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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 files and computed normal modes from quantum programs.
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]
The SHOGUN machine learning toolbox's focus is on large scale kernel methods and especially on Support Vector Machines (SVM). It comes with a generic interface for SVMs, features several SVM and kernel implementations, includes LinAdd optimizations and also Multiple Kernel Learning algorithms. ... [More]
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]
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 effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding ... [More]
A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature.
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 occurrences of words in sequences deviate from their expected values, an can thus single out ... [More]
MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
molsKetch is a molecular drawing tool for 2D molecular structures. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats.
The data and code in this repository were leveraged in the production of several comparative genomics research analyses, including an investigation of rates and mechanisms of intron gain and loss in Cryptococcus, an exploration of genome evolution in the human fungal pathogens Coccidioides, and a ... [More]