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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
LegumeIP
 
Resource Report
Resource Website
10+ mentions
LegumeIP (RRID:SCR_008906) LegumeIP data analysis service, database, service resource, production service resource, data or information resource, analysis service resource LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression. gene function, genome evolution, legume, gene, genome, plant, genomics, transcriptomic, gene annotation, gene family, synteny, gene expression, blast, genomic sequence, microarray, rna-seq, comparative genomics, bio.tools is listed by: 3DVC
is listed by: Debian
is listed by: bio.tools
is related to: UniProt
is related to: InterProScan
is related to: Gene Ontology
is related to: KEGG
has parent organization: Samuel Roberts Noble Foundation
Samuel Roberts Noble Foundation ;
NSF ABI-0960897
PMID:22110036 biotools:legumeip, nlx_151455 https://bio.tools/legumeip SCR_008906 LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes, LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes 2026-02-15 09:19:55 19
Neural Decoding Toolbox
 
Resource Report
Resource Website
10+ mentions
Neural Decoding Toolbox (RRID:SCR_009012) NDT software application, data processing software, software resource, software toolkit, data analysis software Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations. population decoding, neuron, analysis, matlab, data analysis, machine learning, multivariate pattern analysis, neural decoding has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; DARPA ;
IPTO ;
DSO ;
AFSOR-THRL ;
Adobe Systems ;
Honda Research Institute USA ;
King Abdullah University of Science and Technology ;
NEU ;
Sony ;
Eugene McDermott Foundation ;
NSF 0640097;
NSF 0827427;
NSF FA8650-05-C-7262
PMID:23734125 Acknowledgement requested, Account required nlx_152729 SCR_009012 2026-02-15 09:20:00 18
Databrary
 
Resource Report
Resource Website
10+ mentions
Databrary (RRID:SCR_010471) Databrary portal, database, software resource, service resource, storage service resource, data repository, project portal, data or information resource, software repository Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data. behavior, development, data, sharing, audio track, video is listed by: re3data.org
is related to: Datavyu
is related to: Datavyu
has parent organization: New York University; New York; USA
has parent organization: Pennsylvania State University
NSF BCS-1238599;
NICHD U01 HD076595
Restricted nlx_157733 https://github.com/databrary SCR_010471 2026-02-15 09:20:17 13
Brain Observatory
 
Resource Report
Resource Website
Brain Observatory (RRID:SCR_010641) Brain Observatory portal, video resource, service resource, storage service resource, data or information resource, biospecimen repository, material storage repository, topical portal Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health. human, brain, visual cortex, neuroimaging has parent organization: University of California San Diego School of Medicine; California; USA Human immunodeficiency virus, NeuroAIDS, AIDS, Amnesia NIMH ;
NSF ;
The Dana Foundation ;
NEI
Public nlx_69083 http://thebrainobservatory.ucsd.edu/ SCR_010641 The Brain Observatory 2026-02-15 09:20:20 0
GRASSIUS
 
Resource Report
Resource Website
10+ mentions
GRASSIUS (RRID:SCR_012999) GRASSIUS data analysis service, database, service resource, storage service resource, data repository, production service resource, data or information resource, analysis service resource A public resource composed of a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. As knowledge on the interactions of transcription factors (TFs) and cis-regulatory elements in the promoters of the genes that they regulate continues to accumulate, the information is acquired by GRASSIUS, either through contributions by the community, or by literature analysis. The overarching objective of GRASSIUS is to provide a one-stop resource that will facilitate research and communication within the plant community with regards to genome-wide regulation of gene expression processes. transcription factor, coregulator, promoter sequence, transcription factor orf clone, blast, genome browser is listed by: OMICtools
has parent organization: Ohio State University; Ohio; USA
NSF PMID:18987217 Free OMICS_00555 SCR_012999 Grass Regulatory Information Server 2026-02-15 09:20:37 30
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
 
Resource Report
Resource Website
5000+ mentions
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) RCSB PDB database, service resource, storage service resource, data repository, data or information resource Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results. 3-dimensional, annotation, molecule, nucleic acid, protein, visualization, sequence, function, macromolecule, ligand, model, dna, x-ray crystallography, ribosome, structure, oncogene, nucleic acids, molecular structure, cryomicroscopy, gold standard, FASEB list is used by: Structural Genomics Consortium
is used by: Ligand Expo
is used by: DARC - Database for Aligned Ribosomal Complexes
is used by: FireDB
is used by: Protein Data Bank Bind Database
is used by: Protein Data Bank Site
is used by: NIF Data Federation
is used by: ChannelPedia
is used by: MobiDB
is used by: BALBES
is used by: Structural Antibody Database
is used by: BioLiP
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: re3data.org
is affiliated with: EMDataResource.org
is affiliated with: ConSurf Database
is related to: pdb-data
is related to: PDB2MultiGif
is related to: GlyProt
is related to: pdb-care
is related to: pdb2linucs
is related to: GlyVicinity
is related to: GlyTorsion
is related to: GlySeq
is related to: AffinDB
is related to: StatAlign
is related to: Community Structure-Activity Resource
is related to: Binding MOAD
is related to: ConSurf Database
is related to: glycosciences.de
is related to: DOMINE: Database of Protein Interactions
is related to: Jenalib: Jena Library of Biological Macromolecules
is related to: SynSysNet
is related to: EMDataResource.org
is related to: PDBe - Protein Data Bank in Europe
is related to: TFinDIT
is related to: HOLLOW
is related to: ccPDB - Compilation and Creation of datasets from PDB
is related to: DOMMINO - Database Of MacroMolecular INteractiOns
is related to: InterEvol database
is related to: Polbase
is related to: PoSSuM
is related to: ProtChemSI
is related to: RNA CoSSMos
is related to: PDBsum
is related to: Worldwide Protein Data Bank (wwPDB)
is related to: canSAR
is related to: CAPS Database
is related to: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING
is related to: Combinatorial Extension (CE)
is related to: Metalloprotein Site Database
is related to: PDBj - Protein Data Bank Japan
is related to: Statistical Torsional Angles Potentials of NMR Refinement Database
is related to: Metalloprotein Ligand Interaction Database
is related to: CARP
is related to: PDBTM
is related to: RNA FRABASE - RNA FRAgments search engine and dataBASE
is related to: AmiGO
is related to: ConsensusPathDB
is related to: Biological Magnetic Resonance Data Bank (BMRB)
is related to: DNA DataBank of Japan (DDBJ)
is related to: FlyMine
is related to: NCBI Protein Database
is related to: NCBI Nucleotide
is related to: FunTree
is related to: IndelFR - Indel Flanking Region Database
is related to: NMR Restraints Grid
is related to: Enzyme Structures Database
is related to: Electron Microscopy Data Bank at PDBe (MSD-EBI)
is related to: Worldwide Protein Data Bank (wwPDB)
is related to: DNA DataBank of Japan (DDBJ)
is related to: PDBe - Protein Data Bank in Europe
is related to: MINAS - Metal Ions in Nucleic AcidS
is related to: PDBj - Protein Data Bank Japan
has parent organization: University of California at San Diego; California; USA
has parent organization: Rutgers University; New Jersey; USA
is parent organization of: RCSB PDB Software Tools
is parent organization of: Protein Data Bank Markup Language
is parent organization of: Ligand Expo
works with: CellPhoneDB
NIH ;
DOE ;
NSF DBI-1338415
PMID:12037327 Public, Acknowledgement requested nif-0000-00135, SCR_017379 http://www.rcsb.org
http://www.pdb.org
http://www.rcsb.org/pdb/ SCR_012820 RCSB, Research Collaboratory for Structural Bioinformatics Protein Data Bank, The Protein Data Bank, PDB, Protein Databank, RCSB Protein Data Bank, Protein Data Bank 2026-02-15 09:20:36 9870
HDBIG
 
Resource Report
Resource Website
HDBIG (RRID:SCR_014120) software application, data processing software, software resource, image analysis software, software toolkit A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association. image analysis software, genomics, imaging, joint analysis, toolkit, sparse association, sparse regression is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Indiana University; Indiana; USA
NLM R01 LM011360;
NSF IIS-1117335
http://www.iu.edu/~hdbig/ SCR_014120 High Dimensional Brain Imaging Genomics Toolkit 2026-02-15 09:20:55 0
Wisconsin Cortical Thickness Analysis (CTA) Toolbox
 
Resource Report
Resource Website
Wisconsin Cortical Thickness Analysis (CTA) Toolbox (RRID:SCR_014180) software application, data processing software, software resource, software toolkit, data analysis software A Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. It is used for multi-resolutional analysis of such cortical thickness signals and detecting group differences. It is based on the Spectral Graph Wavelet Transform (SGWT) toolbox and provides plug and play methods for deriving Wavelet Multiscale Descriptor (WMD), cortical thickness smoothing using SGWT, Multivariate General Linear Model (MGLM), and False Discovery Rate (FDR). matlab, software toolkit, cortical thickness signal, data analysis software uses: FreeSurfer
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
Wisconsin Partnership Program ;
NIA R01AG040396;
NIA R01AG021155;
NSF RI 1116584;
NSF CAREER 1252725;
UW ADRC NIA P50 AG033514;
UW ICTR NCRR 1UL1RR025011;
NIA P30 AG010129;
NIA K01 AG030514
http://pages.cs.wisc.edu/~wonhwa/code/CTA_toolbox.html
http://pages.cs.wisc.edu/~wonhwa/project/ctdiscrim.html
SCR_014180 2026-02-15 09:20:39 0
NeuroRD
 
Resource Report
Resource Website
10+ mentions
NeuroRD (RRID:SCR_014769) software application, simulation software, software resource Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways. simulation software, simulator, java, neuronal signaling pathway, neuron HFSP ;
NIMH K21-MH01141;
NSF IBN 0077509;
CRCNS program R01 AA16022;
CRCNS program AA18066
Available for download https://github.com/neurord/stochdiff/releases SCR_014769 2026-02-15 09:20:46 13
MITE-Hunter
 
Resource Report
Resource Website
1+ mentions
MITE-Hunter (RRID:SCR_020946) software application, sequence analysis software, data processing software, software resource, data analysis software Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences. Class 2 non-autonomous transposable element, genes non-coding regions, genome evolution, coding sequence, genomic DNA data sets, NSF 0607123 PMID:20880995 Free, Available for download, Freely available https://github.com/jburnette/MITE-Hunter SCR_020946 Miniature Inverted repeat Transposable Elements Hunter 2026-02-15 09:22:23 5
Rcorrector
 
Resource Report
Resource Website
10+ mentions
Rcorrector (RRID:SCR_022011) software application, data processing software, data analysis software, software resource Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads. RNA-seq, k-mer, random sequencing errors correction, kmer based error correction, RNA-seq data, sequencing data, nonuniform read coverage, Illumina RNAseq reads error correction NSF ABI1159078;
NSF ABI1356078
DOI:10.1186/s13742-015-0089-y Free, Available for download, Freely available SCR_022011 RNA-seq error CORRECTOR 2026-02-15 09:22:45 32
ReproNim/containers
 
Resource Report
Resource Website
1+ mentions
ReproNim/containers (RRID:SCR_018467) portal, software resource, training material, software toolkit, data or information resource, narrative resource, knowledge environment resource, workflow Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments. Containerized environment, reproducible neuroimaging, ReproNim, neuroimaging, dataset, DataLad, imaging, data is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) NIBIB P41 EB019936;
NSF 1429999;
German Federal Ministry of Education and Research
Free, Freely available https://github.com/ReproNim/containers SCR_018467 2026-02-15 09:21:37 1
CohortMethod
 
Resource Report
Resource Website
10+ mentions
CohortMethod (RRID:SCR_018511) software application, data visualization software, data processing software, software resource, data analysis software Software R package for performing new user cohort studies in observational database in OMOP Common Data Model. Cohort study, observational database, OMOP Common Data Model, data, drugs, diagnosis, procedure, age, comorbidity index, data visualization NSF IIS 1251151 Free, Available for download, Freely available SCR_018511 2026-02-15 09:21:38 10
BioSimulations
 
Resource Report
Resource Website
BioSimulations (RRID:SCR_018733) web application, software resource Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell. Sharing, reusing, biomodel, simulation, visualization, simulation result, modeling framework support, simulation tool support, model format support, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA
has parent organization: University of Connecticut; Connecticut; USA
NIBIB P41 EB023912;
NSF ;
NIGMS
Restricted biotools:biosimulations https://bio.tools/biosimulations SCR_018733 2026-02-15 09:22:23 0
DiANNA
 
Resource Report
Resource Website
10+ mentions
DiANNA (RRID:SCR_018529) software resource, data access protocol, web service, service resource, production service resource, analysis service resource Neural network and web server, which determines cysteine oxidation state and disulfide connectivity of protein, given only its amino acid sequence. Used to predict disulfide connectivity topology. Predicts which half-cystines are covalently bound to which other half-cystines. DiANNA 1.1 is extension of DiANNA web server for ternary cysteine classification. Ternary cysteine classification, cysteine oxidation, disulfide protein connectivity, amino acid sequence, predict disulfide connectivity, connectivity topology, cysteine covalent bound, NSF DBI 0543506;
Boston College
PMID:16844987
PMID:15980459
Free, Freely available http://bioinformatics.bc.edu/clotelab/DiANNA/ SCR_018529 DiANNA 1.1 2026-02-15 09:22:15 47
BpForms
 
Resource Report
Resource Website
BpForms (RRID:SCR_018653) web service, data access protocol, software toolkit, software resource Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. Molecular structure description, DNA, RNA, protein, modification, epigenetics, transcriptomics, post transcriptional modification, post translational modification, bio.tools uses: BcForms
is used by: ObjTables
is used by: Datanator
is listed by: Debian
is listed by: bio.tools
is related to: BcForms
is related to: ObjTables
NIBIB P41 EB023912;
NSF 1649014;
NIGMS R35 GM119771
PMID:32423472 Free, Freely available biotools:bpforms https://bio.tools/bpforms SCR_018653 2026-02-15 09:22:15 0
ObjTables
 
Resource Report
Resource Website
ObjTables (RRID:SCR_018652) data management software, software application, data processing software, software resource, software toolkit Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort. Creating reusable dataset, combining spreadsheet with schema, spreadsheet, table, supplementary material, schema, object relational map, validation, bio.tools uses: BpForms
uses: BcForms
is listed by: bio.tools
is listed by: Debian
is related to: BpForms
NIBIB P41 EB023912;
NSF 1649014;
NIGMS R35 GM119771
Free, Freely available biotools:objtables https://bio.tools/objtables SCR_018652 2026-02-15 09:22:22 0
DoubletFinder
 
Resource Report
Resource Website
500+ mentions
DoubletFinder (RRID:SCR_018771) software application, data processing software, data analysis software, software resource Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data. Doublet detection in single cell RNA, single cell RNA, doublet detection, RNA sequencing data, gene expression data, artificial nearest neighbors is related to: Seurat
has parent organization: University of California at San Francisco; California; USA
Department of Defense Breast Cancer Research Program ;
NICHD DP2 HD080351;
NSF MCB 1330864;
UCSF Center for Cellular Construction ;
NSF Science and Technology Center ;
Damon Runyon Cancer Research Foundation
PMID:30954475 Free, Available for download, Freely available SCR_018771 2026-02-15 09:21:42 920
ROSIE
 
Resource Report
Resource Website
1+ mentions
ROSIE (RRID:SCR_018764) ROSIE data access protocol, web application, application programming interface, software resource Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community. Web interface for Rosetta, Rosetta online server, Rosetta application serverification, Rosetta user interface works with: Rosetta NIGMS R01 GM073151;
NIGMS R01 GM07822;
NIGMS R21 GM102716;
NCRR R00 RR024107;
NCI U54 CA143907;
NEI PN2 EY016586;
NIGMS T32 GM 88118;
Taiwan Governmental Scholarship for Study Abroad ;
Howard Hughes Medical and Institute International Student Research Fellowship ;
NSF
PMID:23717507 Restricted https://rosie.rosettacommons.org/ SCR_018764 Rosetta Online Server that Includes Everyone 2026-02-15 09:22:18 7
datasets.datalad.org
 
Resource Report
Resource Website
1+ mentions
datasets.datalad.org (RRID:SCR_019089) data set, service resource, storage service resource, data repository, data or information resource DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data. Version control system, data distribution, super dataset, DataLad dataset, neural data is related to: DataLad NSF 1429999;
NSF 1912266;
NIBIB P41 EB019936
Free, Freely available https://www.datalad.org/datasets.html SCR_019089 2026-02-15 09:21:47 8

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