RSS 227 projects tagged "Bioinformatics"

Download No website Updated 30 Mar 2005 libGenome

Screenshot
Pop 19.60
Vit 2.00

libGenome is a development library designed to make common operations on DNA and protein sequences easy. libGenome provides functionality to read and write sequence and annotation data in several file formats. It provides a common manipulation interface for sequence and annotation data in any supported file format. Some of the basic manipulation functionality offered by libGenome is concatenation, truncation, reverse complementation, and translation of sequences. It was intended to be used on genome size sequences and is optimized accordingly. This is a cross platform library written in ANSI C++ and is currently supported on any platform with gcc. Metrowerks CodeWarrior on Windows and Mac OS are also supported.

Download Website Updated 09 Jul 2009 libfid

Screenshot
Pop 26.66
Vit 1.43

The Full-text Index Data structure library, libfid for short, is a portable software library for accessing indexed data through a simple C interface. It implements, among others, functions for reading indexed data from files, and for performing common operations such as fast string matching. Easy alphabet handling for mapping between printable and binary alphabets is integrated from the ground up. Currently, the enhanced suffix array is the only full-text index data structure supported. A very simplistic program for constructing enhanced suffix arrays is included.

Download Website Updated 29 Apr 2005 libmba

Screenshot
Pop 190.33
Vit 4.64

The libmba package is a collection of mostly independent C modules potentially useful to any project. There are the usual ADTs including a linkedlist, hashmap, pool, stack, and varray, a flexible memory allocator, CSV parser, path canonicalization routine, I18N text abstraction, configuration file module, portable semaphores, condition variables, and more. The code is designed so that individual modules can be integrated into existing codebases rather than requiring the user to commit to the entire library. The code has no typedefs, few comments, and extensive man pages and HTML documentation.

Download Website Updated 26 Dec 2012 massXpert mass spectrometry package

Screenshot
Pop 215.17
Vit 16.60

The massXpert software package is a mass spectrometry environment for linear (bio-)polymers. It inherits all the innovations of GNU polyxmass. It allows the detailed definition of new polymer chemistries in the XpertDef module. These chemistry definitions are then used in the desktop calculator-like mass calculator (XpertCalc) and in the sophisticated polymer sequence editor and (bio-)chemical/mass spectrometric simulations module (XpertEdit). Available simulations include polymer and monomer chemical modifications, polymer sequence cleavage, gas-phase fragmentation, m/z ratio calculations, and more.

Download Website Updated 15 Dec 2011 mcl-edge

Screenshot
Pop 120.20
Vit 6.31

MCL-edge is an integrated command-line driven workbench for large scale network analysis. It includes programs for the computation of shortest paths, diameter, clustering coefficient, betweenness centrality, and network shuffles. A module for loading and analyzing gene expression data as a network is provided. The MCL algorithm is a fast and highly scalable cluster algorithm for networks based on stochastic flow. The flow process employed by the algorithm is mathematically sound and intrinsically tied to cluster structure, which is revealed as the imprint left by the process. The threaded implementation has handled networks with millions of nodes within hours and is widely used in the fields of bioinformatics, graph clustering, and network analysis.

Download Website Updated 14 Jul 2009 mkESA

Screenshot
Pop 32.12
Vit 1.75

mkESA is a program for constructing enhanced suffix arrays (ESAs) from biological sequence data. The program is based on an implementation of Manzini's lightweight Deep-Shallow algorithm, which can also utilize multiple CPUs/cores for extra performance. The generated output is compatible with the output of mkvtree from the Vmatch package.

Download Website Updated 01 Feb 2005 mozCellML

Screenshot
Pop 16.73
Vit 2.01

mozCellML is a Mozilla based CellML tool. It can be used to edit boundary conditions, integrate models (using a Runge- Kutta method), and fit parameters to models (using Levenberg-Marquardt). It supports both CellML 1.0 and CellML 1.1 documents.

Download Website Updated 07 Jun 2007 octopus TDDFT

Screenshot
Pop 49.68
Vit 1.54

octopus is a program aimed at the ab initio virtual experimentation on a hopefully ever increasing range of systems types. Electrons are describe quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.

Download Website Updated 08 Nov 2004 open SPEAR

Screenshot
Pop 9.90
Vit 58.72

open SPEAR stands for open Simulator of Physical Environment for Agents Research. It is a C++ library designed to build an efficient multi-agents and robotics simulation. The main audience for this project is the robotics/artificial life community.

No download Website Updated 02 Apr 2014 openModeller

Screenshot
Pop 184.75
Vit 65.66

openModeller is a C++ framework providing tools and an API for ecological niche modeling using a variety of algorithms. It can be used to predict species potential distribution based on a set of georeferenced occurrence points and a set of environmental layers.

Screenshot

Project Spotlight

LeechCraft

A modular live environment.

Screenshot

Project Spotlight

ACE

An object-oriented C++ class library and framework.