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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Appion Package Resource Report Resource Website 10+ mentions |
Appion Package (RRID:SCR_016734) | Appion | image processing software, image analysis software, software resource, software application, data processing software | Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. | processing, analysis, electron, microscope, image | NCRR RR17573; NCRR RR023093; ARCS |
PMID:19263523 | Free, Available for download, Freely available | http://www.appion.org | SCR_016734 | 2026-08-08 12:01:00 | 16 | |||||||
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dCAS Resource Report Resource Website |
dCAS (RRID:SCR_016612) | dCAS | web application, software resource | Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | automate, large, scale, cDNA, sequence, analysis, BLAST, database, gene | is listed by: NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016612 | Desktop cDNA Annotation System | 2026-08-08 12:00:33 | 0 | ||||||||
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RnaSeqGeneEdgeRQL Resource Report Resource Website |
RnaSeqGeneEdgeRQL (RRID:SCR_016699) | software toolkit, software resource, software application, data analysis software, data processing software | Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment. | study, analysis, RNA, sequencing, read, alignment, data | is affiliated with: Bioconductor | Free, Available for download, Freely available | SCR_016699 | 2026-08-08 12:01:01 | 0 | ||||||||||
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CTFFIND Resource Report Resource Website 100+ mentions |
CTFFIND (RRID:SCR_016732) | CTFFIND | software resource, software application, data analysis software, data processing software | Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4. |
is listed by: SoftCite is related to: Janelia Research has parent organization: MRC Laboratory of Molecular Biology |
MRC | PMID:26278980 | SCR_016732 | CTFFinding, CTFFIND4, CTFFIND2, Contrast Transfer Function Finding, Contrast Transfer FunctionFinding, CTFFIND 3 | 2026-08-08 12:00:35 | 114 | ||||||||
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NGlycPred Resource Report Resource Website 1+ mentions |
NGlycPred (RRID:SCR_016610) | NGlycPred | software resource, data access protocol, web service | Web based server to discriminate between glycosylated and non-glycosylated N-X-(T/S) sequons by incorporating structural information and patterns. | predict, classify, glycosylated, nonglycosylate, asparagine, sequons, structure, pattern, information | is listed by: NIAID | Intramural Research Program NIAID | DOI:10.1093/bioinformatics/bts426 | Free, Freely available | SCR_016610 | N linked Glycosylation Prediction server, N linked GLYCosylation PREDiction server | 2026-08-08 12:01:00 | 1 | ||||||
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SpectraVis Resource Report Resource Website |
SpectraVis (RRID:SCR_016691) | web application, network graph visualization software, software resource, network analysis software, software application, data analysis software, data visualization software, data processing software | Web based neuroscience application for analyzing task-related functional networks over time and frequency. Interactive visualization tool for exploring functional brain connectivity. | functional, brain, conectivity, analyzing, network, time, frequency | Free, Available for download, Freely available | http://ericdeno.com/research/SpectraVis/ | SCR_016691 | 2026-08-08 12:00:59 | 0 | ||||||||||
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HASP Resource Report Resource Website |
HASP (RRID:SCR_016615) | HASP | data or information resource, software resource, software application, database, data visualization software, data processing software | Web server to visualize phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of homology models. Database and structural visualization platform for comparative models of influenza A hemagglutinin proteins. | structural, visualization, phylogenetic, biochemical, immunological, hemagglutinin, data, 3D, |
is listed by: NIAID is listed by: NIDDK Information Network (dkNET) |
NIAID | DOI:10.1186/1471-2105-14-197 | Free, Freely available | SCR_016615 | HemAgglutinin Structure Prediction, Hemagglutinin Structure Prediction | 2026-08-08 12:00:58 | 0 | ||||||
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Cleveland Children's Sleep and Health Study Resource Report Resource Website 1+ mentions |
Cleveland Children's Sleep and Health Study (RRID:SCR_016584) | CCSHS | data or information resource, portal, disease-related portal, topical portal | Portal for population based pediatric cohorts studied with objective sleep studies. Includes children with in-home sleep studies, acoustic reflectometry, anthropometry, spirometry, blood pressure (BP), and neuropsychology (NP) and behavioral assessments. Signals recorded include EEG, ECG, EOG, EMG, SpO2, airflow (thermocouple) nasal pressure, respiratory effort, position, plethysmography, light, HR. | data, pediatric, cohort, sleep, study, EEG, ECG, EOG, EMG, SpO2, polysomnography | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | PMID:12712055 PMID:16335483 DOI:10.1080/15402002.2013.825838 |
SCR_016584 | Cleveland Children's Sleep and Health Study | 2026-08-08 12:00:57 | 1 | |||||||
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Imaging WorkBench Resource Report Resource Website 1+ mentions |
Imaging WorkBench (RRID:SCR_016589) | IW | image acquisition software, image analysis software, data acquisition software, software resource, software application, data processing software | Software for multichannel dynamic fluorescence image acquisition and analysis by INDEC BioSystems. | multichannel, fluorescence, image, acquisition, analysis | Commercially available | SCR_016589 | IW 6, Imaging Workbench 6.0, Imaging Workbench (IW) 6, IW 6.0, Imaging Workbench 6 | 2026-08-08 12:00:57 | 5 | |||||||||
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Best Apnea Interventions for Research (BestAIR) sleep study Resource Report Resource Website 1+ mentions |
Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) | BestAIR | data or information resource, portal, disease-related portal, topical portal | Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume. | data, analysis, sleep, apnea, treatment, cardiovascular, disease, risk, factor, polysomnography, ECG, SpO2 | is listed by: National Sleep Research Resource (NSRR) | sleep apnea, cardiovascular disease | ResMed Foundation ; Philips Respironics ; NHLBI U34 HL105277 |
DOI:10.5665/sleep.4266 | SCR_016583 | bestair, , Best Apnea Interventions for Research, Bestair | 2026-08-08 12:00:59 | 3 | ||||||
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kallisto Resource Report Resource Website 100+ mentions |
kallisto (RRID:SCR_016582) | software resource, software application, data analysis software, data processing software | Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads. | bio.tools |
is listed by: Debian is listed by: bio.tools works with: sleuth works with: kb_python |
PMID:27043002 | Free, Available for download, Freely available | biotools:kallisto | https://pachterlab.github.io/kallisto/download.html, https://bio.tools/kallisto, https://sources.debian.org/src/kallisto/ | SCR_016582 | kallisto v0.43.1 | 2026-08-08 12:00:33 | 148 | ||||||
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Traumatic Brain Injury Clinical Trials Network Resource Report Resource Website |
Traumatic Brain Injury Clinical Trials Network (RRID:SCR_013165) | TBI Clinical Trials Network | data or information resource, knowledge environment, topical portal, disease-related portal, portal, research forum portal | The National Center for Medical Rehabilitation Research (NCMRR) established a multi-center network of sites that are working together to design clinical intervention protocols and measures of outcome for TBI. Through rigorous patient evaluation, using common protocols and interventions designed for multiple points of care����??including the accident scene, emergency room, intensive care unit, rehabilitation and long-term follow-up����??the NCMRR TBI Clinical Trials Network can study the required numbers of patients to provide answers more rapidly than individual centers acting alone. This interdisciplinary research Network is designed to evaluate the relationship among acute care practice, rehabilitation strategies, and the long-term functional outcome of TBI patients����??that is, to identify which intervention variables result in improvements in long-term outcomes. Taking advantage of the network model structure has allowed TBI research to progress toward a number of clinical research goals. Specifically, the NCMRR wants to highlight two major achievements to date. First, the TBI Network created a profile of its typical patient to determine the number of patients with different clinical features who might be eligible for future studies and to help estimate recruitment times necessary. Second, Network researchers are developing clinical treatment guidelines and procedures for all points in the continuum of care, including TBI Clinical Trials Network Guidelines for surgical care, systems-based protocol for severe and moderate TBI patients, deep-vein thrombosis prophylaxis procedures, and rehabilitation guidelines for physical therapy, speech-language pathology, occupational therapy, and neuropsychology. | traumatic brain injury, clinical, research, clinical trial, outcome, intervention, one mind tbi | has parent organization: National Institute of Child Health and Human Development | Traumatic Brain Injury | NCMRR | nlx_143904 | http://www.nichd.nih.gov/research/supported/TBI.cfm | SCR_013165 | NCMRR TBI Clinical Trials Network, Traumatic Brain Injury (TBI) Clinical Trials Network | 2026-08-08 12:00:08 | 0 | |||||
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OntoQuest Resource Report Resource Website |
OntoQuest (RRID:SCR_013281) | OntoQuest | software resource | An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework. | ontology, interoperability, owl, middleware, web service, bio.tools, bio.tools |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian is related to: NIFSTD is related to: NIF Web Services has parent organization: Neuroscience Information Framework |
PMID:18958629 | biotools:list_ontologies, biotools:ontoquest_ws, nlx_151737 | https://bio.tools/list_ontologies, https://bio.tools/ontoquest_ws | SCR_013281 | Ontoquest | 2026-08-08 11:59:54 | 0 | ||||||
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Gtk-based Analyze Image Viewer Resource Report Resource Website 1+ mentions |
Gtk-based Analyze Image Viewer (RRID:SCR_013282) | software resource, software application, data visualization software, data processing software | GpetView is light-weight image viewer based on Gtk+ library. The supported image format is ANALYZE(TM) format (Mayo Foundation ). GpetView can run on Unix-systems, such as Linux, Solaris, IRIX, Mac OS-X etc. From Version 2.0, GpetView can also run on Win32 system, if you have installed Glib and Gtk+(2.x). Glib andGtk+ can be found at http://www.gtk.org. For Windows users, you can find Gtk+ libraries at http://gladewin32.sourceforge.net/modules/news/ GpetView has the following features: * very light-weight * view images as transverse, coronal, or sagittal * change color-map (support Analyze lkup file) * zoom images * ROI (Region-Of-Interest) with shapes of circle, ellipse, rectangle, polygon and automatic edge detection * Image histogram and profile Sponsors: This resource is supported by Osaka University. Keywords: Image, Viewer, Software, Transverse, Coronal, Sagittal, Map, Histogram, | has parent organization: Osaka University; Osaka; Japan | nif-0000-00307 | SCR_013282 | GpetView | 2026-08-08 12:00:09 | 2 | ||||||||||
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American Association of Neurological Surgeons Resource Report Resource Website 10+ mentions |
American Association of Neurological Surgeons (RRID:SCR_013209) | professional organization | The American Association of Neurological Surgeons is dedicated to advancing the specialty of neurological surgery and serving as the spokes organization for all practitioners of the specialty of neurosurgery, in order to provide the highest quality of care to our patients. :Founded in 1931 as the Harvey Cushing Society, the American Association of Neurological Surgeons (AANS) is a scientific and educational association with over 7,400 members worldwide. The AANS is dedicated to advancing the specialty of neurological surgery in order to provide the highest quality of neurosurgical care to the public. All Active members of the AANS are board certified by the American Board of Neurological Surgery, the Royal College of Physicians and Surgeons of Canada, or the Mexican Council of Neurological Surgery, A.C. Neurosurgery is the medical specialty concerned with the prevention, diagnosis, treatment and rehabilitation of disorders that affect the spinal column, spinal cord, brain, nervous system and peripheral nerves. For more information on what neurosurgeons do, visit our public pages at : :www.NeurosurgeryToday.org : : :. Visitors to our Web site can find Member Counts under membership including demographic details. | human, neurosurgery, people, surgery | ISNI: 0000 0001 0944 4714, Crossref funder ID: 100008752, nif-0000-10649, Wikidata: Q4743073, grid.469719.4 | https://ror.org/01atcss13 | SCR_013209 | AANS | 2026-08-08 11:59:53 | 20 | |||||||||
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HiTC Resource Report Resource Website 50+ mentions |
HiTC (RRID:SCR_013175) | HiTC | software resource | Software package to explore high-throughput ''C'' data such as 5C or Hi-C. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00524 | SCR_013175 | 2026-08-08 12:00:20 | 87 | ||||||||||
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CoNIFER Resource Report Resource Website 100+ mentions |
CoNIFER (RRID:SCR_013213) | CoNIFER | software resource | Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. |
is listed by: OMICtools has parent organization: SourceForge |
Commercial license | OMICS_00330 | SCR_013213 | Copy Number Inference From Exome Reads | 2026-08-08 11:59:53 | 200 | ||||||||
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RDXplorer Resource Report Resource Website 1+ mentions |
RDXplorer (RRID:SCR_013290) | RDXplorer | software resource | A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
biotools:RDXplorer, OMICS_00349 | https://bio.tools/RDXplorer | SCR_013290 | 2026-08-08 12:00:21 | 7 | ||||||||
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Genolevures Resource Report Resource Website 10+ mentions |
Genolevures (RRID:SCR_013173) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. It provides annotated sequence data and classifications for the genomes of eighteen species of hemiascomycete yeasts, including nine complete genomes. The Gnolevures web resources provides genetic element pages, orthologs defined by syntenic homology, protein families, a genome browser for interspecies comparison, and data sets for downloading. An advanced search facility permits a number of criterion-based and full text queries. Classification data, including protein families and orthologs, and the most up-to-date genome annotations, are for the most part not available in general-purpose sequence data bases such as EMBL/GenBank/DDBJ. | hemiascomycete yeast, protein family |
is listed by: LabWorm is related to: French National Center for Scientific Research |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21161, nif-0000-02862, SCR_013203 | SCR_013173 | Gnolevures | 2026-08-08 11:59:52 | 13 | ||||||||
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3D Brain Resource Report Resource Website |
3D Brain (RRID:SCR_013138) | 3D Brain | data or information resource, narrative resource, software resource, software application, training material, mobile app | iPhone and iPad app that provides a good overview of the brain and its structures allowing you to rotate and zoom around 29 interactive structures with your touch screen. Discover how each brain region functions, what happens when it is injured, and how it is involved in mental illness. Each detailed structure comes with information on functions, disorders, brain damage, case studies, and links to modern research. Compatible with iPhone, iPod touch and iPad. Requires iOS 3.0 or later. | neuroanatomy, brain, gross neuroanatomy |
is related to: Genes to Cognition Online has parent organization: Cold Spring Harbor Laboratory |
The Dana Foundation ; Hewlett Foundation |
Free | nlx_152078 | SCR_013138 | 2026-08-08 12:00:08 | 0 |
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