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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Stereo Investigator - Cleared Tissue Edition Resource Report Resource Website |
Stereo Investigator - Cleared Tissue Edition (RRID:SCR_017668) | data processing software, image analysis software, software application, software resource | Software tool for unbiased stereology to be used on cleared tissue. Used to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Includes number, length, area and volume analyses. | Stereology, cleared, tissue, intact, speciment, imaged, confocal, microscopy, analysis, MBF Bioscience | Restricted | SCR_017668 | SciCrunch Registry | 2026-10-24 12:50:04 | 0 | |||||||||||
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viral_seq Resource Report Resource Website 1+ mentions |
viral_seq (RRID:SCR_018515) | data processing software, software application, software resource | Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis. | Processing viral data, next generation sequencing data, viral data, sequencing, HIV drug resistance analysis, Primer ID sequencing, data | Free, Available for download, Freely available | https://github.com/ViralSeq/viral_seq | SCR_018515 | SciCrunch Registry | 2026-10-24 12:50:05 | 2 | ||||||||||
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EphysExtraction Resource Report Resource Website 1+ mentions |
EphysExtraction (RRID:SCR_018193) | data processing software, software application, software resource | Software tool as code to extract electrophysiological parameters of neurons. Code is continuously being updated to handle more kinds of voltage traces and extract different kinds of features. | electrophysiological parameter, extract parameter, neuron parameter, voltage trace, data | Free, Available for download, Freely available | SCR_018193 | SciCrunch Registry | 2026-10-24 12:50:04 | 3 | |||||||||||
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HTStream Resource Report Resource Website 10+ mentions |
HTStream (RRID:SCR_018354) | data processing software, software application, software resource | Software tool as quality control and processing pipeline for High Throughput Sequencing data. Uses tab delimited fastq format that allows for streaming from application to application. Interoperable with other standard Linux tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Next Generation Sequencing, data processing, quality control, data preprocessing | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018354 | SciCrunch Registry | 2026-10-24 12:50:04 | 13 | |||||||||||
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Science of Behavior Change Research Network Resource Report Resource Website 1+ mentions |
Science of Behavior Change Research Network (RRID:SCR_017385) | SOBC | data or information resource, portal, project portal | Repository for behavioral science measures that have been validated or are in process of being validated in accordance with SOBC Experimental Medicine Approach. | Data, behavioral, science, SOBC, measure, data, medicine | NIH | SCR_017388 | https://scienceofbehaviorchange.org/measures/, https://scienceofbehaviorchange.org/measures/ | SCR_017385 | SciCrunch Registry | SOBC Measures Repository, Science of Behavior Change (SOBC) Research Network | 2026-10-24 12:50:02 | 1 | |||||||
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Registration Software Mitra Lab Resource Report Resource Website |
Registration Software Mitra Lab (RRID:SCR_018353) | data processing software, software application, software resource | Software package to align brain slice images in atlas free manner. | Align, brain, brain slice, brain slice image, atlas free manner | Free, Available for download, Freely available | SCR_018353 | SciCrunch Registry | 2026-10-24 12:50:05 | 0 | |||||||||||
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GeneSyntenyPipeline Resource Report Resource Website |
GeneSyntenyPipeline (RRID:SCR_018198) | data processing software, software application, software resource | Software pipeline was designed to draw gene synteny plot between genomes and obtain 1 to 1 gene pairs from each genome. | Genome, synteny, plot, JCVI, gene pair, data | Free, Available for download, Freely available | SCR_018198 | SciCrunch Registry | 2026-10-24 12:50:03 | 0 | |||||||||||
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halSynteny Resource Report Resource Website 1+ mentions |
halSynteny (RRID:SCR_018127) | data processing software, software application, software resource | Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment. | Conserved synteny, block construction method, genome alignment, DAG based reconstruction, synteny block, chromosome, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:halSynteny | https://bio.tools/halSynteny | SCR_018127 | SciCrunch Registry | Hierarchical Alignment Format Synteny | 2026-10-24 12:50:03 | 4 | |||||||
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Smart-seq2 Multi-Sample Pipeline Resource Report Resource Website 1+ mentions |
Smart-seq2 Multi-Sample Pipeline (RRID:SCR_018920) | data processing software, software application, software resource, software toolkit | Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays. Developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) to process single-nucleus RNAseq (snRNAseq) data generated by Smart-seq2 assays. Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix. | snRNAseq data, Smart-seq2 assays, single nucleus, multi sample, WARP repository |
is related to: Human Cell Atlas has parent organization: University of California at San Diego; California; USA has parent organization: Allen Institute has parent organization: Broad Institute is organization facet of: Terra is organization facet of: BICCN |
Free, Available for download, Freely available | SCR_021312 | https://app.terra.bio/#workspaces/warp-pipelines/Smart-seq2_Single_Nucleus_Muti-Sample | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/smartseq2_multisample | SCR_018920 | SciCrunch Registry | Multi-snSS2, Smart-seq2 Single Nucleus Multi-Sample (Multi-snSS2) | 2026-10-24 12:50:05 | 4 | ||||||
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BALBES Resource Report Resource Website 1+ mentions |
BALBES (RRID:SCR_018763) | software application, software resource, software toolkit, standalone software | Software system for solving protein structures using x-ray crystallographic data. Automatic molecular replacement pipeline for molecular replacement in CCP4. Integrates into one system all components necessary for solving crystal structure by Molecular Replacement. System is automated so that it needs no user intervention when running combination of jobs such as model searching, molecular replacement and refinement. | Molecular replacement pipeline, protein structure, solving protein structure, x-ray crystallographic data, molecular replacement, molecular replacement in CCP4, solving crystal structure, automated system, no user intervention, model searching, refinement |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: CCP4 |
NIGMS R01 GM069758; Wellcome Trust |
PMID:18094476 | Free, Available for download, Freely available | SCR_018763 | SciCrunch Registry | 2026-10-24 12:50:05 | 1 | ||||||||
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CustomCDF Resource Report Resource Website 1+ mentions |
CustomCDF (RRID:SCR_018527) | data processing software, software application, software resource | Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information. | Brainarray, custom CDF, processing raw Affymetrix data, data processing, map probe, probset, oligonucleotide probe, GeneChips, genome, transcriptome, data | PMID:16284200 | Free, Freely available | https://gist.github.com/rmflight/3108891, https://rdrr.io/github/jakejh/metapredict/man/installCustomCdfPackages.html | SCR_018527 | SciCrunch Registry | 2026-10-24 12:50:04 | 8 | |||||||||
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BioCurrents Research Center Resource Report Resource Website |
BioCurrents Research Center (RRID:SCR_002020) | BRC | instrument supplier, material resource | The BioCurrents Research Center (BRC) is an integrated technology resource of the NIH:NCRR. The activities of the Center focus on molecular physiology as it relates to the cell function and disease. Our particular interest is how the dynamics of cell responses are reflected in the chemical profiles of microdomains surrounding single living cells. In order to measure complex cellular boundary layers, the BRC has specialized in the development of extremely sensitive signal acquisition and processing methods along with miniaturized electrochemical sensor designs. The technique is non-invasive and termed self-referencing. Since its establishment in 1996, the BRC has directed its technological research and development to the design and application of ultra-microelectrodes (tip diameters of less than 10m) tailored for the detection of specific chemicals. These have been successfully applied to the boundary layer profiles of many different cell types, with thematic strength in diabetes research, reproductive health and development (see collaborative profiles). More recently, it is changing its focus to technical developments, enhancing the integrative approach to cell function. To understand a cell as a dynamic and integrated whole, BRC must be able to examine responses from different domains as near to real time and as synchronously as possible. To this end, it is developing imaging capabilities to work in parallel with electrochemistry and conventional electrophysiological techniques. Imaging includes a spinning disc confocal, as well as a low light/luminescent imager designed and built within the BRC. The technologies developed or under development are in high demand within the biomedical community. Over 40 investigators work with the Center each year in a collaborative or service capacity. Over 80 of our visitor pool is NIH funded, representing approximately 25 NIH divisions and institutes. As part of our training and dissemination program we host occasional workshops at major national and international meetings, train a significant number of new investigators each year and host graduate students undertaking portions of their thesis dissertation using our technologies. In dissemination we advise on, and install, electrochemical systems in off campus research endeavors, both academic and industrial. | electrochemical, electrochemistry, electrophysiological, function, cell, cellular, chemical, confocal, development, diabetes, disease, health, imager, light, microdomain, microelectrode, physiology, reproductive, research, technique, technology |
has parent organization: Marine Biological Laboratory is parent organization of: Pharmabase - an open content cheminformatics resource linking physiology with pharmacology |
NCRR P41RR001395 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24482 | SCR_002020 | SciCrunch Registry | 2026-10-24 12:52:04 | 0 | |||||||
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Adobe FormsCentral Resource Report Resource Website |
Adobe FormsCentral (RRID:SCR_001729) | FormsCentral | commercial organization, service resource | Service to create PDF and web forms. | pdf, form, template | is listed by: FORCE11 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156027 | SCR_001729 | SciCrunch Registry | Adobe Forms Central | 2026-10-24 12:52:04 | 0 | |||||||
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fMRI Research Center at Columbia Resource Report Resource Website 10+ mentions |
fMRI Research Center at Columbia (RRID:SCR_002658) | PICS | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 7/28/13. Core facility of Columbia Neuroscience with the goal of establishing a collaborative and multi-investigator neuroimaging environment that is focused on the investigation of the neurocircuitry of the brain that underlies cognition, perception and action, and also the development of clinical applications that enhance the goals of personalized medicine. Within this environment the specific current research interests of the Hirsch group include several related directions of investigation. The first is conscious and subconscious neural processes that mediate emotion and cognition in healthy individuals and in patients with psychiatric disorders. This direction also includes neurocircuitry that is characteristic of disorders of consciousness such as minimally conscious or vegetative states, self and visual awareness, and attention. Neurocircuitry of other complex cognitive processes such as decisions, inductive and deductive reasoning, language, truthfulness and top-down influences of expectation, reward, and regulation on early visual and mid-level perceptual and emotional systems. On-going projects targeted for clinical applications include benefits for neurosurgery such as the development of task batteries to map the cortical locations of essential functions such as language, motor, sensation, memory, emotion and sensory functions including visions, audition and the chemical senses. Computational innovations for labeling correspondence between brain structure and specific functional regions are under development to achieve the highest interpretive precision. Current projects include integration of EEG and fMRI techniques to localize seizuregenic cortex in relation to eloquent and functioning cortex for neurosurgical planning; integration of TMS and fMRI to discriminate essential and associative language-sensitive cortical areas; and integration of VEP, EEG and fMRI to inform assessments of visual disease secondary to stroke or neural degeneration. Projects intended to refine and enhance diagnosis of psychiatric disorders such as anxiety, depression, and eating disorders include development of specialized paradigms to target dysfunctional neurocircuitry such as emotional systems (amygdala and basal ganglia) and control and regulatory systems (cingulate and pre-frontal cortex). Comparison of before-treatment images with after-treatment images to inform models of both treatment and disease and investigation of the hypothesis that individual genetic and functional differences have predictive value for treatment options and outcome are currently underway. The lab has pioneered techniques for functional mapping of single patients, and operates an active clinical service for mapping individuals for neurosurgical planning, assessments of the neurocircuitry that underlie acquired or inherited disabilities and the mechanisms of neuroplasticity that restore lost functions are actively investigated using both groups and single subject studies. : | fmri, imaging, neuroscience, cognitive sciences, cognition, perception, action, clinical, personalized medicine, neuroimaging, neurocircuitry, brain, vep, eeg | has parent organization: Columbia University; New York; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00405 | SCR_002658 | SciCrunch Registry | Program for Imaging and Cognitive Sciences, Program for Imaging & Cognitive Sciences | 2026-10-24 12:52:05 | 41 | |||||||
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National Resource for Automated Molecular Microscopy Resource Report Resource Website 1+ mentions |
National Resource for Automated Molecular Microscopy (RRID:SCR_001448) | NRAMM | biomedical technology research center, training resource | Biomedical technology research center that develops, tests and applies technology aimed toward completely automating the processes involved in solving macromolecular structures using cryo-electron microscopy. The goal is to establish a resource that will serve both as a center for high-throughput molecular microscopy as well as for transferring this technique to the research community. Current Core Technology Research and Development is focused on 4 areas: improving grid substrates and specimen preparation; further automation and optimization of image acquisition; development of an integrated single particle analysis and processing pipeline; and the development of automated high throughput EM screening. NRAMM welcomes applications of both collaborative and service projects. | macromolecular structure, cryo-electron microscopy, macromolecule, structure, microscopy, automation, high throughput, specimen handling, image acquisition, data processing, data information integration, structural biology technology center | NIGMS 9 P41 GM103310; NCRR 2P41RR017573 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152671 | SCR_001448 | SciCrunch Registry | 2026-10-24 12:52:04 | 2 | ||||||||
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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 | SciCrunch Registry | Parahippocampal-hippocampal network, TEMPORAL-LOBE, Parahippocampal hippocampal connectivity | 2026-10-24 12:52:05 | 7 | ||||
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National Magnetic Resonance Facility at Madison Resource Report Resource Website 1+ mentions |
National Magnetic Resonance Facility at Madison (RRID:SCR_001449) | NMRFAM | access service resource, service resource, training resource | Provides access and developes NMR technology to advance range of applications and improves the efficiency, rigor and reproducibility of NMR data acquisition and analysis. Houses NMR spectrometers equipped with state-of-the-art probe technology and protocols to support acquisition of high-quality data. Spectrometers range from 500 MHz to 1100 MHz. Service is tailored to the needs of individual users and projects. Provides training and advice on experimental design, best practices for data acquisition, and data analysis. Experienced staff support users with training opportunities including workshops, video tutorials and protocols. | nmr spectrometer, structure, function, protein, rna, dynamics, complex, membrane protein, paramagnetic protein, metabolomics, analysis, spectroscopy, nucleic acid, automation, data analysis, macromolecule, small angle x-ray scattering, structural biology technology center | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | NIGMS P41136463; NIGMS R24GM141526 |
Free, Freely Available | nlx_152672 | SCR_001449 | SciCrunch Registry | 2026-10-24 12:52:03 | 4 | |||||||
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National Biomedical Center for Advanced ESR Technology Resource Report Resource Website 1+ mentions |
National Biomedical Center for Advanced ESR Technology (RRID:SCR_001444) | ACERT | biomedical technology research center, training resource | Biomedical technology research center that develops methods, both experimental and theoretical, of modern electron spin resonance (ESR) for biomedical applications. Center technologies are applicable to the determination of the structure and complex dynamics of proteins. Principal areas of expertise: * Pulsed Fourier Transform and Two Dimensional ESR * High Frequency-High Field (HFHF) ESR * High Resolution ESR Microscopy * Theory and Computational Methods for Modern ESR Activities include: * making resources available to the biomedical community, * publishing results, * running workshops on the new methodologies, * addressing the need to bring these new technologies to other laboratories. | electron spin resonance, spectrometer, electron spin resonance spectrometer, structure, dynamics, protein, structural biology technology center | has parent organization: Cornell University; New York; USA | NIGMS P41GM103521; NCRR P41RR016292 |
Free, Freely Available | nlx_152669 | SCR_001444 | SciCrunch Registry | ACERT National ESR Center, National Biomedical Center for Advanced Electron Spin Resonance Technology | 2026-10-24 12:52:03 | 1 | ||||||
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Center for Integrative Biomedical Computing Resource Report Resource Website 1+ mentions |
Center for Integrative Biomedical Computing (RRID:SCR_001961) | CIBC | biomedical technology research center, training resource | Biomedical technology research center that produces open-source software tools for biomedical image-based modeling, biomedical simulation and estimation, and the visualization of biomedical data. The Center works closely with software users and collaborators in a range of scientific domains to produce user-optimized tools and provides advice, technical support, workshops, and education to enhance user success. Biological projects and collaborations drive their development efforts, all with a single unifying vision: to develop the role of image-based modeling and analysis in biomedical science and clinical practice. The CIBC has a strong, ongoing emphasis on software simulation of bioelectric fields, with clinically oriented collaborations in cardiac defibrillation and the diagnosis/treatment of epilepsy. In addition, the CIBC has expanded in recent years to include applications of statistical shape analysis and three-dimensional visualization to mouse genetics and neuroimaging and applications of image and geometry processing to cell biology. | cardiac defibrillation, epilepsy, software, biomedical, image, modeling, simulation, estimation, visualization, computing, informatics, computing and informatics technology center | has parent organization: University of Utah; Utah; USA | NIGMS P41GM103545 | nif-0000-10535 | SCR_001961 | SciCrunch Registry | NIH/NIGMS Center for Integrative Biomedical Computing | 2026-10-24 12:52:04 | 4 | |||||||
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Human Mortality Database Resource Report Resource Website 100+ mentions |
Human Mortality Database (RRID:SCR_002370) | HMD | data or information resource, data set | A database providing detailed mortality and population data to those interested in the history of human longevity. For each country, the database includes calculated death rates and life tables by age, time, and sex, along with all of the raw data (vital statistics, census counts, population estimates) used in computing these quantities. Data are presented in a variety of formats with regard to age groups and time periods. The main goal of the database is to document the longevity revolution of the modern era and to facilitate research into its causes and consequences. New data series is continually added to this collection. However, the database is limited by design to populations where death registration and census data are virtually complete, since this type of information is required for the uniform method used to reconstruct historical data series. As a result, the countries and areas included are relatively wealthy and for the most part highly industrialized. The database replaces an earlier NIA-funded project, known as the Berkeley Mortality Database. * Dates of Study: 1751-present * Study Features: Longitudinal, International * Sample Size: 37 countries or areas | age, birth, country, demography, health, public health, longevity, longitudinal, international, census data, vital statistics, mortality, population, census, death, FASEB list |
is listed by: re3data.org is listed by: Inter-university Consortium for Political and Social Research (ICPSR) is related to: Human Life-Table Database has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Max Planck Institute for Demographic Research; Mecklenburg-Vorpommern; Germany |
Aging | NIA R01 AG11552 | Free, Registration required, User agreement, Acknowledgement required | nif-0000-21197 | http://www.humanmortality.de/ | SCR_002370 | SciCrunch Registry | The Human Mortality Database | 2026-10-24 12:52:05 | 238 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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