Projects tagged ‘bio-informatics’ and ‘biology’

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 ... [More] support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and 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]

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application ... [More] , is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. [Less]

Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data. The project was started in the Fall of 2001. The Bioconductor core team is ... [More] based primarily at the Fred Hutchinson Cancer Research Center. Other members come from various US and international institutions. [Less]

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. It is a distributed collaborative effort to develop Python ... [More] libraries and applications which address the needs of current and future work in bioinformatics. The source 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 provide web and CVS space for the project. [Less]

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.

This computes protein yield and reading frame displacement given a sequence of codons in addition to writing an infinite amount of tools to analyze or help generate those metrics. Throw in Perl for extra sexiness.

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

The BinBase Database system was created to provide an accurate and fast solution for the analysis of thousand of Chromatograms and to create a library of compounds. Better known as Bins. The system ... [More] is so designed that it can be easily extended and adapted for your specific problems. You also have the possibilities to use it in different runtime configurations like: * using it as standalone system * using it with a cluster * using it with setupX as meta information provider * using with a custom meta information provider BinBase core part is now available in the svn. Websites are down to server error and we are working on it! [Less]

BigRedBin is a web-based tool designed to pre-process metabolomics data generated by a mass spectrometer in an attempt to increase the signal-to-noise ratio. This is accomplished by using information ... [More] from multiple technical replicates of the same sample to identify peaks detected consistently in given sample. BigRedBin then places peaks into bins of a given size to allow the data to be analysed using their preferred software e.g. PCA. [Less]

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