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This site gives you an overview about the project opportunities at the Theoretical Biophysics group at Humboldt University, Berlin.

We will be hosting student projects aiming at an optimized layout for biological reaction networks and their in-browser visualization. For details read below. Please see the guide to students for application instructions.


The deadline is approaching! Find some more application hints here.
The tests are online.
The flyer is online. Please distribute to friends and coworkers!
You can contact us NOW to get in touch and discuss the projects and your applications. Please note that the deadline for submitting your final application to Google is already the 8th of April!
Also have a look at our students discussion forum.
We are accepted to GSoC 2011!

About the group

The Theoretical Biophysics group 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.

As vivid users of open source software we are also eagerly committed to feeding back to the community by conceiving and implementing new software tools or participating in existing projects. Details on our software activities can be found here. The listed tools are used by a large community of biologists of different specializations, including metabolism, signalling and dynamical modelling.  

Since we are a university research group, we do teaching on a daily bases. In addition to lecturing this also includes the mentoring of a graduate students during thesis preparation. Our GSoC student will strongly profit from this experience when working on one of our project proposals.

Biological reaction networks

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.

Part of our research activities center around the creation and analysis of biological reaction networks. These networks provide intuitive views of interactions underlying biological processes which play a role in metabolism or signalling. 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.

Within that context, the visualization of biological networks is a major point of interest. For a given, small to medium scale network a manual layout may be the best choice. Tools for this task exist, the most famous representative is certainly CellDesigner. Nevertheless, creating a manual layout is time consuming and is generally only worth the effort for a well prepared network subject to publication.

With the advent of electronic databases of biological networks (KEGG, Reactome), 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 GraphViz and Cytoscape. Most packages are quite general with respect to the type of graph they accept. This, of course, opens a wide range of possible applications.

The reaction networks mentioned before, however, represent a special kind of graph. 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.

Project ideas

The layout and visualization of these networks is essential for many of our projects. This includes in particular semanticSBML, ModelMaGe, MetaPath Online and NetworkCurator (currently under development). Therefore, we decided to develop the visualization as an independent component, rather than as part of one of our existing projects. In that way it will also be available as component to other projects like the above mentioned databases or graph visualization tools.

We decided to bring this project to the Google Summer of Code program as it can be split up in sub projects which can be handled by GSoC students within the time frame of the program, it provides a research background which may be interesting to the students even beyond the coding and its result will be useful to a large community. Furthermore, the visualization of biological networks as proposed here will bridge researcher on one side and biologically interested people on the other side by helping to understand complex biological relations.

For the project we focus on a Javascript in-browser visualization with a server side network preparation as we tend to publish more and more projects as web applications. Here we collect ideas which can be worked on by individual students. Please note that the order of the ideas also roughly reflects our own priorities for the project.

Idea 1: A graph layout for reaction networks

The goal of this sub project will be to develop a layout algorithm which specifically addresses the features of reaction networks, combining the advantages of previous approaches. The algorithm will be published as independent open source C/C++ library.

For further details see here.

Idea 2: A JavaScript library for interactive reaction graphs

Graph layout is an essential part of network visualization. However, the layout only defines the node positions. It is still necessary to produce the actual image data. As things are moving to the web and many new projects are developed as web applications, we propose to implement a JavaScript library which would display reaction networks following the standart SBGN notation, represents the network structure as SVG elements in the documents DOM structure and provides an API to manipulate structure and appearance.

For further details see here.

Idea 3: The communication layer

The former two proposals can in principle be used as independent projects by other developers. In order to connect both sub projects an integration layer which connects the server side network preparation with in the in-browser visualization is to be developed. This layer should be able to interact with the layout algorithm and to import/export from/to popular graph formats.

For further details see here.

Idea 4: A GUI for interacting with the network

In order to keep the visualization library proposed in idea 2 lightweight, it only provides an API but no user interface. This interface will be the subject of the current proposal. It should provide GUI elements to navigate through or modify the network visualization as well as offer links to other biological web resources.

For further details see here.

Idea 5: The database connection layer

The sub project will extend the communication layer described in idea 3 by interfaces to biological databases. Many of our projects provide networks through databases or fetch them from public resources. Hence, the basic import functionality described in idea 3 can be generalized.

For further details see here.

Idea 6: Plugins to other network graph packages

This proposal has a rather long term perspective. Although the libraries developed by our project can be used by developers of other graph visualization packages, we can also actively develop plugins for popular software like Cytoscape. Here, we invite detailed proposals of students  particularly interested in writing a plugin to a specific application.

For further details see here.

Guide to students

  1. 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.
  2. 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.
  3. 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.
  4. 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++, perl, python or JS) are a prerequisite.
  5. Take one of the tests or provide relevant code examples. Although we do not require you to complete the test, doing so may increase the chances of your application.
  6. Applications to one of our offered projects go through the Google Summer of Code website (http://code.google.com/soc). There you can find all information about the admission. Please note that the application window is open only from March 18 to April 8, 2011.
  7. 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 about 1.5 months of full-time work between May 23 and August 30.
  8. Please check the FAQ and User Guide on the google website for application advise.

Contact information

Contact us through tbp-soc2011@noemail.degooglegroups.com

There is also a students discussion forum: http://groups.google.com/group/tbp-soc2011-stud

The organization’s administrator is Thomas Handorf:  handorf@noemail.dephysik.hu-berlin.de