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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Internet Brain Segmentation Repository Resource Report Resource Website 10+ mentions |
Internet Brain Segmentation Repository (RRID:SCR_001994) | IBSR | data or information resource, data set | Data set of manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the development and evaluation of segmentation methods by providing raw test and image data, human expert segmentation results, and methods for comparing segmentation results. Please see the MediaWiki for more information. This repository is meant to contain standard test image data sets which will permit a standardized mechanism for evaluation of the sensitivity of a given analysis method to signal to noise ratio, contrast to noise ratio, shape complexity, degree of partial volume effect, etc. This capability is felt to be essential to further development in the field since many published algorithms tend to only operate successfully under a narrow range of conditions which may not extend to those experienced under the typical clinical imaging setting. This repository is also meant to describe and discuss methods for the comparison of results. | 3d model, anatomy, brainstem, cerebellum, cortex, gray matter, imaging, morphology, mri, segmentation, volume, white matter, adult human, male, child, image collection, application, magnetic resonance, os independent, php, quality metrics, segmentation, test data, web service |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard Medical School; Massachusetts; USA |
Normal, Tumor | NINDS 1 R01 NS34189-01 | Free, Available for download, Freely available | nif-0000-00032 | http://www.cma.mgh.harvard.edu/ibsr/ | SCR_001994 | 2026-08-08 12:05:41 | 25 | |||||
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Rosetta Bit Resource Report Resource Website 1+ mentions |
Rosetta Bit (RRID:SCR_001906) | Rosetta Bit | data or information resource, data set | Public datasets that have been transcoded into multiple formats. This library of valid file format conversions (DICOM->NIFTI, DICOM->PAR/REC, etc.) will provide a reference for tool developers seeking to support multiple sources of data. | computed tomography, imaging genomics, magnetic resonance, optical imaging, format conversion, dicom, nifti, dicom, par/rec | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155947 | SCR_001906 | 2026-08-08 12:05:46 | 1 | ||||||||
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EEG Database Resource Report Resource Website 1+ mentions |
EEG Database (RRID:SCR_001581) | EEG Database | data or information resource, data set | Data set from a large study to examine EEG correlates of genetic predisposition to alcoholism. It contains measurements from 64 electrodes placed on the scalp sampled at 256 Hz (3.9-msec epoch) for 1 second. There were two groups of subjects: alcoholic and control. Each subject was exposed to either a single stimulus (S1) or to two stimuli (S1 and S2) which were pictures of objects chosen from the 1980 Snodgrass and Vanderwart picture set. When two stimuli were shown, they were presented in either a matched condition where S1 was identical to S2 or in a non-matched condition where S1 differed from S2. There were 122 subjects and each subject completed 120 trials where different stimuli were shown. The electrode positions were located at standard sites (Standard Electrode Position Nomenclature, American Electroencephalographic Association 1990). Zhang et al. (1995) describes in detail the data collection process. There are three versions of the EEG data set. * The Small Data Set (smni97_eeg_data.tar.gz) contains data for the 2 subjects, alcoholic a_co2a0000364 and control c_co2c0000337. For each of the 3 matching paradigms, c_1 (one presentation only), c_m (match to previous presentation) and c_n (no-match to previous presentation), 10 runs are shown. * The Large Data Set (SMNI_CMI_TRAIN.tar.gz and SMNI_CMI_TEST.tar.gz) contains data for 10 alcoholic and 10 control subjects, with 10 runs per subject per paradigm. The test data used the same 10 alcoholic and 10 control subjects as with the training data, but with 10 out-of-sample runs per subject per paradigm. * The Full Data Set contains all 120 trials for 122 subjects. The entire set of data is about 700 MBytes. | genetic predisposition, eeg, gene, heredity, picture, stimuli, match, non-match | has parent organization: University of California at Irvine; California; USA | Alcoholism, Alcoholic, Control | PMID:8590074 | Free, Freely available | nlx_153818 | http://kdd.ics.uci.edu/databases/eeg/eeg.html | SCR_001581 | EEG Database Data Set | 2026-08-08 12:05:46 | 4 | ||||
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PROW Resource Report Resource Website 1+ mentions |
PROW (RRID:SCR_002434) | PROW | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It offers short, structured reviews of proteins and protein families, especially leukocyte surface membrane molecules. Index of information available from PROW includes CD molecule, Alternate names, Current Guides, Past Guides, Entrez Gene and Assigning workshop. Current guides: expanded format including Summary Sentence and Abstract Past guides: older guides with excellent information, some data may be dated | leukocyte, membrane, molecule, protein, protein property, surface | has parent organization: National Cancer Institute | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21340 | SCR_002434 | Protein Reviews On the Web, PROW - Protein Reviews on the Web, Protein Reviews on the Web | 2026-08-08 12:05:48 | 8 | |||||||
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MCIC Resource Report Resource Website 10+ mentions |
MCIC (RRID:SCR_002310) | MCIC | data or information resource, data set | Expertly collected, well-curated data sets consisting of comprehensive clinical characterization and raw structural, functional and diffusion-weighted DICOM images in schizophrenia patients and gender and age-matched controls are now accessible to the scientific community through an on-line data repository (coins.mrn.org). This data repository will be useful to 1) educators in the fields of neuroimaging, medical image analysis and medical imaging informatics who need exemplar data sets for courses and workshops; 2) computer scientists and software algorithm developers for testing and validating novel registration, segmentation, and other analysis software; and 3) scientists who can study schizophrenia by further analysis of this cohort and/or by pooling with other data. | clinical neuroinformatics, dicom, magnetic resonance, image collection, clinical assessment, diagnose, healthy control, neuropsychological test, psychiatric disorder, schizoaffective disorder, schizophrenia, diffusion-weighted |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Mind Research Network - COINS |
Schizophrenia, Normal control | PMID:23760817 | COINS Data Use Agreement | nlx_155657 | SCR_002310 | 2026-08-08 12:05:48 | 34 | ||||||
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EEG time series Data Sets Resource Report Resource Website 1+ mentions |
EEG time series Data Sets (RRID:SCR_001579) | EEG time series data | data or information resource, data set | Five data sets containing quasi-stationary, artifact-free EEG signals both in normal subjects and epileptic patients were put in the web by Ralph Andrzejak from the Epilepsy center in Bonn, Germany. Each data set contains 100 single channel EEG segments of 23.6 sec duration. | eeg, time series, brain, electrical activity, eyes closed, eyes open, intracranial, eeg recording, epileptic seizure |
is related to: Neural Cipher has parent organization: Pompeu Fabra University; Barcelona; Spain |
Epilepsy, Normal | PMID:11736210 | Free, Available for download, Freely available | nlx_153816 | http://epileptologie-bonn.de/cms/front_content.php?idcat=193&lang=3&changelang=3 | SCR_001579 | 2026-08-08 12:05:46 | 1 | |||||
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EBI Genomes Resource Report Resource Website 10+ mentions |
EBI Genomes (RRID:SCR_002426) | data or information resource, data set | The EBI genomes pages give access to a large number of complete genomes including bacteria, archaea, viruses, phages, plasmids, viroids and eukaryotes. Methods using whole genome shotgun data are used to gain a large amount of genome coverage for an organism. WGS data for a growing number of organisms are being submitted to DDBJ/EMBL/GenBank. Genome entries have been listed in their appropriate category which may be browsed using the website navigation tool bar on the left. While organelles are all listed in a separate category, any from Eukaryota with chromosome entries are also listed in the Eukaryota page. Within each page, entries are grouped and sorted at the species level with links to the taxonomy page for that species separating each group. Within each species, entries whose source organism has been categorized further are grouped and numbered accordingly. Links are made to: * taxonomy * complete EMBL flatfile * CON files * lists of CON segments * Project * Proteomes pages * FASTA file of Proteins * list of Proteins | eukaryote genome, gene, gene browser, genome, archaea genome, bacteria genome, phage genome, plasmid genome, viroid genome, viruse genome, sequence, protein, nucleotide, complete genome, gold standard | has parent organization: European Bioinformatics Institute | nif-0000-02778 | SCR_002426 | Genomes Pages - At the EBI, ENA Genomes Server | 2026-08-08 12:05:42 | 26 | |||||||||
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BD FACSDiva Software Resource Report Resource Website 5000+ mentions |
BD FACSDiva Software (RRID:SCR_001456) | BD FACSDiva Software | commercial organization, software resource | A collection of tools for flow cytometer and application setup, data acquisition, and data analysis that help streamline flow cytometry workflows. It provides features to help users integrate flow systems into new application areas, including index sorting for stem cell and single-cell applications, as well as automation protocols for high-throughput and robotic laboratories. | flow cytometry, windows |
is used by: BD Biosciences: LSRFortessa X-20 Cell Analyzer has parent organization: BD Biosciences |
Free, Freely Available | SciRes_000115 | http://www.bdbiosciences.com/instruments/software/facsdiva/index.jsp | SCR_001456 | 2026-08-08 12:05:40 | 8327 | |||||||
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CodonCodes TraceViewer Resource Report Resource Website 1+ mentions |
CodonCodes TraceViewer (RRID:SCR_002304) | TraceViewer | commercial organization, software resource | A Java program that allows you to see, print, and edit DNA sequencing traces. | windows, dna sequencing trace, dna, sequencing, trace | is listed by: OMICtools | Free for academic use | OMICS_01822 | SCR_002304 | CodonCode''s TraceViewer | 2026-08-08 12:05:47 | 1 | |||||||
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ModelRun Resource Report Resource Website |
ModelRun (RRID:SCR_001532) | ModelRun | data or information resource, data set | Data set of output of neuron models through the Trestles supercomputer. | neuron, computational model, simulation, activity pattern, transmitter, receptor, current |
is listed by: ModelDB is listed by: Neuroscience Gateway has parent organization: Neuroscience Information Framework |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152893 | SCR_001532 | 2026-08-08 12:05:46 | 0 | ||||||||
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Amorphium Resource Report Resource Website 1+ mentions |
Amorphium (RRID:SCR_002062) | Amorphium | commercial organization, software resource | Graphics software for a real-time approach to creating 3D graphics that offers a variety of intuitive, powerful design tools to create your 3D masterpiece. The graphics engine allows for a completely interactive environment, where all operations occur on solid objects in real time. A rendering engine allows you to produce stunning 3D imagery at virtually any resolution for Web, print, digital video, and film. Advanced capabilities include Radiosity rendering for photo-realistic scenes, Raytracing for true-to-life surface reflections and refractions, as well as variable smoke and lighting effects. | 3d software, graphics software, graphics, modeling, painting, animation, rendering, design, vector-based 3d | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000164 | http://download.cnet.com/Amorphium-3-0/3000-6677_4-33263.html | SCR_002062 | Amorphium 3, Amorphium 3.0 | 2026-08-08 12:05:47 | 1 | |||||||
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Drug-Interactions Resource Report Resource Website 1+ mentions |
Drug-Interactions (RRID:SCR_002336) | Drug Interactions | data or information resource, data set | Table designed as a hypothesis testing, teaching and reference tool for physicians and researchers interested in drug interactions that are the result of competition for, or effects on the human cytochrome P450 system. The table contains lists of drugs in columns under the designation of specific cytochrome P450 isoforms. A drug appears in a column if there is published evidence that it is metabolized, at least in part, via that isoform. It does not necessarily follow that the isoform is the principal metabolic pathway in vivo, or that alterations in the rate of the metabolic reaction catalyzed by that isoform will have large effects on the pharmacokinetics of the drug., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | drug, cytochrome p450, cytochrome, interaction, isoform, metabolic, p450, pathway, pharmacokinetic, physician, substrate, clincial, inhibitor, inducer, drug interaction, genetics | has parent organization: Indiana University School of Medicine; Indiana; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21132 | http://drug-interactions.com | SCR_002336 | Cytochrome P450 Drug Interaction Table, Cytochrome P450 Drug Interactions, P450 Drug Interactions | 2026-08-08 12:05:42 | 5 | ||||||
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Mammalian Brain Methylomes Resource Report Resource Website |
Mammalian Brain Methylomes (RRID:SCR_001648) | Mammalian Brain Methylomes | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Datasets described in the manuscript: "Global Epigenomic Reconfiguration During Mammalian Brain Development" (Science, 2013 - DOI: 10.1126/science.1237905. This study provides genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis. | epigenetics, methylation, frontal cortex, development, neuron, methylome, maturation, learning, young adult, fetus | has parent organization: Salk Institute for Biological Studies | PMID:23828890 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153926 | SCR_001648 | Mammalian Brain Methylomes | 2026-08-08 12:05:46 | 0 | ||||||
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Paper Rejection Repository Resource Report Resource Website |
Paper Rejection Repository (RRID:SCR_002643) | Paper Rejection Repository | data or information resource, data set | Repository of rejections of papers - letters and comments - that were ultimately accepted by a journal to educate others. Your rejection letters and comments are welcome. Some journals have begun including reviewers' comments with accepted papers to make the views of experts available to the reader. However, often the paper has been submitted to several journals and rejected before it is finally accepted. The rejection letters and comments are equally useful in helping to judge what kind of papers might be acceptable to a journal, and what kind of comments lead to rejections. Rather than hiding these low points in the trajectory of a scientific paper, this forum offers a place to publish these letters and comments to educate others. | rejection, letter, peer review process, manuscript, journal, publish, peer review |
is listed by: FORCE11 has parent organization: Brandeis University; Massachusetts; USA has parent organization: Janelia Research |
Free, Available for download, Freely available | nlx_156072 | SCR_002643 | 2026-08-08 12:05:42 | 0 | ||||||||
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Connectomic reconstruction of the inner plexiform layer in the mouse retina Resource Report Resource Website 1+ mentions |
Connectomic reconstruction of the inner plexiform layer in the mouse retina (RRID:SCR_002246) | MPIN Connectomics | data or information resource, data set | Data set of the dense reconstruction of 950 neurons and their mutual contacts for the mouse inner plexiform layer--the main computational neuropil region in the mammalian retina. This was achieved by applying a combination of crowd-sourced manual annotation and machine-learning-based volume segmentation to serial block-face electron microscopy data. They characterize a new type of retinal bipolar interneuron and show that they can subdivide a known type based on connectivity. Circuit motifs that emerge from their data indicate a functional mechanism for a known cellular response in a ganglion cell that detects localized motion, and predict that another ganglion cell is motion sensitive. A Data browser is also available for download | connectome, retina, retina inner plexiform layer | has parent organization: Max Planck Institute for Biological Intelligence | Max-Planck-Gesellschaft ; DFG ; Gatsby Charitable Foundation |
PMID:23925239 | Free, Freely available | nlx_155563 | SCR_002246 | 2026-08-08 12:05:48 | 1 | ||||||
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EID: Exon-Intron Database Resource Report Resource Website 10+ mentions |
EID: Exon-Intron Database (RRID:SCR_002469) | EID | data or information resource, data set | Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames. | eukaryote genome, exon, exon-intro, gene structure, genome splicing, intron, ortholog, fasta, gene, protein-coding gene, splice, motif, gene prediction, structure, coding region |
is listed by: OMICtools has parent organization: University of Toledo; Ohio; USA |
PMID:16772261 PMID:10592221 |
Free, Available for download, Freely available | OMICS_01886, nif-0000-02793 | http://www.utoledo.edu/med/depts/bioinfo/database.html | http://www.meduohio.edu/bioinfo/eid/, http://mcb.harvard.edu/gilbert/EID | SCR_002469 | The Exon-Intron Database, Exon-Intron Database | 2026-08-08 12:05:42 | 11 | ||||
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HS3D - Homo Sapiens Splice Sites Dataset Resource Report Resource Website 1+ mentions |
HS3D - Homo Sapiens Splice Sites Dataset (RRID:SCR_002939) | HS3D | data or information resource, data set | Data set of Homo Sapiens Exons, Introns and Splice regions extracted from GenBank Rel.123 with an aim of giving standardized material to train and to assess the prediction accuracy of computational approaches for gene identification and characterization. From the complete GenBank (Primate Sequences Division) Rel.123 (162,557 entries), entries of Human Nuclear DNA including Complete CDS and more than one Exon have been selected, and 4523 exons and 3802 introns have been extracted from these entries. Details about extracted exons and introns are reported (Locus, number, Start and End position in the entry, sequence, length, G+C content, presence of not AGCT data (nucleotide scan check)). Statistics are also reported (overall nucleotides, average G+C content, nucleotide scan check results, number of not GT starting / AG ending introns, minimum / maximum / average length, length standard deviation). 3799+3799 donor and acceptor sites, as windows of 140 nucleotides around each splice site have been extracted. After discarding sequences not including canonical GTAG junctions (65+74), including insufficient data (not enough material for a 140 nucleotide window) (686+589), including not AGCT bases (29+30), and redundant (218+226) there are 2796+ 2880 windows. Finally, there are 271,937 + 332,296 windows of false splice sites, selected by searching canonical GTAG pairs in not splicing positions. The false sites in a range of +/- 60 from a true splice site are marked as proximal. | human genome, splice, exon, intron, region, gene, dna, nucleotide, splice region | is related to: GenBank | Free, Available for download, Freely available | nif-0000-02988 | SCR_002939 | Homo Sapiens Splice Sites Dataset, HS3D (Homo Sapiens Splice Sites Dataset) | 2026-08-08 12:05:43 | 7 | |||||||
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Beijing: Short TR Study Resource Report Resource Website 1+ mentions |
Beijing: Short TR Study (RRID:SCR_003502) | Beijing Short TR | data or information resource, data set | Dataset of resting state fMRI scans obtained using two different TR's in healthy college-aged volunteers. Specifically, for each participant, data is being obtained with a short TR (0.4 seconds) and a long TR (2.0 seconds). In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 8-minute resting-state fMRI scan (TR = 2 seconds, # repetitions = 240) * 8-minute resting-state fMRI scans (TR = 0.4 seconds, # repetitions = 1200) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information | nifti, fmri, resting-state fmri, image collection, early adult human, mprage, diffusion tensor imaging, neuroimaging, brain, demographic |
has parent organization: Beijing Normal University; Beijing; China has parent organization: 1000 Functional Connectomes Project |
Healthy | National Natural Science Foundation of China 30770594; National High Technology Program of China 2008AA02Z405 |
Creative Commons Attribution-NonCommercial License | nlx_157642 | SCR_003502 | Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Short TR Sample, BNU Short TR Sample | 2026-08-08 12:05:48 | 6 | |||||
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Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat Resource Report Resource Website 1+ mentions |
Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat (RRID:SCR_002816) | Temporal-lobe.com | data or information resource, data set | Interactive diagram containing existing knowledge of hippocampal-parahippocampal connections in which any connection can be turned on or off at the level of cortical layers. It includes references for each connection. | function, anatomical, connection, cortical, diagram, hippocampus, layer, neuroanatomy, neuroscience, parahippocampal, projection, subfield, temporal, lobe, topological, connectome, magnetic resonance, connectivity, formation, parahippocampal region, retrosplenial cortex, tract tracing |
is used by: NIF Data Federation is used by: Integrated Nervous System Connectivity is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Rat Hippocampus Atlas is related to: Integrated Manually Extracted Annotation has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
Research Council of Norway ; various independent donations |
PMID:21847380 PMID:19300446 |
Freely available, Account required | nif-0000-24805 | http://www.nitrc.org/projects/connectivity | SCR_002816 | Parahippocampal-hippocampal network, TEMPORAL-LOBE, Parahippocampal hippocampal connectivity | 2026-08-08 12:05:48 | 7 | ||||
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Mouse Genome Informatics Transgenes Resource Report Resource Website 1+ mentions |
Mouse Genome Informatics Transgenes (RRID:SCR_003468) | MGI Transgene | data or information resource, data set |
Data set of collected and annotated expression and activity data for recombinase-containing transgenes and knock-in alleles. As the authoritative source of official names for mouse genes, alleles, and strains, MGI makes this list of transgenes available as a service and includes all known transgenes and synonyms. NIF provides a database interface so that researchers may have a better idea whether the trangene or transgenic animal that they are searching for is available. Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice. |
transgene, allele, phenotype |
is used by: NIF Data Federation is related to: Integrated Manually Extracted Annotation has parent organization: Mouse Genome Informatics (MGI) |
Acknowledgement requested, Non-commercial, Commercial with permission, Copyrighted | nif-0000-34000 | SCR_003468 | 2026-08-08 12:05:43 | 3 |
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