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http://sourceforge.net/tracker/?group_id=76834&atid=835555

Open Biomedical Ontologies Tracker that allows users to browse the Plant Ontology (PO) term requests and view their status. Details include a summary, ID, status, Date opened, assignee, submitter, resolution and assigned priority. New requests are accepted from logged in users.

Proper citation: OBO Tracker: Plant Ontology (PO) TERM requests (RRID:SCR_006497) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/chebi/beta/

Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

Proper citation: CHEBI (RRID:SCR_002088) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/metavar/

Software package that enables detection of sequence variation between metagenomic samples.

Proper citation: MaryGold (RRID:SCR_000528) 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://tvap.genome.wustl.edu/tools/varscan/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: VARSCAN (RRID:SCR_006849) 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://hanalyzer.sourceforge.net/

An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download.

Proper citation: Hanalyzer (RRID:SCR_000923) 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://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://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://sybil.sourceforge.net/

A web-based software package for comparative genomics.

Proper citation: Sybil (RRID:SCR_005593) 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

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://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://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