Projects

BioPAX

BioPAX is a collaborative effort to create a data exchange format for biological pathway data. The goal of the BioPAX group is to develop a common exchange format for biological pathways data. The BioPAX project began at the Fourth BioPathways Consortium Meeting, a satellite of the ISMB'02 ... [More] Conference held in Edmonton, Canada in August 2002. It was decided that a pathway exchange format would facilitate sharing of pathway information between databases and users and would be a good first step to building an open source pathway information resource. The project got underway in early October 2002 when Chris Hogue (BIND, UToronto), Peter Karp (BioCyc, SRI), and Chris Sander (MSKCC) organized the BioPAX work group. [Less]

snavi

SNAVI: Desktop Application for Analysis and Visualization of Large-Scale Cell Signaling NetworksAbstractStudies of cellular signaling indicate that signal transduction pathways combine to form large networks of interactions. Viewing protein-protein and ligand-protein interactions as graphs ... [More] (networks), where biomolecules are represented as nodes and their interactions are represented as links, is a promising approach for integrating experimental results from different sources to achieve a systematic understanding of the molecular mechanisms driving cell phenotype. The emergence of large-scale signaling networks provides an opportunity for topological statistical analysis. However, visualization of such networks represents a challenge. SNAVI (Signaling Networks Analysis and Visualization) is Windows-based desktop application that implements standard network analysis methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means to visualize networks and network motifs. SNAVI is capable of generating linked web pages from network datasets loaded in text format. SNAVI can also create networks from lists of gene or protein names. SNAVI is a useful tool for analyzing, visualizing and sharing cell signaling data. SNAVI is open source free software. InstructionsThe installation may be downloaded from: http://code.google.com/p/snavi/downloads/list. The source code can be accessed from: http://snavi.googlecode.com/svn/trunk For the program to work correctly SVG Viewer plug-in version 3.03 should be downloaded and installed from here: http://www.adobe.com/svg/viewer/install/main.html Users should also have WinGraphviz version 1.02.24 installed from here: http://wingraphviz.sourceforge.net/wingraphviz/ An article describing the system has been published in BMC Systems Biology: http://www.biomedcentral.com/1752-0509/3/10 A case study with examples on how to use the software can be downloaded from here: http://www.biomedcentral.com/imedia/6431703032452204/supp1.pdf [Less]