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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
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
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
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
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
http://solexaqa.sourceforge.net/
Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology.
Proper citation: SolexaQA (RRID:SCR_005421) Copy
A web-based software package for comparative genomics.
Proper citation: Sybil (RRID:SCR_005593) Copy
http://sourceforge.net/projects/mipe/
A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file.
Proper citation: MIPE (RRID:SCR_003065) Copy
http://sourceforge.net/projects/genseng/
Software for detecting copy number variations from next generation sequencing data. Used to identify regions of discrete copy number changes while simultaneously accounting for effects of multiple confounders.
Proper citation: GENSENG (RRID:SCR_000378) Copy
http://sourceforge.net/projects/limsforproteomi/
Laboratory information management system for proteomics. The software works with 2DPAGE-based proteomics workflow.
Proper citation: LIPAGE (RRID:SCR_000290) Copy
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
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
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
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
https://sourceforge.net/projects/bva-io/
Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software.
Proper citation: BVA import/export EEGLAB plugin (RRID:SCR_016333) Copy
http://sourceforge.net/projects/cnvhitseq/
A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data.
Proper citation: cnvHiTSeq (RRID:SCR_013160) Copy
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