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