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++.

About biographer

biographer 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.

biographer was started during last year's Google Summer of Code in the Theoretical Biophysics Group at Humboldt University. 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 Reactome database and SBML files.

Visualizations follow the SBGN 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.

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. These tools are used by a large community of biologists of different specializations, including metabolism, signaling and dynamical modeling.

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.

Proposed Ideas

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:

1. Build a front-end for the public databases Reactome and WikiPathway
   Creating a Java Script based library for SBGN files (used by WikiPathways); itegration of the Reactome REST interface

   Knowledge on biochemical interactions is provided through a growing number of public databases. These database represent this data in terms of large reaction networks. This project idea proposes to create an front-end to such databases which enables the user to visually navigate through the stored information. 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.

2. Tablet and gesture support for the visualization

   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.

3. Boolean network simulation

   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.

4. Export to CellDesigner/CytoScape

   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.

5. Extend layout to SBGN-ER formalism

   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.

6. Make a client-side version of the layout module using Google Native Client

   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.

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++, python or JS, depending on the proposal) are a prerequisite.

5. 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.

6. Applications to our offered projects go through the Google Summer of Code website (http://www.google-melange.com/gsoc/homepage/google/gsoc2012). 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.

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 at least 1.5 months of full-time work between May 21 and August 24. Please check the FAQ and User Guide on the google website for application advice.

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 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.

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 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, however, quite general with respect to the type of graph they accept.

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.

Contact information

We opened a group for discussing with us and other prospective students: http://groups.google.com/group/biographer-gsocstud
You can contact us directly through tbp-gsoc@googlegroups.com
The organization's administrator is Thomas Handorf:  handorf@noemail.dephysik.hu-berlin.de