggested by the applicant:
</p>
<ol>
<li><h3><a href="integration.html"><del>Build a front-end for the public databases Reactome and WikiPathway</del><br/>Creating a Java Script based library for SBGN files (used by WikiPathways); itegration of the Reactome REST interface</a></h3>
<p>
Knowledge on biochemical interactions is provided through a growing number of public databases. These database
represent this data in terms of large reaction networks. <del> This project idea proposes to create an front-end to such
databases which enables the user to visually navigate through the stored information. </del>
This project idea proposes to create a JavaScript base version of libSBGN that can read and write SBGN-ML (used by WikiPathways) and jSBGN (used by Biographer) and/or to create a visual navigator for the Reactome database using its REST interface.
</p>
</li>
<li><h3><a href="pad.html">Tablet and gesture support for the visualization</a></h3>
<p>
Tablets provide an easy and intuitive way to access visual information. In particular in lab environments, where space for
regular computers with peripherals is limited, tablets can make complex scientific information available and also easily navigable through
touch gestures.
</p>
</li>
<li><h3><a href="boolnet.html">Boolean network simulation</a></h3>
<p>
Boolean networks are a popular way to investigate the dynamical properties of biological networks. Indeed, such analyses are
a main focus in our research group. In this project we propose to extend the biographer in a way, that allows automatic creation
and simulation of Boolean networks.
</p>
</li>
<li><h3><a href="export.html">Export to CellDesigner/CytoScape</a></h3>
<p>
CellDesigner and Cytoscape are popular tools for visualizing and analyzing reaction networks. However, with respect to providing an optimized
layout for reaction networks they yield mediocre results. biographer provides this capability and hence an export to these tools for further network analysis will
certainly be highly appreciated by the scientific community. This is even more useful if the biographer component is incorporated into
a database front-end as pursued in idea 1.
</p>
</li>
<li><h3><a href="sbgn_er.html">Extend layout to SBGN-ER formalism</a></h3>
<p>
SBGN-ER (Entity Relationship) is an alternative way to graphically represent reaction networks. Although it is initially more complex
than the so far used SBGN-PD (Process Description) it's complexity increases less drastic in highly combinatorial reaction networks,
where a number of species can interact in arbitrary order with one another. Here we propose to extend the layout algorithm to also support this
network type optimally.
</p>
</li>
<li><h3><a href="gnc.html">Make a client-side version of the layout module using Google Native Client</a></h3>
<p>
biographer's layouter is implemented in C++ for speed reasons. Currently this requires the layout to be calculated on the server. In a high load multi-user
scenario this will lead to long response times. A layout calculation on the client side will hence dramatically increase the user capacity of the server. Clearly, the speed
issue exists on the client side as well such that we need to keep the C++ implementation. A way to overcome this issue is to use Google Native client which
allows to execute compiled code within the client's browser.
</p>
</li>
<!-- <li><h3>Implement a Grid-based layout in JavaScript</h3></li>-->
</ol>
<h1>Guide to students</h1>
<ol>
<li><p>We are seeking eager and highly skilled students willing to contribute to open
source in a research environment. Interest in biological or medical engineering
is a strong plus.
</p></li>
<li><p>We recommend you that you contact us already before you send in your
application. In this way you can obtain more information and we can also help
you with your submission.
</p></li>
<li><p>Apart from the ideas presented above we are open to suggestions from students.
If you would like to contribute an idea to the project please include a detailed
description of it in your application.
</p></li>
<li><p>Your application should include a statement of interest (why do you want to
participate), a project proposal (following one of our ideas or an independent
idea) with preliminary timeline, as well as your CV stressing on your
experiences. Please note, the knowledge of the computer languages (C/C++,
python or JS, depending on the proposal) are a prerequisite.
</p></li>
<li><p>We do not require tests this year. However, please tell us on what projects you worked before and if you have also provide us with some meaningful code samples.
We may, however, contact you after the deadline and ask you for a little test if we think that will help us to make a decision.
</p></li>
<li><p>Applications to our offered projects go through the Google Summer of Code
website (<a href="http://www.google-melange.com/gsoc/homepage/google/gsoc2012">http://www.google-melange.com/gsoc/homepage/google/gsoc2012</a>). There you can find all information about
the admission. Please note that the application window is open only from March
26 to April 6, 2011.
</p></li>
<li><p>Google grants a stipend to the accepted students. This comes along with the
liability to proceed as described in the project proposal. Google requires us to
report on your overall progress. For the projects mentioned above you can expect
at least 1.5 months of full-time work between May 21 and August 24.
Please check the <a href="http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/faqs">FAQ</a>
and <a href="http://www.google-melange.com/document/show/gsoc_program/google/gsoc2012/userguide">User Guide</a> on the google website for application
advice.
</p></li>
</ol>
<h1>Biological reaction networks</h1>
</p>
Systems Biology is a field in Biology which studies the components and its
interactions of a biological system as a whole. In the view of Systems Biology,
systems show emergent properties which are due to the complex interplay of the
components and which were not visible by investigating the components
individually.
</p>
<p>
Part of our research activities focus on the creation and analysis of
biological reaction networks. These networks provide intuitive views on the
underlying biological interactions and processes which play a role in metabolism or
signaling. By investigating these networks deep insights can be gained into the
principles of cellular function and diseases like for example cancer.
A typical signaling pathway can represent receptor-binding events, protein
complexes, phosphorylation reactions, translocations and transcriptional
regulation, with only a minimal set of symbols, lines and arrows. These powerful
representations are essential tools, common among the textbooks and review
articles that document any given field of biology.
</p>
<p>
Within that context, the visualization of biological networks is a major point
of interest. For a given, small scale network a manual layout may be
the best choice. Tools for this task exist, the most famous representative is
certainly <a href="http://www.celldesigner.org/">CellDesigner</a>. Nevertheless, creating a manual layout is time consuming
and is generally only worth the effort for a well prepared network subject to
publication.
</p>
<p>
With the advent of electronic databases of biological networks (<a href="http://www.kegg.jp/">KEGG</a>, <a href="http://www.reactome.org/">Reactome</a>),
in principle a large number of network candidates can be generated, creating the
need for automated layouts for the subsequent evaluation and analysis. A lot of
software packages for automated graph layout exist, among the most prominent are
<a href="http://graphviz.org/">GraphViz</a> and <a href="http://www.cytoscape.org/">Cytoscape</a>. Most packages are, however, quite general with respect to the type
of graph they accept.
</p>
<p>
The reaction networks mentioned before represent a special class of
graphs. Specific features include the existence of reactions and metabolites as
special node types, the different meaning of substrate, product and modulator
edges of reactions and the optional locality information. These particularities
justify layout algorithms optimized for this type of graph.
</p>
<h1>Contact information</h1>
<p style="text-align:left">
We opened a group for discussing with us and other prospective students: <a href="http://groups.google.com/group/biographer-gsocstud">http://groups.google.com/group/biographer-gsocstud</a>
<br>
You can contact us directly through [email protected]
<br>
The organization's administrator is Thomas Handorf:
<span>handorf</span><span>@<span style="display:none">noemail.de</span><span>physik.hu-berlin.de</span></span>
</p>
</div>
</div>
</body>
</html>