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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EXCAVATOR-tool Resource Report Resource Website 1+ mentions |
EXCAVATOR-tool (RRID:SCR_012766) | EXCAVATOR-tool | software resource | A software package for the detection of copy number variants (CNVs) from whole-exome sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00332 | SCR_012766 | EXCAVATOR-tool: Tool for detecting CNVs from whole-exome sequencing data | 2026-07-25 12:07:36 | 7 | |||||||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software application, software resource | 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. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-07-26 09:02:49 | 0 | ||||||
|
Xournal Resource Report Resource Website |
Xournal (RRID:SCR_003233) | Xournal | software application, software resource | 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. | annotation, markup |
is listed by: FORCE11 has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_157272 | SCR_003233 | 2026-07-26 09:03:23 | 0 | ||||||||
|
TARQUIN Resource Report Resource Website 50+ mentions |
TARQUIN (RRID:SCR_002598) | TARQUIN | software application, software resource | 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. | magnetic resonance, mrs, mas, molecule, nmr spectroscopy |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
PMID:20878762 | Free, Available for download, Freely available | nlx_156002 | http://www.nitrc.org/projects/tarquin | SCR_002598 | TARQUIN MRS analysis package | 2026-07-26 09:03:14 | 58 | |||||
|
Monte Carlo eXtreme Resource Report Resource Website 1+ mentions |
Monte Carlo eXtreme (RRID:SCR_007001) | MCX | software application, simulation software, software resource | 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. | c, console (text based), macos, microsoft, modeling, monte carlo, optical imaging, other programming language, posix/unix-like, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155817 | http://www.nitrc.org/projects/mcextreme | SCR_007001 | Monte Carlo eXtreme (MCX) | 2026-07-27 09:32:42 | 2 | ||||||
|
GeneVenn Resource Report Resource Website 100+ mentions |
GeneVenn (RRID:SCR_012117) | analysis service resource, service resource, data analysis service, production service resource | A web application creating Venn diagrams from two or three gene lists. | web app |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:17597932 | OMICS_05568 | SCR_012117 | 2026-07-27 09:34:02 | 101 | |||||||||
|
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-07-27 09:31:18 | 35 | ||||||
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Multiscale Object Orientation Simulation Environment Resource Report Resource Website 100+ mentions |
Multiscale Object Orientation Simulation Environment (RRID:SCR_008031) | software application, simulation software, software resource | 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) | cell, computational, molecule, network, neuronal, neuroscience, simulation, subcellular, systems biology |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MUlti SImulation Coordinator has parent organization: SourceForge |
nif-0000-10307 | http://www.nitrc.org/projects/moose | SCR_008031 | MOOSE | 2026-07-27 09:32:58 | 302 | ||||||||
|
cnvHiTSeq Resource Report Resource Website 1+ mentions |
cnvHiTSeq (RRID:SCR_013160) | cnvHiTSeq | commercial organization, software resource | A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23259578 | Commercial license | OMICS_00342 | SCR_013160 | cnvHiTSeq - A set of tools for detecting CNVs using sequencing data | 2026-07-27 09:34:21 | 4 | ||||||
|
MIPE Resource Report Resource Website 10+ mentions |
MIPE (RRID:SCR_003065) | narrative resource, data or information resource, standard specification, software resource, interchange format | 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. | standalone software, pcr, xml, data storage, data exchange |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02358 | http://mipe.sourceforge.net/, https://sources.debian.org/src/mipe/ | SCR_003065 | Minimal Information for PCR Experiments | 2026-07-28 09:40:43 | 31 | |||||||
|
Metabolomics Standards Initiative Resource Report Resource Website 10+ mentions |
Metabolomics Standards Initiative (RRID:SCR_003246) | MSI | narrative resource, data or information resource, standard specification, knowledge environment, ontology, controlled vocabulary | Oversight Committee appointed to monitor, coordinate and review the efforts of working groups (WG) in specialist areas (Biological context metadata WG, Chemical analysis WG, Data processing WG, Ontology WG, Exchange format WG) that will examine standardization and make recommendations. | metabolomics, biological context, metadata, chemical analysis, data processing, exchange format |
is related to: NMR-Instrument Component of Metabolomics Investigations Ontology has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_157308 | https://github.com/MSI-Metabolomics-Standards-Initiative/CIMR | SCR_003246 | 2026-07-28 09:40:45 | 14 | |||||||
|
Vertebrate Trait Ontology Resource Report Resource Website |
Vertebrate Trait Ontology (RRID:SCR_003214) | VT | controlled vocabulary, data or information resource, ontology | A controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms. | trait, morphology, physiology, development, obo |
is listed by: BioPortal is related to: monarch-ontologies is related to: Rat Genome Database (RGD) is related to: Animal QTLdb is related to: Mouse Phenome Database (MPD) has parent organization: SourceForge |
PMID:23937709 | Free, Available for download, Freely available | nlx_156940 | SCR_003214 | VT Ontology | 2026-07-28 09:40:45 | 0 | ||||||
|
Software Ontology Resource Report Resource Website 1+ mentions |
Software Ontology (RRID:SCR_003493) | SWO | controlled vocabulary, data or information resource, ontology | An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to). | owl, software, provenance, version, ontology |
is listed by: BioPortal is listed by: OBO is listed by: SourceForge is related to: Information Artifact Ontology has parent organization: European Bioinformatics Institute has parent organization: University of Manchester; Manchester; United Kingdom |
JISC | The community can contribute to this resource | nlx_157591 | http://www.ebi.ac.uk/efo/swo, http://purl.bioontology.org/ontology/SWO, http://theswo.svn.sourceforge.net/viewvc/theswo/trunk/src/release/swoinowl/swo_merged/swo_merged.owl | SCR_003493 | 2026-07-28 09:40:45 | 2 | ||||||
|
NEMO Ontology Resource Report Resource Website |
NEMO Ontology (RRID:SCR_003386) | NEMO Ontology | controlled vocabulary, data or information resource, ontology | Ontology that describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive / behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Its aim is to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, experiment paradigms, and modalities (EEG/MEG). | eeg, meg, owl, event-related potential, cognitive, behavioral, data sharing, erp |
is listed by: BioPortal is related to: NEMO Analysis Toolkit has parent organization: Neural ElectroMagnetic Ontologies (NEMO) Project has parent organization: SourceForge |
NIH | Free, Available for download, Freely available | nif-0000-32927 | http://purl.bioontology.org/ontology/NEMO, http://sourceforge.net/projects/nemoontologies/ | http://nemo.nic.uoregon.edu/wiki/NEMO#NEMO_Ontology | SCR_003386 | Neural ElectroMagnetic Ontology | 2026-07-28 09:40:43 | 0 | ||||
|
Jmol Resource Report Resource Website 100+ mentions |
Jmol (RRID:SCR_003796) | Jmol | software application, d visualization software, standalone software, software resource | 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. | chemical, crystal, material, biomolecule, java |
is used by: Glyco3D is listed by: SoftCite has parent organization: SourceForge |
PMID:28472503 PMID:28316648 |
GNU Lesser General Public License, Acknowledgement requested | nlx_158093 | SCR_003796 | Jmol: an open-source Java viewer for chemical structures in 3D | 2026-07-28 09:40:49 | 233 | ||||||
|
MGED Ontology Resource Report Resource Website 1+ mentions |
MGED Ontology (RRID:SCR_004484) | MO | controlled vocabulary, data or information resource, ontology | 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. | microarray, biomaterial, treatment, mage, owl |
is listed by: BioPortal is related to: MIAME is related to: MIAME is related to: RNA Abundance Database has parent organization: Functional Genomics Data Society has parent organization: SourceForge |
NIBIB ; NHGRI P41HG003619 |
PMID:16428806 | nlx_47223 | http://purl.bioontology.org/ontology/MO | SCR_004484 | Microarray and Gene Expression Data Ontology | 2026-07-28 09:41:00 | 1 | |||||
|
SolexaQA Resource Report Resource Website 100+ mentions |
SolexaQA (RRID:SCR_005421) | SolexaQA | software application, data analysis software, sequence analysis software, software resource, data processing software, data visualization software | Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20875133 | Acknowledgement requested | biotools:solexaqa, OMICS_01078 | https://bio.tools/solexaqa | SCR_005421 | 2026-07-28 09:41:19 | 291 | ||||||
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Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | data or information resource, database, software resource | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | Sybil: Web-based software for comparative genomics | 2026-07-28 09:41:26 | 37 | ||||||
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Diffusion Tensor Imaging ToolKit Resource Report Resource Website 10+ mentions |
Diffusion Tensor Imaging ToolKit (RRID:SCR_001642) | DTI-TK | software application, software toolkit, software resource, data processing software, image analysis software | 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 | dti, visualization, segmentation, resampling, smoothing, warping, registration, spatial normalization, atlas construction, analysis, atlas application, intersubject, image-to-template, analyze, nifti-1, macos, linux |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury is related to: Camino is related to: MRI Studio has parent organization: University of Pennsylvania; Philadelphia; USA has parent organization: SourceForge |
NIBIB 1R03EB009321-01 | Free, Available for download, Freely available | nlx_153914 | http://www.nitrc.org/projects/dtitk | SCR_001642 | 2026-07-28 09:40:14 | 22 | ||||||
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openADAM Resource Report Resource Website |
openADAM (RRID:SCR_002018) | openADAM | software application, software resource, data management software | 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. | php, perl, front end, affymetrix genechip mapping array, affymetrix genome-wide human snp array, data management, affymetrix, snp, genome-wide association |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19117518 | Free, Available for download, Freely available | OMICS_01921 | SCR_002018 | 2026-07-28 09:40:19 | 0 |
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