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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

http://purl.bioontology.org/ontology/FB-SP

The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.

Proper citation: Fly Taxonomy (RRID:SCR_003317) Copy   

•   Source: SciCrunch Registry

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   

•   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://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://hollow.sourceforge.net/

HOLLOW facilitates the production of surface images of proteins. HOLLOW is a portable command-line utility written in Python 2.4-2.7; it does not have any other dependencies (although running under the PyPy JIT interpreter, it runs much faster). The input is a PDB file. The output is a PDB file of dummy water atoms that forms a cast of the voids and channels of a protein. HOLLOW generates a surface from a cast of the protein surface. HOLLOW fills the interior spaces of a protein structure with dummy atoms defined on an overlapping grid. The surface generated by these dummy atoms can be shown to reproduce the surface of the protein at the ideal limit. The use of the surface of the dummy atoms allows us to focus on a specific piece of the interior surface. Simply by deleting dummy atoms, the interior surface can be trimmed to produce a custom portion of the interior space. For advanced coloring of the surface, the B-factor of the dummy atoms can be calculated as the average of the B-factor of the protein atoms surrounding the dummy atoms. This allows various colorings of the surface to be conveyed through the B-factor field of the PDB files. The volume filling representation facilitated by HOLLOW is meant to complement other programs that identify voids, pockets and channels, such as SPHGEN and CASTp, which identify binding sites but cannot produce output that can be rendered in standard molecular graphics software. HOLLOW can be used to help render these binding pockets.

Proper citation: HOLLOW (RRID:SCR_005729) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/phenofam/

A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.

Proper citation: PhenoFam (RRID:SCR_000640) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/magnolya/

A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets.

Proper citation: Magnolya (RRID:SCR_000164) Copy   

•   Source: SciCrunch Registry

http://utr.sourceforge.net/

Software application that uses change point model for detecting 3-prime UTR changes by RNA-Seq.

Proper citation: UTR (RRID:SCR_000045) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/metabnorm/

Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix.

Proper citation: metabnorm (RRID:SCR_001266) Copy   

•   Source: SciCrunch Registry

http://xournal.sourceforge.net/

Free software application for notetaking, sketching, keeping a journal using a stylus that runs on Linux (recent distributions) and other GTK+/Gnome platforms. It is similar to Microsoft Windows Journal or to other alternatives such as Jarnal, Gournal, and NoteLab. Note: is open source and allows some annotation, but its PDF reading ability is very limited. It also uses its own format to store annotations.

Proper citation: Xournal (RRID:SCR_003233) Copy   

•   Source: SciCrunch Registry

http://tarquin.sourceforge.net/

An analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies, in particular brain tumours, both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS. TARQUIN has the following features: * Free to use and modify under the GPL licence. * Based on a flexible time-domain fitting routine designed to give accurate rapid and automated quantitation for routine analysis. * Cross platform, works on Windows, Linux and OSX. * Comes packaged with a quantum mechanically based metabolite simulator to allow basis set construction optimised for the investigation of particular pathologies sequence parameters. * Includes both GUI and command line interface for one-off and batch analyses.

Proper citation: TARQUIN (RRID:SCR_002598) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/openadam/

A web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Genome-Wide Human SNP Array platforms.

Proper citation: openADAM (RRID:SCR_002018) Copy   

•   Source: SciCrunch Registry

http://dti-tk.sourceforge.net/pmwiki/pmwiki.php

A spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data with special care taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. A 2011 study published in NeuroImage ranks DTI-TK the top-performing tool in its class. Key features include: * open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes * tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization * pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies * built-in cluster-computing support: support for open source Sun Grid Engine (SGE) * Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio * Interoperability with ITK-SNAP: support multi-modal visualization and segmentation

Proper citation: Diffusion Tensor Imaging ToolKit (RRID:SCR_001642) Copy   

•   Source: SciCrunch Registry

http://snver.sourceforge.net/

Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.

Proper citation: SNVer (RRID:SCR_002061) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/virema/

Software Python package for detection, alignment and reporting of recombination events in Next-Generation Sequencing data. Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.

Proper citation: ViReMa (RRID:SCR_000566) Copy   

•   Source: SciCrunch Registry