Projects tagged ‘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]

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.

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]

B-Fabric is an open infrastructure for data and application integration in the life sciences domain. In it is current deployment at FGCZexternal link. It allows to store and access all experimental ... [More] data generated at FGCZ together with its semantic context. B-Fabric acts as the glue between the different instrument PCs and analysis tools at FCGZ, guiding the instrument specialists and researchers through their scientific workflows. B-Fabric is a framework for data management and information integration. B-Fabric allows storing and accessing experimental data generated by instruments that are connected to the framework. The raw data is stored together with all information that is needed to find and correctly interpret the data. [Less]

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

glbase is a unified framework for the analysis of heterogeneous genomic data. It's particularly useful for intersecting any data that can be expressed as a CSV file. Examples are microarray data ... [More] , gene lists, Chip-seq location lists. GLbase excels at integrating these data and then outputting graphical representations of the resulting data. [Less]

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C ... [More] source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. (from the PAML website) [Less]

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]