Projects tagged ‘bio-informatics’

Bioperl is a large, object-oriented toolkit of interacting perl modules useful for building bioinformatics solutions in Perl. The collection of modules in the bioperl-live repository contains the core ... [More] functionality. Additional packages for creating graphical interfaces (bioperl-gui), setting up persistent ORM storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (bioperl-run), and software to automate bioinformatic analyses (bioperl-pipeline) are all available from our Subversion repository. [Less]

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame ... [More] files and computed normal modes from quantum programs. [Less]

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]

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular ... [More] modeling, chemistry, solid-state materials, biochemistry, or related areas. [Less]

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.

The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search ... [More] , SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more. [Less]

JChemPaint is a program for drawing 2D chemical structures like those found in most chemistry textbooks.

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]

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.