Projects

Cytoscape

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

GenoViz

The GenoViz project provides tools for genomics data visualization. It consists of the following: 1) the GenoViz SDK, a library of re-usable components, 2) the Genometry data model to represent relationships between biological sequences, and 3) the Integrated Genome Browser (IGB, "igbee") ... [More] , an application built upon the GenoViz SDK and Genometry for visualization and exploration of genomes and corresponding annotations from multiple data sources. IGB supports the Distributed Annotation System (DAS) protocol, version 1 and 2, as well as other optimized binary data formats that are designed for efficient exploration of large, whole genome data sets. [Less]

nexml

XML-based data exchange standard for phylogenetics. In honor of the commonly-used "nexus" flat file format, the working title for this standard is nexml.

PathVisio

Utility for creating / edit biological pathways and and visualizing high-throughput data (e.g. microarray data) in the context of pathways.

OpenMS

An open source framework for LC-MS based proteomics. OpenMS offers datastructures and algorithms for the processing of mass spectrometry data. The library is written in C++.

Bio::Phylo

Phylogenetic analysis using perl.

BioMart

BioMart is a query-oriented data management system developed jointly by the European Bioinformatics Institute (EBI) and Cold Spring Harbor Laboratory (CSHL). The system can be used with any type of data and comes with a range of query interfaces and administration tools, including 'out of the ... [More] box' website that can be installed, configured and customised according to requirements. The system simplifies the task of creation and maintenance of advanced query interfaces backed by a relational database and it is particularly suited for providing the 'data mining' like searches of complex descriptive (e.g. biological) data. BioMart can work with existing data repositories by converting them to a required BioMart format as well as newly created databases. [Less]

LabKey Server

LabKey Server is open source software that helps scientists manage, analyze and share complex datasets. It supports tandem mass spectrometry, flow cytometry, assays for neutralizing antibodies, Luminex, observational studies, and secure, web-based collaboration. The software is modular ... [More] , configurable, and customizable. Written in Java, it can be installed in your institution on any modern hardware and operating system. It is designed to integrate with your existing systems, instruments, and work flows, and to be readily adapted by skilled programmers to novel methods of inquiry. The project is under active development by a team of professional software engineers and a community of active contributors. We release new versions about four times per year. [Less]

BioDAS

The Distributed Annotation System (DAS) defines a communication protocol used to exchange biological sequence annotations. DAS is a client-server system in which a single client integrates data from multiple servers. Data distribution, performed by DAS servers, is separated from visualization ... [More] , which is done by DAS clients. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community for sharing information about gene and protein sequences as well as protein structures. [Less]

QuteMol

QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilities through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding ... [More] of the 3D shape and structure of large molecules or complex proteins. * Real Time Ambient Occlusion * Depth Aware Silhouette Enhancement * Ball and Sticks, Space-Fill and Liquorice visualization modes * High resolution antialiased snapshots for creating publication quality renderings * Automatic generation of animated gifs of rotating molecules for web pages animations * Interactive rendering of large molecules and protein (>100k atoms) * Standard PDB input [Less]