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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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REDfly Regulatory Element Database for Drosophilia Resource Report Resource Website 10+ mentions |
REDfly Regulatory Element Database for Drosophilia (RRID:SCR_006790) | REDfly | data or information resource, data repository, database, service resource, storage service resource | Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome. | transcriptional cis-regulatory module, transcription factor binding site, dna sequence, gene, expression pattern, genome, gene expression, transcription factor, cis-regulatory module, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Drosophila anatomy and development ontologies is related to: FlyMine has parent organization: University at Buffalo; New York; USA |
NIGMS U24 GM144232; NSF EF0843229 |
PMID:20965965 PMID:18039705 PMID:16303794 |
Acknowledgement requested | OMICS_01870, biotools:redfly, nif-0000-03393 | https://bio.tools/redfly | SCR_006790 | SciCrunch Registry | Regulatory Element Database for Drosophilia, Regulatory Element Database | 2026-10-17 01:26:42 | 15 | ||||
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Open Archives Initiative - Object Reuse and Exchange Initiative Resource Report Resource Website 1+ mentions |
Open Archives Initiative - Object Reuse and Exchange Initiative (RRID:SCR_006982) | OAI-ORE, OAI ORE | data or information resource, narrative resource, standard specification | Initiative which defines standards for the description and exchange of aggregations of Web resources. The intent of the effort is to develop standards that generalize across all web-based information including the increasing popular social networks of web 2.0. The goal of these standards is to expose the rich content in these aggregations (sometimes called compound digital objects, they may combine distributed resources with multiple media types including text, images, data, and video) to applications that support authoring, deposit, exchange, visualization, reuse, and preservation. The specific aim of the ORE effort is to promote (through creation or endorsement) effective and consistent mechanisms which: facilitate discovery of compound digital objects; reference (or link to) these objects (as well as parts thereof); obtain a variety of disseminations of these objects; aggregate and disaggregate objects; and enable processing of objects by automated agents. | compound digital object, aggregation, metadata standard, ontology, interoperability, atom, rdf, xml, rdfa | is listed by: FORCE11 | Open Archives Initiative ; Andrew W. Mellon Foundation ; NSF |
Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported | nif-0000-10391 | http://dltj.org/article/ore-introduction/InSeries-oai-object-reuse-and-exchange | SCR_006982 | SciCrunch Registry | 2026-10-17 01:26:45 | 2 | ||||||
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Comparative Sequencing of Plant Small RNAs Resource Report Resource Website 1+ mentions |
Comparative Sequencing of Plant Small RNAs (RRID:SCR_007003) | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | This project has developed a sequence dataset of plant small RNAs based on the hypothesis that most if not all plants utilize important small RNA signaling networks. Different plant families are likely to have both common and lineage-specific miRNAs or other small RNAs with important biological roles. Comparative genomics approaches can be applied to distinguish potential miRNAs from siRNAs and to match the miRNAs to the target sequences. This project develops an unparalleled resource of millions of plant small RNAs for comparative analyses. The project includes sequencing of small RNAs from a diverse and agronomically-relevant set of plant species, focused analyses of important members of the Solanaceae and Poaceae, and development of a small RNA database and web interface for public access and analysis of data. These data will allow the experimental characterization of the majority of biologically important small RNAs for a range of plant species, and will be tremendously useful to a broad set of plant biologists interested in development, stress responses, epigenetics, evolution, RNA biology and other traits impacted by small RNAs. We offer a variety of tools to query the small RNA data set, with options to identify sequences based on homology, expression levels, conservation, or potential function: 1. Small RNA mapping tool: searches for small RNAs perfectly matching a genomic sequence provided by the user. 2. Small RNA mismatch tool: searches the database for small RNAs or other short sequences provided by the user, allowing mismatches. 3. Library-comparison tool to identify conserved small RNAs. 4. Library-comparison tool to identify differentially regulated small RNAs. 5. Reverse Target Prediction. | has parent organization: University of Delaware; Delaware; USA | NSF 0638525 | nlx_37749 | SCR_007003 | SciCrunch Registry | 2026-10-17 01:26:45 | 1 | ||||||||||
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Lyngby Resource Report Resource Website 1+ mentions |
Lyngby (RRID:SCR_007143) | Lyngby | data analysis software, data processing software, software application, software resource | Matlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files. | functional, statistical, fmri, pet, matlab, neuroimaging |
is listed by: Biositemaps has parent organization: THOR Center for Neuroinformatics |
Human Brain Project ; Danish Research Council ; European Union ; BIOMED2 ; MAPAWAMO ; NASA ; NSF ; DOE ; NIDA R01 DA09246; NIMH P20 MH57180 |
Free, Non-commercial | nif-0000-00324 | SCR_007143 | SciCrunch Registry | Lyngby Toolbox, Lyngby - A Toolbox for Functional Neuroimaging | 2026-10-17 01:26:47 | 2 | ||||||
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ChromHMM Resource Report Resource Website 50+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, data processing software, software application, software resource | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
Alfred P. Sloan Fellowship ; CAREER Award ; NHGRI RC1HG005334; NHGRI U01 HG007912; NHGRI U54 HG004570; NIEHS R01 ES024995; NIMH U01 MH105578; NSF 0905968 |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | SciCrunch Registry | 2026-10-17 01:29:26 | 50 | ||||||
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RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | data access protocol, simulation software, software application, software resource, web service | Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model. | Protein structure predictor, 3D structure, protein sequence, secondary and tertiary structure, binding site, solvent accessibility, disordered region, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
NIGMS R01 GM089753; NSF DBI 0960390 |
PMID:21987485 | Restricted | biotools:raptorx | https://bio.tools/raptorx | SCR_018118 | SciCrunch Registry | 2026-10-17 01:29:26 | 198 | ||||||
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UltraScan Resource Report Resource Website 10+ mentions |
UltraScan (RRID:SCR_018126) | data analysis software, data processing software, software application, software resource | Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis. | Hydrodynamic data, analytical ultracentrifugation experiment, data editing, analysis, sedimentation velocity experiment, spectrum analysis, genetic algorithm, Monte Carlo analysis | Howard Hughes Medical Institute ; NCRR RR 022200 03S1; NCRR RR022200; NIGMS GM120600; NSF ACI 1339649; NSF ANI 228927; NSF DBI 9724273; NSF DBI 9974819; NSF OCI 1032742; NSF TG-MCB 060019T; NSF TG-MCB 070038; NSF TG-MCB 070039; NSF TG-MCB 070040; Robert J. Kleberg Jr. and Helen C. Kleberg Foundation ; San Antonio Life Science Institute |
Free, Available for download, Freely available | SCR_018126 | SciCrunch Registry | 2026-10-17 01:29:21 | 20 | ||||||||||
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ReproNim/containers Resource Report Resource Website 1+ mentions |
ReproNim/containers (RRID:SCR_018467) | data or information resource, knowledge environment resource, narrative resource, portal, software resource, software toolkit, training material, 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) | German Federal Ministry of Education and Research ; NIBIB P41 EB019936; NSF 1429999 |
Free, Freely available | https://github.com/ReproNim/containers | SCR_018467 | SciCrunch Registry | 2026-10-17 01:29:25 | 1 | ||||||||
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DiANNA Resource Report Resource Website 50+ mentions |
DiANNA (RRID:SCR_018529) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | 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, | Boston College ; NSF DBI 0543506 |
PMID:16844987 PMID:15980459 |
Free, Freely available | http://bioinformatics.bc.edu/clotelab/DiANNA/ | SCR_018529 | SciCrunch Registry | DiANNA 1.1 | 2026-10-17 01:29:26 | 55 | |||||||
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CohortMethod Resource Report Resource Website 10+ mentions |
CohortMethod (RRID:SCR_018511) | data analysis software, data processing software, data visualization software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:29:26 | 11 | ||||||||||
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BioSimulations Resource Report Resource Website 1+ mentions |
BioSimulations (RRID:SCR_018733) | software resource, web application | 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; NIGMS ; NSF |
Restricted | biotools:biosimulations | https://bio.tools/biosimulations | SCR_018733 | SciCrunch Registry | 2026-10-17 01:30:08 | 1 | |||||||
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BpForms Resource Report Resource Website |
BpForms (RRID:SCR_018653) | data access protocol, software resource, software toolkit, web service | 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; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bpforms | https://bio.tools/bpforms | SCR_018653 | SciCrunch Registry | 2026-10-17 01:29:35 | 0 | ||||||
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ObjTables Resource Report Resource Website |
ObjTables (RRID:SCR_018652) | data management software, data processing software, software application, 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; NIGMS R35 GM119771; NSF 1649014 |
Free, Freely available | biotools:objtables | https://bio.tools/objtables | SCR_018652 | SciCrunch Registry | 2026-10-17 01:30:07 | 0 | |||||||
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DoubletFinder Resource Report Resource Website 1000+ mentions |
DoubletFinder (RRID:SCR_018771) | data analysis software, data processing software, software application, 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 |
Damon Runyon Cancer Research Foundation ; Department of Defense Breast Cancer Research Program ; NICHD DP2 HD080351; NSF Science and Technology Center ; NSF MCB 1330864; UCSF Center for Cellular Construction |
PMID:30954475 | Free, Available for download, Freely available | SCR_018771 | SciCrunch Registry | 2026-10-17 01:29:47 | 1250 | ||||||||
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ROSIE Resource Report Resource Website 10+ mentions |
ROSIE (RRID:SCR_018764) | ROSIE | application programming interface, data access protocol, software resource, web application | 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 | Howard Hughes Medical and Institute International Student Research Fellowship ; NCI U54 CA143907; NCRR R00 RR024107; NEI PN2 EY016586; NIGMS R01 GM073151; NIGMS R01 GM07822; NIGMS R21 GM102716; NIGMS T32 GM 88118; NSF ; Taiwan Governmental Scholarship for Study Abroad |
PMID:23717507 | Restricted | https://rosie.rosettacommons.org/ | SCR_018764 | SciCrunch Registry | Rosetta Online Server that Includes Everyone | 2026-10-17 01:29:47 | 10 | |||||
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datasets.datalad.org Resource Report Resource Website 1+ mentions |
datasets.datalad.org (RRID:SCR_019089) | data or information resource, data repository, data set, service resource, storage service 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 | NIBIB P41 EB019936; NSF 1429999; NSF 1912266 |
Free, Freely available | https://www.datalad.org/datasets.html | SCR_019089 | SciCrunch Registry | 2026-10-17 01:29:53 | 8 | ||||||||
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runBioSimulations Resource Report Resource Website 1+ mentions |
runBioSimulations (RRID:SCR_019110) | software resource, web application | Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource. | Executing modeling studies, visualization, model reusing, simulation, bio.tools |
uses: BioSimulators is listed by: bio.tools is listed by: Debian |
Center for Reproducible Biomodeling Modeling ; National Institute of Bioimaging and Bioengineering ; National Institute of General Medical Sciences ; NIH ; NSF |
Free, Freely available | biotools:runbiosimulations | https://bio.tools/runbiosimulations | SCR_019110 | SciCrunch Registry | 2026-10-17 01:29:43 | 3 | |||||||
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HDBIG Resource Report Resource Website |
HDBIG (RRID:SCR_014120) | data processing software, image analysis software, software application, software resource, 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 | SciCrunch Registry | High Dimensional Brain Imaging Genomics Toolkit | 2026-10-17 01:28:36 | 0 | ||||||||
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Wisconsin Cortical Thickness Analysis (CTA) Toolbox Resource Report Resource Website |
Wisconsin Cortical Thickness Analysis (CTA) Toolbox (RRID:SCR_014180) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | SciCrunch Registry | 2026-10-17 01:28:44 | 0 | |||||||||
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NeuroRD Resource Report Resource Website 10+ mentions |
NeuroRD (RRID:SCR_014769) | simulation software, software application, 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 | SciCrunch Registry | 2026-10-17 01:28:49 | 13 |
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