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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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LTR_FINDER_parallel Resource Report Resource Website 10+ mentions |
LTR_FINDER_parallel (RRID:SCR_018969) | data processing software, software application, software resource, data analysis software | Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. | Parallelization, rapid identification, retrotransposons identification, repetitive sequences, large genomes, long terminal repeat, retrotrnsposon, parallel operation, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF IOS 1740874; United States Department of Agriculture National Institute of Food ; Agriculture and AgBioResearch at Michigan State University |
PMID:31857828 | Free, Available for download, Freely available | biotools:LTR_FINDER_parallel | https://bio.tools/LTR_FINDER_parallel | SCR_018969 | 2026-08-04 09:44:29 | 14 | ||||||
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Open Science Chain Resource Report Resource Website 1+ mentions |
Open Science Chain (RRID:SCR_018773) | OSC | data processing software, portal, software resource, software application, data or information resource | Provides data integrity using blockchain. Used for protecting integrity and provenance of research data.Open science chain utilizes distributed ledger technology (consortium blockchain) to securely store information about scientific data including its provenance to enable independent verification of its authenticity to establish trust in the research community. | ASWG, data integrity, research data, authenticity, data integrity protection, data protection, data verification | has parent organization: University of California at San Diego; California; USA | NSF 1840218 | DOI:10.1145/3332186.3332203 | Free, Freely available | SCR_018773 | 2026-08-04 09:44:24 | 2 | |||||||
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ANTIGENpro Resource Report Resource Website 100+ mentions |
ANTIGENpro (RRID:SCR_018779) | data access protocol, software resource, service resource, web service | Web tool as sequence-based, alignment-free and pathogen-independent predictor of protein antigenicity.Predicts likelihood that protein is protective antigen. Integrated in SCRATCH suite of predictors. | Protein antigenicity, sequence based predictior, alignment free predictor, pathogen independent predictor, protein antigenicity predictor, SCRATCH suite, predictor | has parent organization: University of California at Irvine; California; USA | NLM LM 07443; NSF EIA 0321390; NSF 0513376; Microsoft Faculty Research Award |
PMID:20934990 | Free, Freely available | SCR_018779 | 2026-08-04 09:44:24 | 247 | ||||||||
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DE-Sim Resource Report Resource Website |
DE-Sim (RRID:SCR_018770) | simulation software, software application, software resource | Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models. | Object oriented, discrete event simulation, data driven modeling, oriented discrete event simulation, computation model simulation |
is related to: NumPy is related to: SciPy is related to: Pandas is related to: SIMULA has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NSF 1649014; NIGMS R35 GM119771; Icahn Institute for Data Science and Genomic Technology |
Free, Available for download, Freely available | SCR_018770 | Discrete Event Simulation, object oriented Discrete Event-Simulation tool | 2026-08-04 09:44:24 | 0 | ||||||||
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Tracer Resource Report Resource Website 1000+ mentions |
Tracer (RRID:SCR_019121) | data processing software, data analysis software, software resource, software application, data visualization software | Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more. | Analysing trace files, files generated by Bayesian MCMC runs, MCMC trace files, conditional posterior distribution summary, demographic trajectory reconstruction, Bayesian phylogenetic inference, kernel density estimation, multivariate visualisation | Wellcome Trust ; European Union Seventh Framework Programme ; NSF DMS 1264153; NIAID R01 AI107034; NIAID U19 AI135995 |
PMID:29718447 | Free, Available for download, Freely available | https://github.com/beast-dev/tracer, http://gensoft.pasteur.fr/docs/Tracer/v1.6, http://beast.community/tracer, https://github.com/beast-dev/tracer/releases/tag/v1.7.1 | SCR_019121 | Tracer v1.7.1, Tracer v1.6 | 2026-08-04 09:44:32 | 1582 | |||||||
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brainlife Resource Report Resource Website 10+ mentions |
brainlife (RRID:SCR_020940) | portal, storage service resource, project portal, data repository, service resource, data or information resource | Free cloud platform for secure neuroscience data analysis. Allows to manage data, processing and results, sharing projects privately with collaborators or publicly with brainlife.io community.Promotes engagement and education in reproducible neuroscience.You can share your neuroimaging data publicly or privately. Data on brainlife.io is organized as Datatypes to allow interoperability between Apps. | Secure neuroscience data analysis, manage data, sharing projects, data files mapping, interoperate | works with: brainlife.io | NSF OAC 1916518; NSF IIS 1912270; NSF IIS 1636893; NSF BCS 1734853; NIBIB R01 EB029272; Google Cloud ; Microsoft Research Award ; Microsoft Investigator Fellowship ; Indiana University |
Free, Freely available | r3d100012397, r3d100013223 | https://github.com/brainlife, https://github.com/brainlife/brainlife, https://doi.org/10.17616/R3KV0P, https://doi.org/10.17616/R31NJMP3 | SCR_020940 | Brainlife | 2026-08-04 09:44:41 | 15 | ||||||
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BindingDB Resource Report Resource Website 10+ mentions |
BindingDB (RRID:SCR_000390) | database, data or information resource | Web accessible database of data extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in Protein Data Bank . Website supports query types including searches by chemical structure, substructure and similarity, protein sequence, ligand and protein names, affinity ranges and molecular weight . Data sets generated by BindingDB queries can be downloaded in form of annotated SDfiles for further analysis, or used as basis for virtual screening of compound database uploaded by user. Data are linked to structural data in PDB via PDB IDs and chemical and sequence searches, and to literature in PubMed via PubMed IDs . | drug, drug discovery, drug target, binding affinity, protein interaction, small molecule-protein interaction, interaction, protein, small molecule, FASEB list |
is related to: PSICQUIC Registry is related to: canSAR has parent organization: University of California at San Diego; California; USA |
NIGMS GM070064; NSF 9808318; National Institute of Standards and Technology ; NIGMS R24 GM144232 |
PMID:26481362 PMID:17145705 |
Free, Freely available | r3d100012074, nif-0000-02603 | https://doi.org/10.17616/R3ZS9T | SCR_000390 | BindingDB | 2026-08-04 09:40:07 | 41 | |||||
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Southern California Earthquake Data Center Resource Report Resource Website |
Southern California Earthquake Data Center (RRID:SCR_000663) | SCEDC | database, data or information resource | Archive of earthquake data for research in seismology and earthquake engineering in Southern California recorded or processed by the Southern California Seismic Network (SCSN). Users can access information on: * Recent earthquakes detected by the SCSN * Significant southern California earthquakes and faults * The southern California earthquake catalog, spanning from 1933 to present * Waveform and metadata files of SCSN seismic stations from 1977 to present * Data sets created by SCEC scientists to assist in ongoing and future research | southern california, earthquake, fault, waveform, seismic, data set | is listed by: CINERGI | U.S. Geological Survey G10AP00091; NSF EAR-0529922; Southern California Earthquake Center 07HQAG0008 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154718, r3d100011575 | https://doi.org/10.17616/R3ZS8F | SCR_000663 | 2026-08-04 09:40:11 | 0 | ||||||
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MCScanX Resource Report Resource Website 100+ mentions |
MCScanX (RRID:SCR_022067) | data processing software, data analysis software, software resource, software application, software toolkit | Software toolkit for detection and evolutionary analysis of gene synteny and collinearity. | gene synteny and collinearity, detection and evolutionary analysis, | NSF DBI 0849896; NSF MCB 0821096; NSF MCB 1021718; NIAID R01 AI068908 |
PMID:22217600 | Free, Available for download, Freely available | SCR_022067 | Multiple Collinearity Scan toolkit X version | 2026-08-04 09:44:56 | 257 | ||||||||
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Polar Rock Repository Resource Report Resource Website |
Polar Rock Repository (RRID:SCR_002212) | PRR | database, data or information resource | National facility for permanent curatorial preservation of rock collections from Antarctica and Southern Ocean. Repository preserves existing rock/dredge/unconsolidated/terrestrial core/photo archive collections for research use. Database allows online requests for sample loans. Mapping tool combines existing PRR database with high resolution satellite images of Antarctica, REMA or USGS topographic layers. PRR created Polar Rock Boxes for educators who are teaching about Earth science and Antarctica. Each Polar Rock Box contains samples with binder full of teaching information about Earth science and Antarctica. These boxes are freely available as short loans to US schools. | Sampling in polar regions, rock, polar, antarctica, dredge, southern ocean, glacial sediment, volcano, metadata |
is listed by: CINERGI has parent organization: Ohio State University; Ohio; USA |
NSF | Free, Freely available | nlx_154740, r3d100011627 | https://doi.org/10.17616/R3JD0W | SCR_002212 | Polar Rock Repository Database, U.S. Polar Rock Repository | 2026-08-04 09:40:35 | 0 | |||||
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Scholarometer Resource Report Resource Website |
Scholarometer (RRID:SCR_004279) | Scholarometer | source code, data set, web service, software resource, data access protocol, data or information resource | Scholarometer (beta) is a social tool to facilitate citation analysis and help evaluate the impact of an author''s publications. It is a social (crowdsourcing) application that leverages the wisdom of the crowds. Scholarometer makes visualization of author and discipline networks available on the web site. It requires users to tag their queries with one or more discipline names, choosing from predefined ISI subject categories or arbitrary tags. This generates annotations that go into a database, which collects statistics about the various disciplines, such as average number of citations per paper, average number of papers per authors, etc. This data is publicly available. Scholarometer users can save the finding into formats appropriate for local reference management software (e.g., EndNote), or for social publication sharing systems (e.g., BibSonomy). Currently, our system supports the following export formats: BibTex (BIB), RefMan (RIS), EndNote (ENW), comma-separated values (CSV), tab-separated values (XLS), and BibJSON. Export data is dynamically generated in response to any filter, merge or delete actions performed by the user. Since Scholarometer is a browser extension that provides a smart interface for Google Scholar, it does not have the limitations of server based citation analysis tools that sit between the user and Google Scholar. At the same time Scholarometer is not an application, such as Publish or Perish, and therefore it is platform independent and runs on every system that supports the Firefox or the Chrome browser. Still, Scholarometer uses Google Scholar, which provides the most comprehensive source of citation data across the sciences and social sciences. Scholarometer provides a RESTful web API so that other developers can make use of our crowdsourced data. Select the method on the left panel to see corresponding documentation. The extension/add-on code is available in the Mozilla Firefox Add-ons and Google Chrome Extensions repositories. Additional server-side code is not available at this time. | has parent organization: Indiana University Bloomington; Indiana; USA | NSF IIS-0811994 | PMID:22984414 | nlx_29330 | SCR_004279 | 2026-08-04 09:41:06 | 0 | ||||||||
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AntWeb Resource Report Resource Website 100+ mentions |
AntWeb (RRID:SCR_004851) | AntWeb | image repository, storage service resource, data repository, service resource, database, data or information resource | Database of images, specimen records, and natural history information on ants including Search Tools, Regional Lists, In Depth Information, Ant Image Comparison Tool, PDF Field Guides, Maps on AntWeb and Google Earth, and Ant Genera of the World Slideshow. It is community driven and open to contribution from anyone with specimen records, natural history comments, or images. As of February of 2013, AntWeb has 97,814 ant images, of 23,272 specimens representing over 10,549 species. AntWeb provides tools for submitting images, specimen records, annotating species pages, and managing regional species lists. AntWeb contains information on the ant faunas of several areas in the Nearctic and Malagasy biogeographic regions, and global coverage of all ant genera. AntWeb provides tools for exploring the diversity and identification of ants (Hymenoptera: Formicidae). These tools have been developed to encourage the study of ants, to facilitate the use of ants in inventory and monitoring programs, and to provide ant taxonomists with access to images of type specimens. AntWeb illustrates the diversity of ants by providing information and high quality color images of many of the approximately 10,000 known species of ants. AntWeb currently focuses on the species of the Nearctic and Malagasy biogeographic regions, and the ant genera of the world. Over time, the site will grow to describe every species of ant known. | image, FASEB list | has parent organization: California Academy of Sciences | Private donations ; NSF DEB-0344731; NSF EF-0431330 |
nlx_84285 | SCR_004851 | 2026-08-04 09:41:14 | 195 | ||||||||
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DataONE Resource Report Resource Website 10+ mentions |
DataONE (RRID:SCR_003999) | DataONE | portal, database, storage service resource, software resource, data repository, service resource, catalog, data or information resource | A distributed framework and cyberinfrastructure for open, persistent, and secure access to Earth observational data. It ensures the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program. The DataONE Investigator Toolkit is a collection of software tools for finding, using, and contributing data in DataONE. DataONE currently hosts three Coordinating Nodes that provide network-wide services to enhance interoperability of the Member Nodes and support indexing and replication services. Coordinating Nodes provide a replicated catalog of Member Node holdings and make it easy for scientists to discover data wherever they reside, also enabling data repositories to make their data and services more broadly available to the international community. DataONE Coordinating Nodes are located at the University of New Mexico, the University of California Santa Barbara and at the University of Tennessee (in collaboration with Oak Ridge National Laboratory). DataONE comprises a distributed network of data centers, science networks or organizations. These organizations can expose their data within the DataONE network through the implementation of the DataONE Member Node service interface. In addition to scientific data, Member Nodes can provide computing resources, or services such as data replication, to the DataONE community. | earth, environment, data sharing, cyberinfrastructure, earth observational data, data management, data set, FASEB list |
uses: DataUp is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: University of New Mexico; New Mexico; USA |
NSF 0830944; NSF 1430508 |
Acknowledgement requested | DOI:10.25504/FAIRsharing.yyf78h, nlx_158410, DOI:10.17616/R3101G, r3d100010478, DOI:10.2586 | https://doi.org/10.17616/R3101G, https://doi.org/10.17616/r3101g, https://doi.org/10.2586/, https://dx.doi.org/10.2586/, https://fairsharing.org/10.25504/FAIRsharing.yyf78h, https://doi.org/10.17616/R3TG83 | SCR_003999 | Data Observation Network for Earth | 2026-08-04 09:41:02 | 44 | |||||
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Cell Type Ontology Resource Report Resource Website 1+ mentions |
Cell Type Ontology (RRID:SCR_004251) | CL | ontology, data or information resource, controlled vocabulary | Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. | cell ontology, ontology repository |
is listed by: BioPortal is listed by: Ontology Lookup Service is related to: CELDA Ontology is related to: OBO is related to: Cell Line Knowledge Base |
BBSRC ; MRC ; NIH ; NSF DBI-9978564; NSF PGRP-0321666 |
PMID:15693950 | Free, Freely available | nlx_26501 | http://purl.bioontology.org/ontology/CL | http://cellontology.org, http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell, | SCR_004251 | cellontology.org, Obo-cell-type, Cell Ontology | 2026-08-04 09:41:06 | 6 | |||
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BioMart Project Resource Report Resource Website 100+ mentions |
BioMart Project (RRID:SCR_002987) | portal, web service, software resource, data access protocol, project portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse. | biology, data, management, data mining, search, descriptive, graphical, application, perl, java, gold standard |
is used by: Blueprint Epigenome is related to: Mouse Genome Informatics (MGI) is related to: biomaRt has parent organization: Ontario Institute for Cancer Research has parent organization: European Bioinformatics Institute |
Wellcome Trust ; Spanish Government ; Sandra Ibarra Foundation for Cancer ; Breast Cancer Campaign Tissue Bank ; U.S. Department of Energy ; NSF NRF 2013M3A6A4043695; Center for Genome Regulation ; Center for Mathematical Modelling ; European Molecular Biology Laboratory |
PMID:21930506 PMID:19144180 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30184 | SCR_002987 | BioMart software | 2026-08-04 09:40:47 | 284 | ||||||
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PONDR Resource Report Resource Website 50+ mentions |
PONDR (RRID:SCR_023691) | data access protocol, software resource, web service | Web tool to predict order and disorder from amino acid sequence. Used to predict of natural disordered regions in proteins. | amino acid sequence, predict sequence order and disorder, protein natural disordered regions prediction, protein, | NLM R01 LM06916; NSF ; DOE ; MRC of Canada |
DOI:10.1016/S1093-3263(00)00138-8 | Free, Freely available | SCR_023691 | Predictor of Natural Disordered Regions | 2026-08-04 09:45:19 | 90 | ||||||||
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Open Tree of Life Resource Report Resource Website 1+ mentions |
Open Tree of Life (RRID:SCR_024603) | portal, web service, software resource, data access protocol, project portal, data or information resource | Project aims to construct comprehensive, dynamic and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data. | construct tree of life, digitally available tree of life, published phylogenetic trees, taxonomic data, |
is listed by: DataCite has parent organization: University of California; California; USA |
NSF | Free, Freely available | https://opentreeoflife.github.io/, https://api.datacite.org/dois?prefix=10.48699 | SCR_024603 | 2026-08-04 09:45:33 | 2 | ||||||||
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microbeMASST Resource Report Resource Website 1+ mentions |
microbeMASST (RRID:SCR_024713) | data access protocol, software resource, web service | Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. | Identification of microbial derived metabolites, microbial metabolomics data, microbial metabolite annotation, taxonomy, mass spectrometry search tool, searching tool, bacteria, fungi, metabolomics, microbiome, search known and unknown MS/MS spectra, | is related to: GNPS MASST | NIDDK U24DK133658; NIA U19AG063744; NIGMS 1DP2GM137413; Korean Government ; Austrian Science Fund ; German Research Foundation ; Sao Paulo Research Foundation ; Mexican National Council of Science and Technology ; NIGMS R01GM107550; NSF ; Research Council of Norway ; NIAID R01AI167860; NIDDK T32DK007202; NIGMS 1R01GM132649; NIGMS R35GM142938; NIDDK U01DK119702; NIH Office of the Director S10 OD021750; NLM 1R01LM013115 |
PMID:37577622 | Free, Freely available, | SCR_024713 | 2026-08-04 09:45:35 | 6 | ||||||||
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Sheep Brain Atlas Resource Report Resource Website 1+ mentions |
Sheep Brain Atlas (RRID:SCR_001752) | portal, atlas, data or information resource | Online portal and image database of coronal sections of the sheep brain. Each image contains stained sections of cell bodies and myelinated fibers; nuclei and tracts are labeled. | sheep brain, atlas, images, coronal section, stain, anatomy |
has parent organization: Michigan State University; Michigan; USA has parent organization: National Science Foundation |
NSF 0131267; NSF 0131826; NSF 0131028 |
Free, Freely available | nif-0000-00102 | https://www.msu.edu/~brains/brains/sheep/index.html | SCR_001752 | Sheep Brain Atlas, The Navigable Atlas of the Sheep Brain | 2026-08-04 09:40:28 | 4 | ||||||
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Dynamic Regulatory Events Miner Resource Report Resource Website 1+ mentions |
Dynamic Regulatory Events Miner (RRID:SCR_003080) | DREM | data processing software, software application, software resource | The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations | transcription, gene regulation, dynamics, time series, gene expression, static, dynamic, transcription factor-gene interaction, chip-chip, transcription factor, regulatory network, hidden markov model, systems biology, gene regulatory network, times series expression data, dynamic network, chip-seq | has parent organization: Carnegie Mellon University; Pennsylvania; USA | NIH ; NIGMS 1RO1 GM085022; NIAID DNO1 AI-5001; NSF 0448453 |
PMID:22897824 | Free, Available for download, Freely available | nif-0000-30478 | SCR_003080 | Dynamic Regulatory Events Miner (DREM) | 2026-08-04 09:40:48 | 5 |
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