Projects

BioJava

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and ... [More] powerful analysis and statistical routines including a dynamic programming toolkit. BioJava is used in several real-world bioinformatics applications and has been used for bioinformatics analysis in a number of published studies. [Less]

Biopython

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source ... [More] code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. We work along with the Open Bioinformatics Foundation, who generously host our website, bug tracker, and mailing lists. [Less]

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.

Bio::Phylo

Phylogenetic analysis using perl.

mdanalysis

MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, NAMD, LAMMPS, or Gromacs. It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively fast ... [More] framework for complex analysis tasks. In addition, CHARMM-style atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out. Some time-critical routines are written in C or Cython and require a working C compiler. MDAnalysis comes with an expanding library of analysis functions such as RMSD-fitting or analysis of lipid membrane bilayers. [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]

Adun

Adun currently includes tools for the calculation and analysis of several dynamic properties of macromolecules. Several force fields have already been implemented (Enzymix, Charmm and AMBER) and a sophisticated distributed database of simulations results that can be directly accessed by the program ... [More] is in development. Simulations methods currently include Newtonian and Langevin molecular dynamics. [Less]

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]

Cipres-perl

Perl stack for the Cyber-Infrastructure for Phylogenetic Research (CIPRES)