Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MultiLoc Resource Report Resource Website 10+ mentions |
MultiLoc (RRID:SCR_003151) | MultiLoc | service resource, data analysis service, software resource, production service resource, analysis service resource | An extensive high-performance subcellular protein localization prediction system that incorporates phylogenetic profiles and Gene Ontology terms to yield higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. A downloadable version of MultiLoc2 for local use is also available. | subcellular localization, protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tubingen; Tubingen; Germany |
PMID:19723330 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01628, biotools:multiloc2 | https://bio.tools/multiloc2 | SCR_003151 | 2026-07-28 09:40:37 | 40 | ||||||
|
Primer3 Resource Report Resource Website 10000+ mentions |
Primer3 (RRID:SCR_003139) | Primer3 | service resource, data analysis service, software resource, production service resource, analysis service resource | Tool used to design PCR primers from DNA sequence - often in high-throughput genomics applications. It does everything from mispriming libraries to sequence quality data to the generation of internal oligos. | primer, primer design, polymerase chain reaction, pcr primer, dna sequence, c, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Primer3Plus is related to: Primer-BLAST has parent organization: University of Tartu; Tartu; Estonia |
NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:22730293 PMID:17379693 DOI:10.1385/1-59259-192-2:365 DOI:10.1385/1-59259-192-2:365 |
Free, Freely available | nlx_156833, OMICS_02325, biotools:primer3 | http://bioinfo.ut.ee/primer3-0.4.0/, http://sourceforge.net/projects/primer3/, http://frodo.wi.mit.edu/primer3, https://bio.tools/primer3, https://sources.debian.org/src/primer3/, https://sources.debian.org/src/primer3/ | SCR_003139 | Primer3web - Pick primers from a DNA sequence, Primer3 - PCR primer design tool, Primer3web | 2026-07-28 09:40:44 | 10957 | ||||
|
Database of Interacting Proteins (DIP) Resource Report Resource Website 100+ mentions |
Database of Interacting Proteins (DIP) (RRID:SCR_003167) | DIP | service resource, data or information resource, data repository, data analysis service, storage service resource, database, production service resource, analysis service resource | Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available. | blast, cellular network, ligand-receptor complex, ligand, network, protein, protein interaction, protein ligand, protein-protein interaction, protein receptor, receptor, sequence, interaction, regulatory pathway, signaling pathway, protein binding, bio.tools, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: NIH Data Sharing Repositories is related to: PSICQUIC Registry is related to: Agile Protein Interactomes DataServer has parent organization: University of California at Los Angeles; California; USA |
NIGMS | PMID:14681454 | Free, Available for download, Freely available | OMICS_01905, nif-0000-00569, r3d100010882, biotools:dip | https://dip.doe-mbi.ucla.edu/dip/Main.cgi, https://bio.tools/dip, https://doi.org/10.17616/R3431F | SCR_003167 | , Database of Interacting Proteins, DIP, Database of Interacting Proteins (DIP) | 2026-07-28 09:40:37 | 153 | ||||
|
Solas Resource Report Resource Website 1+ mentions |
Solas (RRID:SCR_003168) | software application, data analysis software, sequence analysis software, source code, software resource, data processing software | Software package for the statistical language R, devoted to the analysis of next generation short read data of RNA-seq transcripts. It provides predictions of alternative exons in a single condition/cell sample, predictions of differential alternative exons between two conditions/cell samples, and quantification of alternative splice forms in a single condition/cell sample. | r statistical package, rna seq, exon prediction, exon splicing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
Free, Available for download, Freely available | biotools:solas, OMICS_01339 | https://bio.tools/solas | SCR_003168 | 2026-07-28 09:40:38 | 8 | ||||||||
|
DIALIGN Resource Report Resource Website 10+ mentions |
DIALIGN (RRID:SCR_003041) | DIALIGN | service resource, data analysis service, data access protocol, software resource, production service resource, web service, analysis service resource | Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/ | dna, protein, sequence alignment, sequence, alignment, fasta, genome, genomic sequence, homology, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15215344 PMID:23620293 DOI:10.1186/1748-7188-3-6 |
Free, Available for download, Freely available | nif-0000-30417, OMICS_24606, OMICS_00973, biotools:dialign-tx | http://dialign.gobics.de/, https://bio.tools/dialign-tx | https://sources.debian.org/src/dialign-tx/ | SCR_003041 | DIALIGN at GOBICS | 2026-07-28 09:40:36 | 43 | ||||
|
PIRSF Resource Report Resource Website 10+ mentions |
PIRSF (RRID:SCR_003352) | PIRSF | narrative resource, data or information resource, database, standard specification | A SuperFamily classification system, with rules for functional site and protein name, to facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors. The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. There are different PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network. The FTP site provides free download for PIRSF. | protein annotation, classification, protein, superfamily, functional site, protein name, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: UniProtKB has parent organization: Protein Information Resource |
NHGRI U01-HG02712; NSF DBI-0138188; NSF ITR-0205470 |
PMID:19455212 PMID:14681371 |
Free, Freely available | biotools:pirsf, nif-0000-03294, OMICS_01697 | https://bio.tools/pirsf | http://pir.georgetown.edu/pirsf/ | SCR_003352 | PIR SuperFamily, Protein Information Resource SuperFamily | 2026-07-28 09:40:46 | 28 | |||
|
SplicingCompass Resource Report Resource Website 1+ mentions |
SplicingCompass (RRID:SCR_003249) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software for detection of differential splicing between two different conditions using RNA-Seq data. | differential splicing, splicing event, exon removal, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23449093 | Free, Available for download, Freely available | biotools:splicingcompass, OMICS_01340 | https://github.com/KoenigLabNM/SplicingCompass | SCR_003249 | Splicing Compass | 2026-07-28 09:40:45 | 2 | ||||||
|
deFuse Resource Report Resource Website 50+ mentions |
deFuse (RRID:SCR_003279) | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | 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 | 2026-07-28 09:40:45 | 95 | |||||
|
Mouse Phenome Database (MPD) Resource Report Resource Website 100+ mentions |
Mouse Phenome Database (MPD) (RRID:SCR_003212) | MPD | service resource, narrative resource, data or information resource, data repository, database, experimental protocol, storage service resource | Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility. | female, genomic location, genotype, inbred strain, male, mouse strain, phenome, phenotype, qtl, reference data, single-nucleotide polymorphism, strain allele, strain characteristic, strain, trait, gene expression, variation, hypothesis testing, data set, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Special Mouse Strains Resource is related to: Vertebrate Trait Ontology is related to: GenomeMUSter has parent organization: Jackson Laboratory |
NIDA ; NHGRI HG003057; NHLBI HL66611; NIA AG025707; NIA AG038070; NIMH MH071984; NIDA DA028420 |
PMID:24243846 PMID:22102583 PMID:18987003 PMID:17151079 |
Free, Freely available | biotools:mpd, nif-0000-03160, r3d100010101 | https://bio.tools/mpd, https://doi.org/10.17616/R3PC7F | http://www.jax.org/phenome | SCR_003212 | Mouse Phenome Database | 2026-07-28 09:40:38 | 221 | |||
|
Piano Resource Report Resource Website 100+ mentions |
Piano (RRID:SCR_003200) | software application, software resource, data analysis software, data processing software | Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses. | r, omics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chalmers University of Technology; Gothenburg; Sweden has parent organization: Bioconductor |
PMID:23444143 | Free, Available for download, Freely available | OMICS_01558, biotools:piano | https://bio.tools/piano | SCR_003200 | 2026-07-28 09:40:39 | 182 | |||||||
|
GenePattern Resource Report Resource Website 1000+ mentions |
GenePattern (RRID:SCR_003201) | GenePattern | software application, software resource, data analysis software, data processing software | A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. | gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is affiliated with: GenePattern Notebook is related to: TIGRESS has parent organization: Broad Institute |
NCI ; NIGMS |
PMID:16642009 | Free, Freely available | biotools:genepattern, OMICS_01855, nif-0000-30654 | https://bio.tools/genepattern | SCR_003201 | 2026-07-28 09:40:44 | 1078 | |||||
|
Cell Image Library (CIL) Resource Report Resource Website 10+ mentions |
Cell Image Library (CIL) (RRID:SCR_003510) | CIL | service resource, data or information resource, data repository, image repository, database, storage service resource | Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment. | microscopic image repository, microscopic video repository, cell animation repository, bio.tools |
is used by: NIF Data Federation is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Cell Centered Database is related to: Cell Centered Database is related to: OME-TIFF Format is related to: Integrated Manually Extracted Annotation has parent organization: American Society for Cell Biology has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR has parent organization: University of California at San Diego; California; USA is parent organization of: Biological Imaging Methods Ontology |
NIGMS RC2 GM092708 | PMID:34218671 PMID:34218673 |
Free, Freely available | biotools:cellimagelibrary, nif-0000-37639, r3d100011601 | http://www.cellimagelibrary.org/pages/about, https://bio.tools/cellimagelibrary, https://doi.org/10.17616/R3N92J | SCR_003510 | Cell Image Library. CIL, Cell Image Library (CIL) | 2026-07-28 09:40:45 | 19 | ||||
|
Proteomics Identifications (PRIDE) Resource Report Resource Website 500+ mentions |
Proteomics Identifications (PRIDE) (RRID:SCR_003411) | PRIDE | service resource, data or information resource, data repository, database, storage service resource | Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester. | proteomics, protein, peptide, mass spectrometry, annotation, standard, spectra, protein-protein interaction, amino acid, amino acid sequence, post-translational modification, biomart, bio.tools |
is used by: ProteomeXchange is used by: BioSample Database at EBI is recommended by: NIDDK Information Network (dkNET) is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: HUPO Proteomics Standards Initiative is related to: ProteomeXchange has parent organization: European Bioinformatics Institute |
Wellcome Trust WT085949MA; European Union FP7 LSHG-CT-2006-036814; European Union FP7 260558; European Union FP7 262067; European Union FP7 202272; BBSRC BB/I024204/1 |
PMID:23203882 PMID:19662629 |
Free, Available for download, Freely available | nif-0000-03336, biotools:pride, r3d100011515 | https://www.ebi.ac.uk/pride/archive/, https://bio.tools/pride, https://doi.org/10.17616/R3F330 | SCR_003411 | PRoteomics IDEntifications database, PRIDE Archive - proteomics data repository, PRIDE Archive, PRIDE, Proteomics Identifications, Proteomics Identifications (PRIDE), PRoteomics IDEntifications database (PRIDE) | 2026-07-28 09:40:42 | 642 | ||||
|
Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
Ontario Research Fund ; European Molecular Biology Laboratory ; NHGRI P41 HG003751; European Union FP6 ENFIN LSHG-CT-2005-518254; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome, https://doi.org/10.17616/R3V59P | SCR_003485 | Reactome Functional Interaction Network | 2026-07-28 09:40:48 | 4282 | |||||
|
L-Measure Resource Report Resource Website 10+ mentions |
L-Measure (RRID:SCR_003487) | LM | software application, service resource, software resource, data processing software, image processing software, image analysis software | A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux. | neuronal morphology, neuroinformatics, branching analysis, digital reconstruction, analysis, comparison, bio.tools |
is listed by: 3DVC is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Computational Neuroanatomy Group |
Human Brain Project ; NINDS R01 NS39600 |
PMID:18451794 | Public | nif-0000-00003, biotools:l-measure | http://www.nitrc.org/projects/lmeasure, https://bio.tools/l-measure | SCR_003487 | 2026-07-28 09:40:44 | 30 | |||||
|
eTRIKS Resource Report Resource Website 10+ mentions |
eTRIKS (RRID:SCR_003765) | eTRIKS | service resource, data or information resource, organization portal, consortium, portal | Research informatics and analytics platform for the IMI OncoTrack consortium. | data sharing, drug discovery, translational research, informatics, knowledge management, metadata standard, platform, analytics, tool development, bio.tools |
uses: tranSMART is used by: U-BIOPRED is used by: Predict-TB is used by: OncoTrack is used by: ABIRISK is used by: RA MAP is listed by: Consortia-pedia is listed by: Debian is listed by: bio.tools is related to: Roche is related to: Janssen Research and Development is related to: Merck is related to: Pfizer Animal Genetics is related to: Imperial College London; London; United Kingdom is related to: French National Center for Scientific Research is related to: Clinical Data Interchange Standards Consortium is related to: University of Luxembourg; Luxembourg; Luxembourg is related to: IDBS is related to: BioSci Consulting is related to: TraIT is related to: EMIF is related to: Open PHACTS has parent organization: Imperial College London; London; United Kingdom |
Innovative Medicines Initiative ; EFPIA |
PMID:29482119 | biotools:eTRIKS, nlx_158034 | https://bio.tools/eTRIKS | SCR_003765 | European Translational Information and Knowledge Management Services, European Translational Information & Knowledge Management Services | 2026-07-28 09:40:51 | 10 | |||||
|
QuPath Resource Report Resource Website 1000+ mentions |
QuPath (RRID:SCR_018257) | software application, image analysis software, software resource, data processing software | Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images. | Digital pathology, image analysis, whole slide image, batch processing, tissue image, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Queens University Belfast; Ireland; United Kingdom |
Invest Northern Ireland ; Experimental Cancer Medicine Centre Network ; Sean Crummey Memorial Fund ; Tom Simms Memorial Fund ; Friends of the Cancer Centre ; Cancer Research UK Accelerator |
PMID:29203879 | Free, Available for download, Freely available | biotools:qupath | https://bio.tools/qupath | SCR_018257 | 2026-07-27 09:35:42 | 1590 | ||||||
|
GeSeq Resource Report Resource Website 100+ mentions |
GeSeq (RRID:SCR_017336) | software application, service resource, software resource, data processing software | Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes. | rapid, accurate, annotation, organelle, genome, chloroplast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Human Frontier Science Program ; Max Planck Society ; German Science Foundation |
PMID:28486635 | Free, Freely available | biotools:geseq | https://bio.tools/geseq | SCR_017336 | 2026-07-27 09:35:31 | 375 | ||||||
|
SeWeR - SEquence analysis using WEb Resources Resource Report Resource Website |
SeWeR - SEquence analysis using WEb Resources (RRID:SCR_004167) | service resource, data or information resource, software resource, topical portal, portal | Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C. | nucleic acid, protein, pcr, alignment, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Centre for Cellular and Molecular Biology; Hyderabad; India |
PMID:11395442 | biotools:sewer, nlx_18981 | https://bio.tools/sewer | SCR_004167 | SEquence analysis using WEb Resources, SeWeR | 2026-07-28 09:40:55 | 0 | |||||||
|
BSRD Resource Report Resource Website 10+ mentions |
BSRD (RRID:SCR_004249) | BSRD | service resource, data or information resource, data repository, database, storage service resource | A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets. | srna target, srna, small regulatory non-coding rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23203879 | Acknowledgement requested, The community can contribute to this resource | biotools:bsrd, OMICS_01533 | https://bio.tools/bsrd | SCR_004249 | BSRD - Bacterial Small Regulatory RNA Database, Bacterial Small Regulatory RNA Database | 2026-07-28 09:40:55 | 29 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the SPARC SAWG Resources search. From here you can search through a compilation of resources used by SPARC SAWG and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that SPARC SAWG has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on SPARC SAWG then you can log in from here to get additional features in SPARC SAWG such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into SPARC SAWG you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
