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]

pathway-commons

This project hosts source code related to the Pathway Commons project. Pathway Commons is a collection of publicly available pathways from multiple organisms. It provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common ... [More] language. Access is via a web portal for browsing, query and download. Database providers can share their pathway data via a common repository and avoid duplication and reduce software development costs. Bioinformatics software developers can increase efficiency by sharing software components. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. http://www.pathwaycommons.org [Less]

intrinsic Noise Analyzer

iNA is a computational tool for quantitative analysis of fluctuations in biochemical reaction networks. Such fluctuations, also known as intrinsic noise, arise due to the stochastic nature of chemical reactions and cannot be ignored for when some molecules are present only in very low copy numbers ... [More] as is the case in living cells. The SBML-based software computes statistical measures such as means and standard deviations of concentrations within a given accuracy using the analytical system size expansion. The result of iNA’s analysis can be tested against the computationally much more expensive stochastic simulation algorithm. [Less]

amino-acid-substitution-rates

The aim of this project is to take an open and collaborative approach to investigating the evolution of proteins based on the biosynthetic cost of amino acids. A more details description can be found on the wiki while current progress can be tracked by following current issues.

phydotnet

WelcomePhy.net is collection of classes which implement many of the most widely known phylogenetic and bioinformatic search tools available. A full roster of its current implementation is available from the Project Specification. Mission Overview: Gene AlignmentNeedleman-Wunsch Smith-Waterman ... [More] Phylogenetic Tree ConstructionNeighbour-Joining UPGMA Maximum Parsimony Maximum Likelihood UtilityEnterez Sequence Aqcuisition Cladogram Rendering Visual Algorithm Profiling News31st October 2008: Phy.net project conceived [Less]

conip

This is an effort for finding a better and efficient method for finding Consensus for a set of binding sites for a protein. This would be helpful for finding potential binding sites.

megamicrobase

Code for managing and analyzing large numbers of microarray platforms

bio-itermap

This project implements four algorithms that maps short reads to one reference sequence or a set of reference sequences. The primary objective is to measure the performance of the algorithms. However, the code and result can be easily adopted and used in other projects.

pathwaycommons

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. Biologists can browse and search Pathway Commons pathways. Computational biologists can download all pathways in BioPAX format for global ... [More] analysis. Software developers can build software on top of Pathway Commons using our web service API. You can also download and install the cPath software to create a local mirror of Pathway Commons. All data is freely available, under the license terms of each contributing database. This site is intended to be a one-stop spot for all things related to Pathway Commons development, including: cPath software: the main engine that runs Pathway Commons. Bug / Issue Tracker Requirements documents [Less]

icoresoc

This site keeps track of the open source projects that are being submitted to Google Summer of Code 2009. The Informatics Core at the Institute for Systems Biology is the mentoring organization.