GSoC/GCI Archive
GSoC/GCI Archive
Google Summer of Code 2009

GenMAPP

Web Page: http://genmapp.cgl.ucsf.edu/wiki/Google_Summer_of_Code_2009

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

We are an academically based organization that develops and supports GenMAPP (Gene Map Annotator and Pathway Profiler), a 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. Over 21,000 people from >70 countries have registered to download the GenMAPP program. There are over 430 publications that reference GenMAPP or use GenMAPP to display data in the context of biological pathways. GenMAPP is 100% open source. All new development is in Java, MySQL, Derby, XML, and Web technologies such as MediaWiki in collaboration with the UCSF library, BiGCaT Bioinformatics, and the Cytoscape Consortium. Our development team is composed of individuals who are both biologists and programmers, providing a unique perspective on building and using open source tools. As in past years, GenMAPP is serving as an umbrella organization for Cytoscape and WikiPathways projects as well. All three projects are at exciting crossroads, making this an ideal time to get involved in development.

Projects

  • Biopax plugin(import, layout, export) for PathVisio Biopax plugin implementation for PathVisio.
  • CyAnimator: A general purpose animation tool for Cytoscape A tool that cycles through and animates a user specified list of features would help to visually differentiate datasets, pathways, and attributes from and within large biological networks. These features would be sets of nodes and edges that would be generated based upon the network topology and data attributes. They would then be made available for the user to specify which features to animate within the network along with what visual attributes should be assigned to each feature.
  • Cytoscape GPU Assisted Graph Layout Plugin The aim of this project is to create a Cytoscape plugin capable of performing fast and accurate graph representations, using the GPU to accelerate the computations and taking only a fraction of the time that the traditional implementations require.
  • ID mapper API and plugin for Cytoscape This project is to develop an ID mapping plugin and publish the corresponding ID mapping API for other plugin developers. Different sources of ID information will be supported including local/remote files, databases and web services.
  • Idea 5: Superpathways in Cytoscape Biologists want to study interactions across multiple pathways. We propose to address some existing issues by implementing a Cytoscape plugin with following features: -Use GpmlPlugin to query and load data from WikiPathways -Provide two methods for users to select a group of pathways to merge -Present a novel layout to show pathways and the number of shared nodes among them -Create interactions to help biologists make connections between the merged and origin pathways
  • Integrated data mining in Cytoscape 3.0 Cytoscape is an open-source platform for complex network analysis and visualization. Filters and Search are part of analysis feature. Filters are currently based on Quick Find plugin. For searching it has two plugins Quick Find and Enhanced Search Plugin (ESP). I will be integrating both Quick Find and ESP which when combined can offer a faster and efficient indexing and searching. The Filters interface will be modified to perform complex queries. Auto completion can also be implemented.
  • Ontologies for Wiki Pathways In any application, be it a website or a video game, UI & Accessibility are the most important things to keep in any mind. According to me any information should be properly organized and indexed, so that people can make the best use out of it.
  • Phylogenetic tree plugin for Cytoscape Proposed here is a plan for a plugin for Cytoscape which takes in a phlyogenetic tree as and displays it in Cytoscape. Several of Cytoscape’s original features are supported in this plugin, such as the ability to manipulate nodes, zooming and exporting a view of the network. New functions that would be beneficial to analyzing phylogenetic trees are proposed such as the ability to collapse subtrees, swap subtrees with the same ancestors and display included information about nodes in the tree.
  • Processing-Based New Visualizer for Cytoscape 3 Current Cytoscape(CS) has issue such as timeseries data visualization. To cover such usecase, CS needs a new visualizer. Processing is a good toolkit to quickly implement such renderer and new CS3 has cleaner view model and its rendering engine is pluggable. The goal of my project is design and implement simple renderer for CS3 based on Processing and integrating it to CS3's new view-model/VizMapper. This project will be a good test case for CS3's "multiple-view per network model" design.