Projects tagged ‘bio-informatics’ and ‘research’

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]

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.

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.

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 ... [More] effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins. * Real Time Ambient Occlusion * Depth Aware Silhouette Enhancement * Ball and Sticks, Space-Fill and Liquorice visualization modes * High resolution antialiased snapshots for creating publication quality renderings * Automatic generation of animated gifs of rotating molecules for web pages animations * Interactive rendering of large molecules and protein (>100k atoms) * Standard PDB input [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]

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 ... [More] relationships between biological sequences, and 3) the Integrated Genome Browser (IGB, "igbee"), 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]

R'MES is a set of command-line tools to assess the exceptionality of words or families of words in biological sequences. Using different mathematical models it gives a statistical measure of how much ... [More] occurrences of words in sequences deviate from their expected values, an can thus single out words having a potential biological interest. It has already been used to prove on a statistical basis that a specific motif (called CHI) is over-represented in certain kind of bacteria. R'MES is an initiative of the Applied Mathematics and Computing division of the french Agronomical Research Institute (INRA). [Less]

PD - Molecular Simulation Software