Search Results for "beta"

CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files.

Lush is a Lisp dialect with extensions for object-oriented and array-oriented programming. Lush is intended for prototyping numerically intensive applications and is designed for easy integration of existing C/C++/Fortran codes.

The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.

mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.

ESTScan is a program that can detect coding regions in DNA/RNA sequences, even if they are of low quality (e.g. EST sequences). ESTScan will also detect and correct sequencing errors that lead to frameshifts.

Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.

CUDASW++ software is a public open source software for Smith-Waterman protein database searches on Graphics Processing Units with CUDA. This software have been added to the NVIDIA Tesla Bio Workbench (http://www.nvidia.com/object/swplusplus_on_tesla.html

Tagger is a tool which allows searching fixed-sequence tags (or sequence branches) against entire genomes or mRNA reference sequence databases.

MrBayes is a program for the Bayesian estimation of phylogeny. The project has been moved to GitHub: https://github.com/NBISweden/MrBayes

GPU MrBayes implements MrBayes MC(3) on the GPU using CUDA. When using our program in your article, please cite our paper "Efficient Implementation of MrBayes on multi-GPU" (http://mbe.oxfordjournals.org/content/early/2013/03/14/molbev.mst043.abstract.html?papetoc).

BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.

NOTE: Use of this codebase is NOT RECOMMENDED. This project has been migrated to github at http://jaerproject.net (or https://github.com/SensorsINI/jaer for the Java code). Commits have been disabled for the subversion sourceforge repository and new development is being done on the github repository. Java tools for Address-Event Representation (AER) neuromorphic processing. Uses USB hardware. See wiki at https://sourceforge.net/p/jaer/wiki/

Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS

Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.

SoundRuler is a tool for acoustic analysis, graphing and teaching. It interactively recognizes and measures 35 temporal and spectral properties of each sound in a file. It also features several measurement, graphing and didactic modules.

OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast...

Atlas is a suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequecing (WECS) data.

PANorama is a Linux-compatible, open-source software package for panicle image acquisition, processing, and phenotyping. PANorama 2.0 contains new phenotype measurements and is available for download within the "Files" tab listed above. Installation and user instructions are located within the "Wiki" tab. How to videos are available for streaming at the link below, or for download in the "Files" tab above. Information regarding the project and funding can be found at...

The General Hidden Markov Model Library (GHMM) is a C library with additional Python bindings implementing a wide range of types of Hidden Markov Models and algorithms: discrete, continous emissions, basic training, HMM clustering, HMM mixtures.

TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.

Efficient tool for clustering and assembling short reads, especially for RAD.

This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps...

Toolchain for quantification of fluorescence intensity and morphological parameters in single cells using microscope based cytometry.

RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.

AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.