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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Bridger Resource Report Resource Website 1+ mentions |
Bridger (RRID:SCR_017039) | data analysis software, data processing software, software application, software resource | Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcripto, assembler, RNAseq, data, short, read, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCRR P20 RR016460; NIGMS P20 GM103429; NSFC 61272016; NSFC 61432010 |
PMID:25723335 | Free, Available for download, Freely available | biotools:bridger, OMICS_07535 | https://bio.tools/bridger | SCR_017039 | 2026-09-12 12:58:47 | 6 | ||||||
|
nanoPOTS Resource Report Resource Website 1+ mentions |
nanoPOTS (RRID:SCR_017129) | instrument resource | Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes. | nanodroplet, processing, platform, quantitative, proteome, profiling, analysis, mammalian, cell, small, volume | has parent organization: Pacific Northwest National Laboratory | JDRF ; NCI R33 CA225248; NIBIB R21 EB020976; NIDDK DP3 DK110844; NIDDK UC4 DK104167; NIGMS P41 GM103493; NIH Office Of The Director S10 OD016350 |
PMID:29491378 | SCR_017129 | 2026-09-12 12:58:48 | 1 | |||||||||
|
PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | data access protocol, data or information resource, data repository, service resource, software resource, storage service resource, web service | Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents. | repository, software, targeted, mass, spectrometry, data, proteomic, quantitative, viewing, sharing, disseminating, result, , bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA works with: Skyline |
NHGRI U54 HG008097; NIGMS R01 GM103551; NIGMS R01 GM121696; NIH R01 AR071762; University of Washington Proteomics Resource |
DOI:10.1074/mcp.RA117.000543 | Free, Freely available | biotools:panorama | https://bio.tools/panorama | SCR_017136 | 2026-09-12 12:58:49 | 0 | ||||||
|
CWL-Airflow Resource Report Resource Website 1+ mentions |
CWL-Airflow (RRID:SCR_017196) | CWL DAG | data processing software, software application, software resource, workflow software | Software Python package to extend Airflow functionality with Common Workflow Language support. Lightweight pipeline manager supporting Common Workflow Language. Can be used to run workflows on standalone MacOS/Linux servers, on clusters, or on cloud platforms. | airflow, common workflow language, cwl, pipeline, workflow, docker | is listed by: OMICtools | NCATS UL1 TR001425; NIGMS DP2 GM119134 |
DOI:10.1101/249243 DOI:10.1093/gigascience/giz084 |
Free, Available for download, Freely available | OMICS_26560 | SCR_017196 | CWL-Airflow v 1.0.16, Common Workflow Language-Airflow | 2026-09-12 12:58:49 | 3 | |||||
|
FoXS Resource Report Resource Website 10+ mentions |
FoXS (RRID:SCR_017269) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for computing theoretical scattering profile of structure and fitting of experimental profile. Computes SAXS profile of given atomistic model and fits it to experimental profile. Used for structural modeling applications with small angle X-ray scattering data. | computing, theoretical, scattering, profile, structure, fitting, small, angle, X ray, data | has parent organization: University of California at San Francisco; California; USA | Lawrence Berkeley National Lab IDAT program ; NCRR U54 RR022220; NIGMS P41 GM109824; NIGMS R01 GM083960; NIGMS R01 GM105404; Rinat (Pfizer) Inc. ; Weizmann Institute Advancing Women in Science |
PMID:23972848 PMID:27151198 |
Free, Available for download, Freely available | SCR_017269 | Fast X-Ray Scattering | 2026-09-12 12:58:50 | 24 | |||||||
|
Protein Cross-Linking Database Resource Report Resource Website 1+ mentions |
Protein Cross-Linking Database (RRID:SCR_021027) | ProXL, proxl, Protein XL | data access protocol, data or information resource, database, software resource, web service | Web application and database designed for sharing, visualizing, and analyzing protein cross-linking mass spectrometry data with emphasis on structural analysis and quality control. Includes public and private data sharing capabilities, project based interface designed to ensure security and facilitate collaboration among multiple researchers. Used for private collaboration and public data dissemination. | Protein cross-linking, mass spectrometry data, analysis, visualization, sharing, structural analysis, quality control, private collaboration, public data dissemination |
uses: Kojak has parent organization: University of Washington; Seattle; USA |
NIGMS P41 GM103533; University of Washington Proteomics Resource |
PMID:27302480 | Free, Available for download, Freely available | https://github.com/yeastrc/proxl-web-app | SCR_021027 | Protein XL Database | 2026-09-12 12:59:49 | 5 | |||||
|
Kojak Resource Report Resource Website 1+ mentions |
Kojak (RRID:SCR_021028) | data analysis software, data processing software, software application, software resource | Software tool for identification of cross-linked peptides from mass spectra. Used for analysis of chemically cross-linked protein complexes. Used to analyze both novel and existing data sets. | Mass spectra, cross-linked peptides identification, protein complexes analysis, novel data analysis, existing data analysis |
is used by: Protein Cross-Linking Database has parent organization: University of Washington; Seattle; USA |
National Science Foundation MRI grant 0923536; NCRR S10 RR027584; NIGMS P41 GM103533; NIGMS P50 GM076547; NIGMS P50 GM08722150 |
PMID:25812159 | Free, Available for download, Freely available | SCR_021028 | 2026-09-12 12:59:49 | 4 | ||||||||
|
Modeling Infectious Disease Agents Study online portal for COVID-19 Resource Report Resource Website 1+ mentions |
Modeling Infectious Disease Agents Study online portal for COVID-19 (RRID:SCR_018281) | data or information resource, portal, topical portal | Portal for COVID-19 modeling research. Public access data collections with documented metadata.Computational models to study transmission dynamics of broad range of infectious diseases. | COVID-19, COVID-19 data, modeling research, public data, metadata, infectious disease | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | NIGMS | Free, Freely available | https://github.com/midas-network/COVID-19 | SCR_018281 | MIDAS online portal for COVID-19 | 2026-09-12 12:58:59 | 4 | ||||||
|
Recombination Detection Program Resource Report Resource Website 500+ mentions |
Recombination Detection Program (RRID:SCR_018537) | RDP | data analysis software, data processing software, software application, software resource | Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes. | DNA sequence, alignment, phylogenetic tree, nucleotide analysis, sequence data analysis, genetic recombination identification, DNA sequence alignment, recombinant pattern analysis, virus genome | Carnergie Corporation ; European Research Council ; Fund for Scientific Research Flanders ; NIAID AI090970; NIAID AI100665; NIGMS U01 GM110749; Polyomielitis Research Foundation ; South African Centre of High Performance Computing ; South African National Research Foundation ; Spanish Ministry of Science and Education ; University of Cape Town ; Wellcome Trust |
PMID:27774277 PMID:20798170 |
Free, Available for download, Freely available | SCR_018537 | Recombination Detection Program, RDP4, RDP3 | 2026-09-12 12:59:02 | 507 | |||||||
|
BcForms Resource Report Resource Website |
BcForms (RRID:SCR_018654) | data access protocol, software resource, software toolkit, web service | Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models. | Molecular structure description, molecular complex, atom, bond, protein, complex, modification, crosslinked residue, semantic meaning description, bio.tools |
is used by: BpForms is used by: ObjTables is listed by: Debian is listed by: bio.tools is related to: BpForms |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bcforms | https://bio.tools/bcforms | SCR_018654 | 2026-09-12 12:59:04 | 0 | ||||||
|
Datanator Resource Report Resource Website 1+ mentions |
Datanator (RRID:SCR_018651) | application programming interface, data access protocol, data or information resource, database, software resource, web application | Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition. | Data discovering, cell model, model cellular biochemistry, modeling specific organism, specific environmental condition, genomics, proteomics, epigenomics, metabolomics, system biology, bio.tools |
uses: BpForms is listed by: Debian is listed by: bio.tools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NIBIB P41 EB023912; NIGMS R35 GM119771 |
DOI:10.1101/2020.08.06.240051 | Free, Freely available | biotools:datanator, r3d100013339 | https://github.com/karrlab/datanator, https://bio.tools/datanator, https://doi.org/10.17616/R31NJMSB | SCR_018651 | 2026-09-12 12:59:04 | 2 | ||||||
|
Edtsurf Resource Report Resource Website 1+ mentions |
Edtsurf (RRID:SCR_016083) | data processing software, data visualization software, software application, software resource, source code | Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening. | construct, triangulate, surface, macromolecule, van der Waals, solvent, accessible, molecular, cavities, program |
is listed by: Debian is listed by: OMICtools |
NIGMS GM083107; NIGMS GM084222; NSF 0746198; the Alfred P. Sloan Foundation |
PMID:19956577 | Free, Available for download, Freely available | OMICS_16795 | https://sources.debian.org/src/edtsurf/ | SCR_016083 | EDTSurf: Quick and accurate construction of macromolecular surfaces | 2026-09-12 12:58:35 | 4 | |||||
|
fermi-lite Resource Report Resource Website 1+ mentions |
fermi-lite (RRID:SCR_016112) | algorithm resource, alignment software, data processing software, image analysis software, software application, software resource, standalone software | Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling. | assembling, short, read, small, region, sequencing, retain, heterozygous, event, diploid, variant, calling | is related to: Illumina | NHGRI U54 HG003037; NIGMS GM100233 |
PMID:26220959 | Free, Available for download | SCR_016112 | FermiKit, Fml-asm | 2026-09-12 12:58:35 | 4 | |||||||
|
Glam2 Resource Report Resource Website 100+ mentions |
Glam2 (RRID:SCR_016129) | Glam2 | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets. | motif, analysis, sequence, find, amino acid, nucleotide, set, alignment, gapped, recurring, variable, letnght, pattern, DNA, protein, output, discovery, dataset | is related to: MEME Suite - Motif-based sequence analysis tools | NIGMS R01 GM103544 | PMID:18437229 | Free, Freely available for non-commercial use | http://meme-suite.org/ | SCR_016129 | Glam2: Gapped local alignment of motifs 2 | 2026-09-12 12:58:35 | 203 | |||||
|
Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | data or information resource, data processing software, data visualization software, database, software application, software resource, web application | Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources. | gene, protein, visualization, search, prediction, functional | BD2K-LINCS Data Coordination and Integration Center ; Illuminating the Druggable Genome ; Knowledge Management Center ; NCI U54 CA189201; NHLBI U54 HL127624; NIGMS R01 GM098316 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | 2026-09-12 12:58:36 | 142 | |||||||||
|
ASHLAR Resource Report Resource Website 1+ mentions |
ASHLAR (RRID:SCR_016266) | Ashlar | data processing software, image processing software, software application, software resource | Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration. | cycif, registration, software, python, cyclic, immunofluorescence, fluorescence, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS P50 GM107618 | Free, Available for download | biotools:ASHLAR | https://bio.tools/ASHLAR | SCR_016266 | ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration | 2026-09-12 12:58:37 | 6 | |||||
|
lilikoi Resource Report Resource Website 1+ mentions |
lilikoi (RRID:SCR_016361) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction. | personalized, medicine, metabolomics, data, classification, clustering, biomarker, prediction, algorithm, calculating, microarray, enrichment |
is listed by: OMICtools is related to: University of Hawaii; Hawaii; USA |
NICHD R01 HD084633; NIEHS K01 ES025434; NIGMS GM103457; NLM R01 LM012373 |
DOI:https://doi.org/10.1101/283408 | Free, Available for download, Freely available | https://omictools.com/lilikoi-tool | SCR_016361 | 2026-09-12 12:58:38 | 3 | |||||||
|
EcoGene Resource Report Resource Website 50+ mentions |
EcoGene (RRID:SCR_002437) | ECK, ECOGENE, ECOGENE G | data or information resource, database | Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries. | life sciences, genomics, proteomics, gene, gene expression, genetics, protein, protein binding, protein-protein interaction, membrane, rna, dna, structure, function, functional annotation, annotation, blast, FASEB list |
is listed by: re3data.org is related to: RefSeq is related to: Colibri has parent organization: University of Miami Miller School of Medicine; Florida; USA |
NIH ; Lucille P. Markey Foundation ; NIGMS 5-R01-GM58560-05 |
PMID:23197660 PMID:10592181 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02784, r3d100010546 | https://doi.org/10.17616/R3KP5V | http://bmb.med.miami.edu/ http://bmb.med.miami.edu/EcoGene/EcoWeb/ http://www.ecogene.org/old/ | SCR_002437 | EcoGene Database of Escherichia coli Sequence and Function | 2026-09-12 01:01:25 | 58 | |||
|
EcoCyc Resource Report Resource Website 500+ mentions |
EcoCyc (RRID:SCR_002433) | EcoCyc, EcoCyc REF | data or information resource, database | Database for the bacterium Escherichia coli K-12 MG1655, the EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms. | genome, metabolic pathway, transcription, transporters, escherichia coli, transcriptional regulation, metabolism, pathway, FASEB list |
uses: Pathway Tools is used by: NIF Data Federation is listed by: OMICtools is listed by: BioCyc is related to: MultiFun is related to: BioCyc is related to: BioCyc is related to: AmiGO is related to: NCBI BioSystems Database is related to: Pathway Tools has parent organization: Stanford Research Institute International |
NCRR ; NIGMS GM077678; NIGMS GM71962 |
PMID:23143106 PMID:21097882 |
Free, Freely available | OMICS_01645, nif-0000-02783, r3d100011277 | https://doi.org/10.17616/R34K99 | SCR_002433 | EcoCyc REF | 2026-09-12 01:01:25 | 511 | ||||
|
Allopathfinder Resource Report Resource Website |
Allopathfinder (RRID:SCR_002702) | AlloPathFinder | software application, software resource, source code | Software application and code base that allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space. The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins. It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or "walking" of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. They are investigating which residues are likely to participate in allosteric communication pathways. The application is a collection of C++/QT code, suitable for reproducing the computational results of the paper. (PMID 17900617) In addition, they provide input and alignment information to reproduce Figure 3 (a key figure) in the paper. Examples provided will show users how to use AlloPathFinder with other protein families, assumed to exhibit an allosteric communication. To run the application a multiple sequence alignment of representative proteins from the protein family is required along with at least one protein structure. | allosteric communication, allostery, allosteric, pathway, protein, residue, prediction, myosin, computational model, protein model, structure-based protein classification, protein classification, myosin allosteric communication |
is listed by: Biositemaps has parent organization: Simtk.org |
NIH Roadmap for Medical Research ; Jane Coffin Childs Memorial Fund ; NIGMS U54 GM072970; NIGMS GM33289 |
PMID:17900617 | Free, Available for download, Freely available | nif-0000-23327 | SCR_002702 | Predicting allosteric communication in myosin via a conserved residue pathway | 2026-09-12 01:01:26 | 0 |
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
