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http://samtools.sourceforge.net/

A generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.

Proper citation: SAM format (RRID:SCR_012093) Copy   

•   Source: SciCrunch Registry

http://mzmatch.sourceforge.net/

A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java.

Proper citation: mzMatch (RRID:SCR_000543) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/htqc/

A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc..

Proper citation: HTQC (RRID:SCR_006448) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/avalontoolkit/

Software toolkit containing tools to render and canonicalize SMILES and manipulate MOL file and related formats, as well as structure fingerprinting.

Proper citation: Avalon Cheminformatics Toolkit (RRID:SCR_014273) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://broadinstitute.github.io/picard/

Java toolset for working with next generation sequencing data in the BAM format.

Proper citation: Picard (RRID:SCR_006525) Copy   

•   Source: SciCrunch Registry

http://neurospy.org

neurospy is a free software for functional imaging of fast neuronal activity. neurospy is a modular cross-platform application framework written in Java for the NetBeans Platform. At this time it runs on Windows XP-based LeCroy oscilloscopes and drives acousto-optic scanners via USB using the Analog Devices 9959 Direct Digital Synthesis chip. This combination makes one of the most powerful systems for scanning microscopy available today at any price. neurospy is very easy to port to other kinds of acquisition and scanning hardware.

Proper citation: neurospy (RRID:SCR_007016) Copy   

•   Source: SciCrunch Registry

http://cudasw.sourceforge.net/

CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher

Proper citation: CUDASW++ (RRID:SCR_008862) Copy   

•   Source: SciCrunch Registry

http://fmatoolbox.sourceforge.net

Matlab toolbox used to help analyze electrophysiological and behavioral data recorded from freely moving animals.

Proper citation: FMAToolbox (RRID:SCR_015533) Copy   

•   Source: SciCrunch Registry

http://jmol.sourceforge.net/

An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component.

Proper citation: Jmol (RRID:SCR_003796) Copy   

•   Source: SciCrunch Registry

http://mged.sourceforge.net/ontologies/MGEDontology.php

An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed.

Proper citation: MGED Ontology (RRID:SCR_004484) Copy   

•   Source: SciCrunch Registry

http://moose.sourceforge.net/

MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology. MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. it is backwards-compatible with GENESIS, and forward compatible with Python and XML-based model definition standards like SBML and MorphML. MOOSE is coordinating with the GENESIS-3 project towards the goals of developing educational resources for modeling. MOOSE is open source software, licensed under the LGPL (Lesser GNU Public License). It has absolutely no warranty. Sponsors: - National Center of Biological Sciences (NCBS) - National Institutes of Health (NIH) Collaboration - EU-India grid - Department of Atomic Energy Science Research Council (DAE/SRC) - Department of Biotechnology (DBT)

Proper citation: Multiscale Object Orientation Simulation Environment (RRID:SCR_008031) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/blox/

A quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Programming Language: Java, JavaScript, Scheme

Proper citation: Blox (RRID:SCR_006667) Copy   

•   Source: SciCrunch Registry

http://bionerds.sourceforge.net/

A named entity recognizer for the recovery of bioinformatics databases and software from primary literature. The entity recognizer achieved an F-measure of between 63% and 91% on different datasets (63%78% at the document level). Results from full-text literature analysis for both Genome Biology and BMC Bioinformatics journals are available as well as a full list of references and links for the various major resources mentioned. Data generated data can be used for exploration of bioinformatics database and software usage. This tool makes heavy use of GATE (version 6.1). It can be run in sandbox mode, which means a installation of GATE is not a prerequisite, but you will instead need to point the config to a unzipped gate_plugins directory instead (located in the bin/BMC_Files directory).

Proper citation: bioNerDS (RRID:SCR_006784) Copy   

•   Source: SciCrunch Registry

http://deconseq.sourceforge.net/

Software tool to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. The user can upload FASTA or FASTQ files and select the databases used for contamination screening, including seven human genomes, bacterial genomes, and viral genomes. The user can set the thresholds interactivly and see the results directly using the functionality of the graphical interface. The results can be downloaded in joined or separated files in different formats. The coverage-identity plots provide additional information that can guide the selections of the thresholds using color coded points and connecting lines.

Proper citation: DeconSeq (RRID:SCR_007006) Copy   

•   Source: SciCrunch Registry

http://mcx.sourceforge.net/

A Monte Carlo simulation software for photon migration in 3D turbid media. It uses Graphics Processing Units (GPU) based massively parallel computing techniques and is extremely fast compared to the traditional single-threaded CPU-based simulations. Using an nVidia 8800GT graphics card (14MP/114Cores), the acceleration is about 300x~400x compared to a single core of Xeon 5120 CPU; this ratio can be as high as 700x with a GTX 280 GPU and 1400x with a GTX 470.

Proper citation: Monte Carlo eXtreme (RRID:SCR_007001) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/rdpframebot/

A frameshift correction and nearest neighbor classification tool for use with high-throughput amplicon sequencing. It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline.

Proper citation: RDP FrameBot (RRID:SCR_013083) Copy   

•   Source: SciCrunch Registry

http://libeep.sourceforge.net/

Software library that deals with reading and writing RIFF-format CNT/AVR-files. This file format is also called EEProbe data format, and is used in the software packages EEProbe, ASA, ASA-Lab, Cognitrace, eemagine EEG, Visor, by ANT Neuro B.V., The Netherlands. The file format provides for storage of EEG/ERP/MEG data as 32-bit values, and includes a very efficient compression algorithm. Encoding/decoding from the compressed data is performed automatically through the LIBEEP interface functions.

Proper citation: LIBEEP (RRID:SCR_009591) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/w2mhs/

An open source MATLAB toolbox designed for detecting and quantifying White Matter Hyperintensities(WMH) in Alzheimer?s and aging related neurological disorders.Our toolbox provides a self-sufficient set of tools for segmenting these WMHs reliably and further quantifying their burden for down-processing studies. WMHs arise as bright regions on T2-weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer?s disease (AD) with regard to its prognosis.

Proper citation: Wisconsin White Matter Hyperintensities Segmentation Toolbox (RRID:SCR_009652) Copy   

•   Source: SciCrunch Registry

http://cpfp.sourceforge.net/

Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics.

Proper citation: CPFP (RRID:SCR_012043) Copy   

•   Source: SciCrunch Registry

http://bionotate.sourceforge.net/

An open source annotation tool for the distributed creation of a large corpus.

Proper citation: Bionotate (RRID:SCR_012098) Copy   

•   Source: SciCrunch Registry