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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Educational Resources in Neuroscience Resource Report Resource Website |
Educational Resources in Neuroscience (RRID:SCR_000169) | ERIN | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A database that lists, reviews, and rates resources for teaching neuroscience at the graduate and undergraduate level. | education, neuroscience, training material, clinical |
is used by: NIF Data Federation lists: UCSC Genome Browser lists: ReMoto lists: Neurofly lists: Free Statistical Software is related to: ReMoto is related to: Neurofly is related to: Free Statistical Software has parent organization: Society for Neuroscience |
NSF DUE-1043553 | PMID:26240519 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143786 | SCR_000169 | ERIN: Educational Resources In Neuroscience, ERIN Resources | 2026-09-12 01:02:23 | 0 | |||||
|
Antarctic Marine Geology Research Facility Resource Report Resource Website |
Antarctic Marine Geology Research Facility (RRID:SCR_002213) | AMGRF, ARF | biomaterial supply resource, material resource |
National repository for geological materials collected in polar regions housing over 20,000 meters of deep-sea core sediment and over 5,000 kg of dredge, trawl, and grab samples, the largest such Southern Ocean collection in the world. These materials have been acquired from over 90 USAP research vessel cruises. The Facility also houses and curates nearly 3,000 meters of rotary cored geological material acquired by NSF supported drilling programs in the Antarctic. Replacement cost of this core inventory in terms of ship and ice-based drilling is conservatively estimated to be in the range of $150 to $200M. SESAR or the the System for Earth Sample Registration is a service provided by the IDEA. SESAR operates the registry that distributes the International Geo Sample Number IGSN. SESAR catalogs and preserves sample metadata profiles, and provides access to the sample catalog via the Global Sample Search. Facility services include: * curation of the existing collections at the facility * onsite ship and land based curatorial services * receipt and processing of new cores * core description and publication of core descriptions * distribution of samples from the collection to authorized scientists * hosting of scientific meetings and workshops * tours, lectures, and student education and training in Antarctic geoscience * maintenance of: ** a core and sample database ** an Antarctic geology and marine geology reference library and a searchable End Note computer database of the entire collection ** a satellite IODP/MRC for nannofossils and diatoms |
marine, sediment, deep freeze, polar, international geosample number, geosample, x-ray, antarctic, x-radiograph, map, nannofossil, diatom, data set, metadata |
is listed by: CINERGI has parent organization: Florida State University; Florida; USA |
NSF 838901 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154735 | SCR_002213 | Antarctic Research Facility | 2026-09-12 01:02:27 | 0 | ||||||
|
ShapeComplexAtlas Resource Report Resource Website |
ShapeComplexAtlas (RRID:SCR_002553) | ShapeComplexAtlas | software application, software resource | A Matlab demo for constructing a neuro-anatomical shape complex atlas from 3D MRI brain structures, based on the paper Ting Chen, Anand Rangarajan, Stephan J. Eisenschenk and Baba C. Vemuri, Construction of a Neuroanatomical Shape Complex Atlas from 3D MRI Brain Structures. In NeuroImage, Volume 60, Page 1778-1787, 2012 | atlas application, matlab, magnetic resonance, mri, shape complex atlas |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Florida; Florida; USA |
NSF RI-IIS 0954032; NSF IIS 1143963 |
PMID:22305953 PMID:20879384 |
Free, Available for download, Freely available | nlx_155960 | http://www.nitrc.org/projects/shapecomplex | SCR_002553 | 2026-09-12 01:02:28 | 0 | |||||
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total impact.org Resource Report Resource Website |
total impact.org (RRID:SCR_005952) | Total impact | service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 8, 2017. Service that aggregates altmetrics: diverse impacts from articles, datasets, blog posts, and more, to create a measure of the impact of scholarly output. * view metrics: Point to research products in Slideshare, GitHub, and Dryad. Import items from Google Scholar profiles or a BibTex file and the output is a metrics report that can be viewed and shared. * embed anywhere: Use the full-featured API to add metrics to projects. Or drop the embeddable Javascript widget into a publishing platform''s HTML. * Free - metrics data (and source code). They believe open altmetrics are key for building the coming era of Web-native science. | alternative metric, impact factor, altmetric, altmetric provider, metric, code, widget | is listed by: FORCE11 | Alfred P. Sloan Foundation ; NSF ; JISC |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151310 | SCR_005952 | 2026-09-12 01:02:35 | 0 | |||||||
|
CloVR Resource Report Resource Website 10+ mentions |
CloVR (RRID:SCR_005290) | CloVR | service resource, software resource | A desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. | cloud computing, next-generation sequencing |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
Amazon Web Services in Education Research Grants program ; National Human Genome Research Institute ; NHGRI RC2 HG005597-01; NSF 0949201 |
PMID:21878105 | OMICS_01216 | SCR_005290 | CloVR - Automated Sequence Analysis from Your Desktop, Cloud Virtual Resource | 2026-09-12 01:02:34 | 26 | ||||||
|
PlantGDB Resource Report Resource Website 100+ mentions |
PlantGDB (RRID:SCR_013166) | data or information resource, database | Software tools and databases for plant genomics. | FASEB list | NSF IOS-1126267; NSF IOS-0606909; NSF DBI-0110254; NSF DBI-0321600 |
nlx_156925 | SCR_013166 | 2026-09-12 01:02:09 | 227 | ||||||||||
|
Planteome Resource Report Resource Website 10+ mentions |
Planteome (RRID:SCR_014411) | data or information resource, database | An international collaborative effort to develop and enrich new and existing reference ontologies for plants, improve ontology use and cross-references, and to develop data annotation standards. Users can search for ontology terms and bioentities and submit the ontology-related term requests by visiting the following GitHub request trackers. | database, ontology, plant, genome | NSF IOS:1340112 | Available to the research community, Only registered users of the GitHub website are allowed to submit requests and make suggestions or comments | SCR_014411 | 2026-09-12 01:02:14 | 28 | ||||||||||
|
iPTMnet Resource Report Resource Website 10+ mentions |
iPTMnet (RRID:SCR_014416) | data or information resource, database | A protein database which connects multiple disparate bioinformatics tools and systems text mining, data mining, analysis and visualization tools, and databases and ontologies. | database, protein, phosphorylation, bioinformatics, text mining, ontology | NSF ABI-1062520 | Available to the research community | SCR_014416 | 2026-09-12 01:02:14 | 31 | ||||||||||
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Algal Resources Collection Resource Report Resource Website 1+ mentions |
Algal Resources Collection (RRID:SCR_014942) | ARC | biomaterial supply resource, material resource, tissue bank | Supplier of algae strains that aims to be a resource to both the HAB research community and biotechnological applications. Researchers can order and deposit strains with the ARC. | algae, algal, strain, biotechnology, culture, biospecimen | NSF 1756414 | SCR_016468 | SCR_014942 | Algal Resource Collection (ARC), Algal Resources Collection | 2026-09-12 01:02:15 | 3 | ||||||||
|
TheCellMap Resource Report Resource Website 10+ mentions |
TheCellMap (RRID:SCR_018728) | data or information resource, database, service resource | Web accessible database for visualizing and mining global yeast genetic interaction network. Allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize sub networks, using data driven network layouts in intuitive and interactive manner. Used for storing and visualizing genetic interactions in S. cerevisiae. | Genetic interactions, genetic network, yeast genetics, synthetic genetic array, network visualization, annotation, data, genetic interaction visualization | has parent organization: University of Toronto; Ontario; Canada | Canadian Institutes of Health Research ; NHGRI R01 HG005084; NHGRI R01 HG005853; NSF DBI 0953881 |
PMID:28325812 | Free, Freely available | SCR_018728 | TheCellMap.org | 2026-09-12 01:02:19 | 41 | |||||||
|
nanoHUB Resource Report Resource Website 10+ mentions |
nanoHUB (RRID:SCR_013963) | data or information resource, portal | A portal which provides simulation programs for nanoscale phenomena, online presentations, courses, learning modules, podcasts, animations, and teaching materials. Researchers can also collaborate with others and publish content. | portal, nanotechnology, simulation program, educational material |
is listed by: Connected Researchers is related to: Connected Researchers |
NSF EEC-0228390; NSF EEC-0634750; NMI NSF OCI-0438246; SDCI NSF OCI-0721680; NSF OCI-0944665; NSF OCI-0749140; NSF EEC-1227020 |
Free, Public | SCR_013963 | 2026-09-12 01:01:01 | 24 | |||||||||
|
Whole Tale Resource Report Resource Website 1+ mentions |
Whole Tale (RRID:SCR_017537) | data or information resource, portal, project portal | Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility. | Reproducible, data, merging, science, cyberinfrastructure, pathway, tale, capture, code, finding, analysis | NSF 1541450 | DOI:10.1016/j.future.2017.12.029 | Free, Freely available | https://github.com/whole-tale/wt-design-docs//blob/stable/README.rst | SCR_017537 | 2026-09-12 01:01:06 | 1 | ||||||||
|
LTR_retriever Resource Report Resource Website 100+ mentions |
LTR_retriever (RRID:SCR_017623) | data processing software, software application, software resource | Software package for identification of long terminal repeat retrotransposons (LTR-RTs). Removes false positives from initial software predictions. Achieves very high specificity, accuracy, and precision without significantly sacrificing sensitivity, hence significantly outperforming existing methods. Can construct LTR libraries directly from self-corrected PacBio reads prior to genome assembly. | Identification, long, terminal, repeat, retrotransponson, remove, false, positive, prediction, LTR, library, PacBio, read | NSF ; United States Department of Agriculture National Institute of Food and Agriculture and AgBioResearch at Michigan State University |
PMID:29233850 | Free, Available for download, Freely available | SCR_017623 | Long Terminal Repeat retriver | 2026-09-12 01:01:06 | 112 | ||||||||
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PyMVPA Resource Report Resource Website 100+ mentions |
PyMVPA (RRID:SCR_006099) | PyMVPA | software application, software resource, software toolkit | A Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run. Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. This Python-based, cross-platform, open-source software toolbox software toolbox for the application of classifier-based analysis techniques to fMRI datasets makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. | python, machine learning, fmri, eeg, neuroimaging, image analysis, scripting, multivariate pattern analysis, brain, meg, extracellular recording, algorithm, reusable library, analyze, c, console (text based), eeg, meg, electrocorticography, frequency domain, independent component analysis, linear, modeling, magnetic resonance, multivariate analysis, nifti, nonlinear, os independent, pet, spect, principal component analysis, python, regression, spatial transformation, statistical operation, temporal transformation, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: neurodebian is related to: CoSMoMVPA has parent organization: Dartmouth College; New Hampshire; USA has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany |
German Academic Exchange Service PPP-USA D/05/504/7; NIMH MH080526; NSF SBE 0751008; James McDonnell Foundation 220020127 |
PMID:19184561 PMID:19212459 PMID:20582270 |
MIT License | nlx_151596 | http://www.nitrc.org/projects/pymvpa | SCR_006099 | Python MVPA, Multivariate Pattern Analysis in Python, PyMVPA - Multivariate Pattern Analysis in Python | 2026-09-12 01:02:35 | 144 | ||||
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rMATS Resource Report Resource Website 10+ mentions |
rMATS (RRID:SCR_023485) | software resource | Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design. | detection of differential alternative splicing, replicate RNA-Seq data, analysis of paired and unpaired replicates, clinical RNA-Seq datasets, genome studies, | Alfred Sloan Research Fellowship ; NIEHS R01ES024995; NIGMS R01GM088342; NIGMS R01GM105431; NINDS R01NS076631; NSF DMS1055286; NSF DMS1310391 |
PMID:25480548 | Free, Available to download, Freely available | SCR_023485 | 2026-09-12 01:00:39 | 22 | |||||||||
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ContainerProfiler Resource Report Resource Website 1+ mentions |
ContainerProfiler (RRID:SCR_023770) | software resource | Software tool supports profiling resource utilization including CPU, memory, disk, and network metrics of containerized tasks. Resource utilization metrics are obtained across three levels: virtual machine (VM)/host, container, and process. Implementation leverages facilities provided by Linux operating system that is integral with Docker containers. | Resource profiling, resource utilization, containerized tasks, resource utilization metrics, | NIH R01GM126019; NIH R01GM126019-02S2; NIH R03AI159286; NIH U24HG012674; NSF OAC-1849970 |
DOI:10.48550/arXiv.2005.11491 | Free, Available for download, Freely available | SCR_023770 | 2026-09-12 01:00:42 | 2 | |||||||||
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PONDR Resource Report Resource Website 100+ 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, | DOE ; MRC of Canada ; NLM R01 LM06916; NSF |
DOI:10.1016/S1093-3263(00)00138-8 | Free, Freely available | SCR_023691 | Predictor of Natural Disordered Regions | 2026-09-12 01:00:41 | 171 | ||||||||
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Open Tree of Life Resource Report Resource Website 1+ mentions |
Open Tree of Life (RRID:SCR_024603) | data access protocol, data or information resource, portal, project portal, software resource, web service | 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 | 2026-09-12 01:00:49 | 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 | Austrian Science Fund ; German Research Foundation ; Korean Government ; Mexican National Council of Science and Technology ; NIAID R01AI167860; NIA U19AG063744; NIDDK T32DK007202; NIDDK U01DK119702; NIDDK U24DK133658; NIGMS 1DP2GM137413; NIGMS 1R01GM132649; NIGMS R01GM107550; NIGMS R35GM142938; NIH Office of the Director S10 OD021750; NLM 1R01LM013115; NSF ; Research Council of Norway ; Sao Paulo Research Foundation |
PMID:37577622 | Free, Freely available, | SCR_024713 | 2026-09-12 01:00:50 | 7 | ||||||||
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Sheep Brain Atlas Resource Report Resource Website 1+ mentions |
Sheep Brain Atlas (RRID:SCR_001752) | atlas, data or information resource, portal | 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 | 2026-09-12 01:00:52 | 4 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
