Projects

Jmol

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

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] 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]

SHOGUN

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] SHOGUN also implements a number of linear methods. It allows the input feature-objects to be dense, sparse or strings and of type int/short/double/char. It provides efficient implementations several kernels but also linear methods, hidden markov models etc. and interfaces to matlab,octave,python,R and has a cmdline interface and allows C++ extensions via a library. [Less]

GenoViz

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] , 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]

QuteMol

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] 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]

PPI Benchmark

A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature.

R'MES

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] 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]

MOLGENIS model-driven database platform

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

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.

sharpton-thesis

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] fungal kingdom-wide analysis of simple sequence repeat evolution. This project was initialized by Dr. Thomas J. Sharpton from Professor John W. Taylor's lab at the University of California at Berkeley. [Less]