National Resource for Network Biology (GenMAPP, Cytoscape and WikiPathways)

Web Page: http://nrnb.org/gsoc

Mailing List: http://groups.google.com/group/cytoscape-discuss

The National Resource for Network Biology (NRNB) is organizing the joint efforts of GenMAPP, Cytoscape, and WikiPathways. This is a great opportunity to work at the intersection of biology and computing. GenMAPP is a pathway visualization and analysis tool for biological data. GenMAPP illustrates the relationships between various genes and proteins to help researchers understand their data in terms of connected, biological pathways. Tens of thousands of people from a hundred countries have registered to download the GenMAPP program. The GenMAPP group is coordinated by the Conklin Lab at the Gladstone Institutes (UCSF). Our development team is composed of biologists and programmers, providing a unique perspective on building and using open source tools. Cytoscape is a general network visualization tool that integrates network topology with data about the network into the visualization. Cytoscape is rapidly becoming a systems biology standard. Cytoscape consists of a plugin framework which extends functionality in new ways. Our team consists of programmers and biologists from both academia and industry including: UC San Diego, UC San Francisco, U of Toronto, Agilent, Institute for Systems Biology, Sloan-Kettering, Institut Pasteur and others. WikiPathways is a wiki for biological pathways. The wiki approach allows biologists and domain experts to easily create and update pathways. Pathways can be directly modified from a web browser using an embedded applet where you can draw genes, proteins and their interactions like in any popular drawing tool. The pathways can be used as images for publication and in data analysis tools such as GenMAPP, PathVisio and Cytoscape. WikiPathways itself is completely open source and is built on top of MediaWiki, using PathVisio as the pathway editor and BridgeDb as the backend database. WikiPathways is developed and maintained by BiGCaT Bioinformatics (University of Maastricht) and the Conklin Lab at the Gladstone Institutes (UCSF).

Our code repository can be found here: http://code.google.com/p/google-summer-of-code-2011-nrnb/

Projects

• (IDEA 17) Cytoscape Web - HTML5 Prototype This project will attempt to produce a version of the Cytoscape Web program using only JavaScript and HTML5. This version will no longer use Adobe Flash which is the core of the current Cytoscape Web program. This change will attempt to increase the portability of Cytoscape Web (since operating systems such as iOS do not support Adobe Flash) and explore the feasibility of a Cytoscape Web that only uses web standards. The time-efficiency of HTML5 versus Adobe Flash will also be explored.
• A Cytoscape build with a fused (Annotation + Basic) editor based on an improved CyNetworkView with Neo4j interoperability My aim is to combine the two plugins, CyAnnotator and CytoscapeEditor and create a fused editor. I will also design an improved CyNetworkView which can be exploited by this fused editor. I also intend to use some of this editor's functionality to load and save networks with annotations to a Neo4j graph database.
• Connecting Cytoscape with igraph The aim of this project is to allow Cytoscape's users to benefit from igraph. This would be achieved by providing both a straightforward way of invoking igraph from Cytoscape, as well as a plugin featuring it.
• GOLayout: Network partitioning and layout driven by GO ontology The GO is a major bioinformatics initiative to unify the representation of gene and gene product attributes. And Cytoscape is a widely used open source bioinformatics software platform for visualizing molecular interaction networks and integrating multiple types of state data. But there is not any software can integrate those two wonderful resources. I am planning to develop GO Layout plugin for Cytoscape, which can be used to partition and layout biological network driven by GO annotation.
• HTML5 prototype for Cytoscape Web Project aiming to create a prototype of a web-standards-based implementation of Cytoscape Web in HTML5 and JavaScript.
• Integrate Pathway Visualization and Analysis into Savant This project involves developing a plugin for the Savant Genome Browser that can be used to visualize and annotate WikiPathways data.
• New PathVisio Plug-in Manager I picked up idea 22 from the ideas page. Currently the installation of new plug-ins for PathVisio is cumbersome and does not work for the Java Web Start version. So I would like to develop a plug-in manager for the PathVisio OSGi version that makes the installation of new plug-ins as easy as possible for the user.
• Real-time Validation Framework for Pathvisio Real-time syntax validation helps programmers prevent careless mistakes, such as missing semi-colons and using undefined symbols, by highlighting these errors as they happen. In the project, this idea is to be extended in Pathvisio for biological pathway diagrams. Thus, there's a need to develop a view in Pathvisio which highlights the errors. This validation framework needs to be generic, allowing other developers to create their own rule-sets against which the pathway diagrams are validated.