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Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.
3D medical image platform for visualization and image processing. Segmentation with Levels sets. Surface reconstruction with marching Cubes, texture Mapping and Raycasting,DICOM support. Integration environment for VTK, ITK and vtkInria3D under wxWidgets
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A population-based method for DNA copy number analysis: recurrent copy number aberration indentification in multiple samples (with no need of single-sample calling). Developed for a quick analysis of high resolution and large population data.
Open Source project for visualizing protein structure. Written in C++ with Qt and OpenGL the software is designed to be multi-platform (Linux, FreeBSD and Windows). On web: www.msprot.com Copyright 2008 Federal University of Sao Paulo - UNIFESP
This library is a lightweight implementation of genetic algorithm, contains the most popular types of chromosomes and the basic algorithms for selection, elitism, crossing and mutation.
Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.
Accurately convert voice to text in over 125 languages and variants by applying Google's powerful machine learning models with an easy-to-use API.
New customers get $300 in free credits to spend on Speech-to-Text. All customers get 60 minutes for transcribing and analyzing audio free per month, not charged against your credits.
Given low-density genotypes for pedigrees, and dense genotypes for some people in those pedigrees, computes high-density genotypes for some other people in those pedigrees. This reduces genotyping effort.
The SBML ODE Solver is a command-line tool and programming library (ISO/ANSI C) for construction and numerical integration of an ODE system, derived from an SBML based description of a biochemical reaction network.
Development has moved to https://github.com/raim/SBML_odeSolver . Please download the latest version from there!
This is a C library with a set of functions that allow the user to evolve biological networks. The user provides a fitness function in C, and the library will do the rest. A few simulation algorithms and examples are included.
CheMecher is a fully-featured chemical simulator that supports an arbitrary number of reaction steps and chemical species. Uses the Runge-Kutta algorithm for numeric solutions.
A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
LocalMotif is a bioinformatics tool for discovering nucleotide motifs in a set of gene regulatory sequences. It takes into account the positional distribution of the motifs relative to a biological landmark. Look out for an updated version in May.
Biodiversity Information Group develops software tools and data standards that enable herbaria and museums to create dynamic distributed queries of their online databases. See http://bit.ly/bfirSh and http://bit.ly/bwpnSY for latest developments.
AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general.
AnnaF was build upon the pipeline framework Anna.
An efficient implementation of the Smith-Waterman algorithm that takes advantage of SIMD instruction sets in modern CPUs. The Smith-Waterman algorithm is used for sequence alignment in bioinformatics.
A repository linking to eight Bioinformatics Resource Centers (BRCs) sponsored by the NIAID. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of bioterrorism
Tandem mass spectral peptide identification and validation software, similar to X!Tandem, OMSSA, MyriMatch. Suitable for single hosts through large clusters. Written in Python for simplicity, with performance-critical sections in C++.