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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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iso2mesh Resource Report Resource Website 10+ mentions |
iso2mesh (RRID:SCR_013202) | iso2mesh | software application, software resource, software toolkit | A Matlab / Octave-based mesh generation toolbox designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images. It contains a rich set of mesh processing scripts/programs, functioning independently or interfacing with external free meshing utilities. Iso2mesh toolbox can operate directly on 3D binary, segmented or gray-scale images, such as those from MRI or CT scans, making it particularly suitable for multi-modality medical imaging data analysis or multi-physics modeling. | matlab, mesh generation, modeling, magnetic resonance, optical imaging, os independent, mri, computed tomography, octave |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155855 | http://www.nitrc.org/projects/iso2mesh | SCR_013202 | 2026-02-16 09:48:18 | 25 | |||||||
|
deFuse Resource Report Resource Website 50+ mentions |
deFuse (RRID:SCR_003279) | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Software package for gene fusion discovery using RNA-Seq data. It uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. | rna sequencing, gene fusion, paired end alignment, split read, fusion boundary, bio.tools |
uses: SAMTOOLS uses: Bowtie uses: BLAT uses: GMAP uses: R Project for Statistical Computing is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
British Columbia Cancer Foundation ; Vancouver General Hospital Foundation ; Genome Canada ; Michael Smith Foundation for Health Research ; Canadian Breast Cancer Foundation ; Canadian Institutes of Health Research's Bioinformatics Training Program |
PMID:21625565 | Free, Available for download, Freely available | biotools:defuse, OMICS_01345 | https://sourceforge.net/projects/defuse/ http://compbio.bccrc.ca/software/defuse/ https://bio.tools/defuse |
http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page | SCR_003279 | 2026-02-16 09:46:11 | 95 | |||||
|
Clinical Measurement Ontology Resource Report Resource Website |
Clinical Measurement Ontology (RRID:SCR_003291) | CMO | ontology, data or information resource, controlled vocabulary | An ontology designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs. | obo, phenotype, clinical, measurement, morphology, physiology |
is listed by: SourceForge is listed by: BioPortal is listed by: OBO has parent organization: Medical College of Wisconsin; Wisconsin; USA |
PMID:22654893 | Free, Freely available | nlx_157364 | http://sourceforge.net/projects/phenoonto/ ftp://rgd.mcw.edu/pub/ontology/clinical_measurement/clinical_measurement.obo |
SCR_003291 | 2026-02-16 09:46:11 | 0 | ||||||
|
Niftilib Resource Report Resource Website 1+ mentions |
Niftilib (RRID:SCR_003355) | Niftilib | source code, software toolkit, software library, software resource | Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. nifti-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. Niftilib currently has C, Java, MATLAB, and Python libraries; we plan to add some MATLAB/mex interfaces to the C library in the not too distant future. Niftilib has been developed by members of the NIFTI DFWG and volunteers in the neuroimaging community and serves as a reference implementation of the nifti-1 file format. In addition to being a reference implementation, we hope it is also a useful i/o library. Niftilib code is released into the public domain, developers are encouraged to incorporate niftilib code into their applications, and, to contribute changes and enhancements to niftilib. Please contact us if you would like to contribute additonal functionality to the i/o library. | image data, mri, fmri, brain image, image, brain, neuroimaging |
is related to: NIfTI Data Format Working Group has parent organization: SourceForge |
Free, Available for download, Freely available | nif-0000-32011 | SCR_003355 | The Nifti Libraries, Nifti Libraries | 2026-02-16 09:46:12 | 3 | |||||||
|
Measurement Method Ontology Resource Report Resource Website |
Measurement Method Ontology (RRID:SCR_003373) | MMO | ontology, data or information resource, controlled vocabulary | An ontology designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms. | obo, phenotype, clinical |
is listed by: SourceForge is listed by: BioPortal is listed by: OBO |
PMID:22654893 | Free, Available for download, Freely available | nlx_157468 | http://sourceforge.net/projects/phenoonto/ ftp://rgd.mcw.edu/pub/ontology/measurement_method/measurement_method.obo |
SCR_003373 | 2026-02-16 09:46:00 | 0 | ||||||
|
Mindtouch DekiWiki Resource Report Resource Website 1+ mentions |
Mindtouch DekiWiki (RRID:SCR_003425) | MindTouch | source code, commercial organization, software resource | A web based social authoring and publishing environment that adheres to open standards and RESTful design principals. It provides wiki-like ease of use with a sophisticated web services framework for rapid application development, creating flexible workflows and rapid integration. MindTouch creates a vibrant real-time information fabric by federating content from across enterprise silos, such as CRM, ERP, file servers, email, databases, web services and more. | authoring, publishing, standard, web service, cloud |
is listed by: FORCE11 is listed by: Biositemaps has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: SourceForge |
Free, Freely available | nif-0000-33097 | http://sourceforge.net/projects/dekiwiki/ https://www.force11.org/node/4733 |
SCR_003425 | MindTouch Core, DekiWiki, MindTouch Deki Wiki, Deki Wiki, MindTouch (frmly deki wiki) | 2026-02-16 09:46:12 | 2 | ||||||
|
MIAPA Resource Report Resource Website 1+ mentions |
MIAPA (RRID:SCR_003777) | MIAPA | data or information resource, standard specification, narrative resource | Central hub for resources related to developing and deploying a Minimal Information for a Phylogenetic Analysis (MIAPA) standard. | phylogeny, dna, amino acid sequence |
is listed by: Minimum Information for Biological and Biomedical Investigations is listed by: GitHub is listed by: SourceForge |
PMID:16901231 | nlx_158100 | https://github.com/miapa/miapa/blob/master/checklist/MIAPA-checklist.md http://mibbi.sourceforge.net/projects/MIAPA.shtml |
SCR_003777 | Minimal Information for a Phylogenetic Analysis | 2026-02-16 09:46:07 | 1 | ||||||
|
FastSemSim Resource Report Resource Website 1+ mentions |
FastSemSim (RRID:SCR_006919) | FastSemSim | software resource, software toolkit, software library | A package that implements several semantic similarity measures. It is both a library and an end-user application, featuring an intuitive graphical user interface (GUI). It has been implemented with the aim of being fast, expandable, and easy to use. It allows the user to work with the most updated version of GO database and customizable annotation corpora. It provides a set of logically-organized classes that can be easily exploited to both integrate semantic similarity into different analysis pipelines and extend the library with new measures. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, functional similarity, semantic similarity, graphical user interface, gene ontology, annotation, parse, gene, protein |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Padua; Padua; Italy has parent organization: SourceForge |
Open unspecified license - Free for academic use. GNU GPL license. However, This software is currently unpublished work. You must contact us before using it or its results or any work/app. based on top of it in any published work. | nlx_149309 | SCR_006919 | 2026-02-16 09:46:50 | 6 | ||||||||
|
Adverse Event Ontology Resource Report Resource Website |
Adverse Event Ontology (RRID:SCR_006807) | AEO | ontology, data or information resource, controlled vocabulary | AEO represents the Adverse Event Ontology, a community-driven ontology developed to standardize and integrate data on biomedical adverse events (e.g., vaccine adverse events) and support computer-assisted reasoning. The AEO also can be found in BioPortal, http://bioportal.bioontology.org/ontologies/45534?p=terms | has parent organization: SourceForge | nlx_44108 | SCR_006807 | 2026-02-16 09:46:48 | 0 | ||||||||||
|
Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | software development tool, software application, software development environment, community building portal, software resource, portal, data or information resource | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | NIPY Community | 2026-02-16 09:48:33 | 24 | ||||
|
UnoSeq Resource Report Resource Website 1+ mentions |
UnoSeq (RRID:SCR_005116) | UnoSeq | software resource, software toolkit, software library | A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists. | java, expression profile, next generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20194116 | OMICS_01296 | SCR_005116 | UnoSeq - Expression profiling with next generation sequencing without a reference genome | 2026-02-16 09:46:25 | 1 | |||||||
|
SeqAnt Resource Report Resource Website 1+ mentions |
SeqAnt (RRID:SCR_005186) | SeqAnt | data analysis service, analysis service resource, software resource, production service resource, service resource | A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest. | annotation, dna sequence variant, single base mutation, insertion, deletion, sequencing, mutation, variant, sequence variant, perl, sequence, genome |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA has parent organization: SourceForge |
PMID:20854673 | GNU General Public License, v2 | OMICS_00182 | SCR_005186 | SeqAnt - Sequence Annotator | 2026-02-16 09:46:24 | 2 | ||||||
|
Sequence Read Format Resource Report Resource Website 1+ mentions |
Sequence Read Format (RRID:SCR_000132) | SRF | data or information resource, standard specification, interchange format, narrative resource | A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology. | dna sequence, dna sequencing, interchange format |
is listed by: OMICtools has parent organization: SourceForge |
Public, A C++ implementation of Sequence Read Format is available | OMICS_05130 | SCR_000132 | Sequence Read Format (SRF) | 2026-02-16 09:45:11 | 1 | |||||||
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GMATo Resource Report Resource Website 1+ mentions |
GMATo (RRID:SCR_000165) | software application, data processing software, sequence analysis software, data analysis software, software resource | A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable. | simple sequence repeat, ssr, microsatellite, genomic, marker design, sequence analysis software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23861572 | Free, Available for download, Freely available | OMICS_00106 | SCR_000165 | Genome-wide Microsatellite Analyzing Tool, Genome Microsatellite Analyzing Tool, Genome-wide Microsatellite Analyzing Tool (GMATo) | 2026-02-16 09:45:12 | 1 | |||||||
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BlackOPs Resource Report Resource Website |
BlackOPs (RRID:SCR_000032) | software application, data processing software, sequence analysis software, data analysis software, software resource | Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls. | rna seq, false positive, genome editing, rna editing, mismapped reads | has parent organization: SourceForge | PMID:23935067 | Free, Available for download, Freely available | OMICS_01229 | SCR_000032 | BlackOPs: RNA-Seq Variant Blacklist Tool | 2026-02-16 09:45:10 | 0 | |||||||
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PAZAR Resource Report Resource Website 10+ mentions |
PAZAR (RRID:SCR_005410) | PAZAR | data repository, database, storage service resource, software resource, service resource, data or information resource | Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, target gene, regulatory sequence, transcription factor profile, annotation, sequence, profile, transcription factor binding profile, chip, chip-seq, gene, cis-regulatory element, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of British Columbia; British Columbia; Canada has parent organization: SourceForge |
PMID:18971253 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00540, biotools:pazar | https://bio.tools/pazar | SCR_005410 | 2026-02-16 09:46:27 | 32 | ||||||
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Maqview Resource Report Resource Website |
Maqview (RRID:SCR_005632) | MaqView | software application, data processing software, data visualization software, software resource | A graphical read alignment viewer specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. It is highly efficient in speed, memory and disk usage. Maqview is based on OpenGL and is known to work on both Mac OS X and Linux. Porting to Windows is in principle easy. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License | OMICS_00889, biotools:maqview | https://bio.tools/maqview https://sources.debian.org/src/maqview/ |
SCR_005632 | Mapping and Assembly with Qualities Viewer, M.A.Q Viewer | 2026-02-16 09:46:40 | 0 | |||||
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Brain Networks Resource Report Resource Website 1+ mentions |
Brain Networks (RRID:SCR_005841) | Brain Networks | software application, data processing software, data analysis software, source code, software resource | Brain Networks: Code to perform network analysis on brain imaging data. | brain, imaging, network analysis, brain imaging, neuroimaging | has parent organization: SourceForge | PMID:21031030 | Open unspecified license - GNU General Public License (GPL) | nlx_149364 | SCR_005841 | brainnetworks | 2026-02-16 09:46:41 | 1 | ||||||
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Predictive Networks Resource Report Resource Website |
Predictive Networks (RRID:SCR_006110) | PN | data analysis service, analysis service resource, database, software resource, source code, production service resource, service resource, data or information resource | A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model. | gene interaction network, gene, interaction, gene expression, graph, visualization, gene interaction, gene network, predictive network analysis, model, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: SourceForge |
NLM 1R01LM010129 | PMID:22096235 | Apache License, v2 | nlx_151582, biotools:predictivenetworks | https://bio.tools/predictivenetworks | SCR_006110 | 2026-02-16 09:46:43 | 0 | |||||
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BLESS Resource Report Resource Website 10+ mentions |
BLESS (RRID:SCR_005963) | BLESS | software application, data processing software, sequence analysis software, data analysis software, algorithm resource, software resource | Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory. | c++, next-generation sequencing, bloom-filter, error correction, ngs, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24451628 | GNU General Public License v3 | OMICS_02246, biotools:bless | https://bio.tools/bless | SCR_005963 | BLoom-filter-based Error correction Solution for high-throughput Sequencing reads, BLESS - Bloom-filter-based Error Correction Tool for NGS reads | 2026-02-16 09:46:42 | 45 |
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