National Resource for Network Biology (NRNB)

License: Apache License, 2.0

Web Page: http://nrnb.org/gsoc/index.html#ideas-tab

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

The National Resource for Network Biology (NRNB) is organizing the joint efforts of Cytoscape, WikiPathways and other network biology tools. This is a great opportunity to work at the intersection of biology and computing. Cytoscape is a general network visualization tool that integrates network topology with data about the network into the visualization. Cytoscape has become 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, Gladstone Institutes, U of Toronto, Agilent, Institute for Systems Biology, Memorial Sloan-Kettering Cancer Center, 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-CS, PathVisio and Cytoscape. WikiPathways itself is completely open source and is built on top of MediaWiki, using PathVisio as the pathway editor and BridgeDb for the backend databases. WikiPathways is developed and maintained by BiGCaT Bioinformatics at University of Maastricht and Gladstone Institutes.

Projects

• ADAM Variation Services and Visualizations for Cytoscape 3 Variation App Variation, a Cytoscape 3 app under development, will enable users to load genetic variation data from multiple sources (Ensembl, ADAM, and GEMINI) and integrate them to create visual mappings for these variations. I would like to contribute by implementing the variation service based on ADAM, a set of formats and APIs for distributed processing of genomic file formats. In addition, I’d like to add visualization support for variation counts and consequences at the gene level.
• Connect PathVisio and WikiPathways to Expression Atlas! The core idea is to build a PathVisio plugin that connects to Expression Atlas in order to directly load data sets and visualize the data on pathways in PathVisio. Next focus is a plugin on human tissue data available from Expression Atlas in order to determine which pathways are active in which tissues or have different levels of activity between certain tissues. As a final step in the project, the 'tissue' plugin is used to determine the ‘tissue-profile’ for each pathway on WikiPathways.
• Connecting Neo4j and Cytoscape Neo4j provides a potential computational backend for more performance intensive tasks required of Cytoscape. The idea is to allow the user to connect and upload a local Cytoscape graph to a Neo4j instance (on a high performance machine) and then invoke operations on this instance via Cytoscape. The necessary calculations are executed on the Neo4j instance and then streamed back to the client. This approach aims to turn Cytoscape into a thin client and treats a Neo4j server as a mainframe.
• Developing An Interface For The Cancer Network Altering Variant Database This proposal is the development of a web interface for The Cancer Network Altering Variant Database using traditional search and browse methods combined with a comparative visualization of the interaction networks between both wild type and mutant proteins involved with cancers. Being able to visualize the differences between cancerous and wild type protein-protein interaction networks would help researchers gain understanding of how cancers develop and have an effect on the protein level.
• Hierarchical Models in Segway Segway aims to find patterns in genomic data by segmenting the data, and assigning a small number of labels to each segment, and then using an unsupervised learning algorithm to discover patterns in the data. I aim to improve Segway’s ability to describe genome patterns by implementing features of a Dynamic Bayesian Network, specifically its ability to further segment into hierarchical labels, to reveal patterns at different scales.
• IDEA #12: New Features for Interference App Interference is a Cytoscape plug-in which is well know for virtual knock-out experiments on complex networks,implementing New Features in current Interference App will be provide advance level experience to user for performing calculation on Markov Shannon entropies and new layout for node descriptor based on node ranking.user also select node list for generate plot and eliminate one node and see metabolic info, notations, semantics, via Interactive plot
• Idea 14: Graph Analysis Algorithms for Cytoscape.js The aim of this project is to improve Cytoscape.js network analysis capabilities, by implementing and integrating several graph algorithms.
• Idea 15: Work on the Pathway Database Converters for the Expansion of Pathw Pathway Commons (PC) aggregates biological pathway information from several pathway databases; the data are stored primarily in the format known as BioPAX. The PC database currently includes data from resources that already provide data in BioPAX format, such as Reactome and HumanCyc. The aim of this project is to extend Pathway Commons framework by implementing importers/converters for other data resources that do not provide their data in BioPAX but are of high interest to biologists.
• Idea 26: Porting Interference App to Cytoscape 3 Interference is a Cytoscape plug-in for virtual knock-out experiments on complex networks.It is based on some features of the CentiScaPe plugin and is currently available for Cytoscape 2.8. So the main aim of the Project is to port the plugin to Cytoscape3. Goals of the project are 1. Port Interference plugin to Cytoscape3. 2. Provide the Eigenvector, Bridging Centrality and Edge Betweenness centrality Interference. 3. Add support for directed and weighted networks
• Idea 38: Network Analysis Enhancements While the Network Analyzer and the Centiscape app between them offer a number of important and useful measures to analyse networks, it is still a challenge for users and developers to make use of the existing code in their apps. Thus comes the need to develop an API to expose Network Analyzer and Centiscape functions. Google Pagerank and HITS algorithms would be good additions to the existing suit of algorithms and functionality provided by Network Analyzer.
• Implementation of new clustering techniques into Cytoscape The process of clustering assigns similar objects to the same group and dissimilar objects to different groups and the resulting data partition enhances data understanding. In biological domains, we are often interested in determining the group structure in data but the results can depend on chosen method's assumptions. Algorithms need to be compared on the basis of desirable clustering features, and outline algorithms’ benefits and drawbacks to match them to biomedical applications.
• Implementing TieDIE algorithm as a CYTOSCAPE App ( IDEA- 43 ) TieDIE is an algorithm that finds "subnetworks" connecting genomic perturbations to transcriptional changes in large gene interaction networks. This algorithm is useful in optimizing cancer treatment by viewing cancer from a gene network perspective thus enhancing our understanding of disease initiation, progression and therapy. This project deploys TieDIE algorithm into cytoscape as an app.
• PathVisio Plugin to Load Additional Information about Data Nodes With the introduction of BioMart implementation support by Ensembl it has become easy to view more correlation tables between datasets and the Ensembl Genes 75, Ensembl Variation 75, Ensembl Regulation 75, Vega 55 and PRIDE databases. Although they can be viewed online using BioMart online browser PathVisio still lacks a way to show this information. This plugin aims at displaying this information for annotated gene products in a pathway that have Ensembl as their database.
• Pathvisiojs Diff Viewer Pathvisiojs comes to replace obsolete Pathvisio web applet. Diff Viewer allows to see differences between different versions of the same path. It is also based on old Java web applet. Implementing Diff Viewer as a plugin for Pathvisiojs will bring: * Expanding accessibility of plugin to all devices supported by Pathvisiojs * Testing and improving Pathvisiojs API and multi-instance * Serving as an example with documentation for Pathvisiojs plugins development
• Porting Pesca App to Cytoscape 3 with new features (Idea: 27) In biological networks, identification of shortest paths between proteins may help to detect and score highly communicating nodes. Pesca currently supports single-source shortest path problem, single-destination shortest path problem and finding SP clusters for undirected graphs. Adding additional features to the app like support for directed and weighted graphs as well as provision to download the human interactome would highly increase the application of the app in the biological world.
• PSFC: a Cytoscape app for calculating pathway signal flows Signaling pathways are sets of directed interactions between biomolecules, initiated by input signals and resulting in realization of target processes. Assessment of pathway activities is crucial for identification of pathways which contribute to disease development. This project is aimed at creating a Cytoscape app for calculation of pathway signal flow based on gene expression data and pathway topology. The app should incorporate both existing algorithms and provide framework for new ones.
• Virtual Cell iPhone App Enhancements Improving the current VCell iOS App prototype to include new set of features more useful for VCell users on the mobile device.