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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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CALIB Resource Report Resource Website 100+ mentions |
CALIB (RRID:SCR_001338) | CALIB | software resource | Software package that contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:17485432 | Free, Available for download, Freely available | OMICS_02003 | http://www.bioconductor.org/packages/release/bioc/html/CALIB.html | SCR_001338 | 2026-08-08 11:57:40 | 141 | ||||||
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Morpholino Database Resource Report Resource Website 1+ mentions |
Morpholino Database (RRID:SCR_001378) | MODB | data or information resource, database, service resource, storage service resource, data repository | Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External linkage of our morpholino sequences to ZFIN and Ensembl. To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password. | morpholino, target mrna, embryonic zebrafish, sequence, target, blast, phenotype, anatomy, development, behavior, morphology, pigmentation, toxicity, pax2 expression, craniofacial structure, eye, kidney, pituitary, skin, name, target name, target sequence, gene target, genetic, mortality, toxicity, defect, function, gene annotation, genome, data analysis service |
uses: Zebrafish Information Network (ZFIN) uses: PATO has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
NIGMS GM63904; NIA CA65493 |
PMID:18179718 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152566 | SCR_001378 | MODB (MOprholino DataBase) | 2026-08-08 11:57:27 | 1 | |||||
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Brede Wiki Resource Report Resource Website |
Brede Wiki (RRID:SCR_001411) | wiki, data or information resource, narrative resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 10, 2025. Semantic wiki with structured information, primarily from functional and molecular neuroimaging papers, but there are also other types of papers, e.g., from personality genetics. It lists results from neuroimaging studies, such as Talairach coordinates and brain volume measurements, as well as software packages and brain regions. SQL dumps of the structured information in the wiki is available so complex queries can be formed. The Brede Wiki templates store the structured information from neuroscience papers and editors may add free format text. Template definitions format the data so it is presented as tables on the formatted wiki-page. From a given PMID a web-service can format information from PubMed for inclusion in the Brede Wiki. A Matlab script can extract coordinates from SPM5 and format them in the Talairach coordinate template format. | neuroinformatics, neuroscience, functional neuroimaging, molecular neuroimaging, fmri, mri, talairach, brain region, data sharing, mediawiki, sql |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Brede Database is related to: Brede Toolbox is related to: Brede Database has parent organization: Technical University of Denmark; Lyngby; Denmark |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-08130 | http://www.nitrc.org/projects/bredewiki | SCR_001411 | Brede Wiki - a neuroinformatics wiki | 2026-08-08 11:57:29 | 0 | |||||||
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Open metadata mark up language Resource Report Resource Website 10+ mentions |
Open metadata mark up language (RRID:SCR_001376) | odML | data or information resource, standard specification, narrative resource, markup language, interchange format | Mark up language for collecting and exchanging metadata in an automated, computer-based fashion, developed for neuroscience, specifically, neurophysiology experiments. In odML arbitrary metadata information is stored as extended key-value pairs in a hierarchical structure. Central to odML is a clear separation of format and content, i.e., neither keys nor values are defined by the format. This makes odML flexible enough for storing all available metadata instantly without the necessity to submit new keys to an ontology or controlled terminology. Common standard keys can be defined in odML-terminologies for guaranteeing interoperability. | mark-up language, electrophysiology, neurophysiology, terminology, metadata, data sharing, interoperability, annotate, ontology |
is used by: NIX is used by: EEGbase is used by: odMLtables has parent organization: German Neuroinformatics Node (G-Node) |
BMBF 01GQ0802; BMBF 01GQ0801 |
PMID:21941477 | Free, Available for download, Freely available | nlx_152533 | SCR_001376 | open metadata Markup Language | 2026-08-08 11:57:40 | 27 | |||||
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Integrated Content Environment Resource Report Resource Website |
Integrated Content Environment (RRID:SCR_001369) | ICE | software resource, collaboration tool | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The Integrated Content Environment (ICE) is a free Word-processor based system that allows authors to work individually or collaboratively on material for the Web, CD and print. This free web content management system, produced by the University of Southern Queensland, was initially developed by staff at the university to produce course content for online and print delivery. It has also been used for general web site development, and to manage documents in project intranets. | integrated content, word processor, collaboration, content management | has parent organization: University of Southern Queensland; Queensland; Australia | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-07757 | http://ice.usq.edu.au/default.htm https://eprints.usq.edu.au/697/ | http://www.usq.edu.au/lrds/tech/ice | SCR_001369 | Integrated Content Environment (ICE) | 2026-08-08 11:57:26 | 0 | |||||
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Integrated DNA Technologies OligoAnalyzer Resource Report Resource Website 500+ mentions |
Integrated DNA Technologies OligoAnalyzer (RRID:SCR_001363) | OligoAnalyzer | web application, sequence analysis software, software resource, software application, data analysis software, data processing software | Web-based application for analyzing oligonucleotides. Analysis proceeds after the sequence has been entered and the calculations modified based on target type, oligo concentration, sodium ion concentration, magnesium ion concentration, and dNTP concentration. | oligos, oligonucleotides, sequence, web, analyzer | Free, Freely Available | nif-0000-07754 | SCR_001363 | IDT OligoAnalyzer, OligoAnalyzer, IDT Oligo Analyzer, OligoAnalyzer 3.1 | 2026-08-08 11:57:26 | 620 | ||||||||
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UNAFold Resource Report Resource Website 100+ mentions |
UNAFold (RRID:SCR_001360) | software resource, software application, data analysis software, data processing software | Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows. | software, nucleic acid, folding, hybridization, prediction, rna, dna, stochastic sampling, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University at Albany; New York; USA |
Free, Available for download, Freely available | biotools:unafold, nif-0000-07753 | http://mfold.rna.albany.edu/ | SCR_001360 | The UNAFold Web Server, UNAFold Web Server | 2026-08-08 11:57:40 | 373 | |||||||
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THOR Center for Neuroinformatics Resource Report Resource Website 1+ mentions |
THOR Center for Neuroinformatics (RRID:SCR_001400) | THOR Center | data or information resource, software resource, software application, topical portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Center hosting a number of related projects concerning neural networks, functional neuroimaging, multimedia signal processing, and biomedical signal processing. Neuroinformatics is a research field rooted in classical disciplines like signal processing, biology, physics, computer science and engineering. Neuroinformatics combines learning from the brain and learning about the brain. By studying information processing in the brain neuroinformatics invents new computing paradigms (e.g., artificial neural networks) with the objective of understanding the dynamics of the conscious mind. Artificial neural networks is an active neuroinformatics research field, which combines many approaches to adaptive signal processing in solving real world problems. They began using neural networks for general nonlinear adaptive signal processing. Since 1991 the CONNECT groups have participated in the development of neural computing as an advanced, non-linear statistical tool, which has been applied to forecasting within dynamical systems, pattern recognition, and medical image analysis, particularly functional neuroimages. While neural computing has largely been viewed as a black box approach, they have initiated research aimed at opening this black box, using hypertext, multimedia, and interactivity. Their key objective is to convert abstract models into intuitive knowledge through interactive visualization. | neuroinformatics, neural network, functional neuroimaging, multimedia, signal processing, biomedical, neuroscience, biomedical, brain |
has parent organization: Technical University of Denmark; Lyngby; Denmark is parent organization of: MRIWarp is parent organization of: Brede Toolbox is parent organization of: Lyngby |
Danish Research Council | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-08128 | SCR_001400 | Technology by Highly Oriented Research Center for Neuroinformatics | 2026-08-08 11:57:29 | 1 | ||||||
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LPE Resource Report Resource Website |
LPE (RRID:SCR_001364) | LPE | software resource | Software library used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional "BH" or "BY" procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. | differential expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18450812 | Free, Available for download, Freely available | OMICS_01978 | SCR_001364 | Local Pooled Error | 2026-08-08 11:57:40 | 0 | ||||||
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Happy Resource Report Resource Website 10+ mentions |
Happy (RRID:SCR_001395) | HAPPY | software resource, software application, source code, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download). | qtl, quantitative trait locus, r, c, gene, genetic, genomic, ansi c, unix, irix, sunos, linux, animal model, trait, map, genotype, phenotype, haplotype, linear regression, data set, qtl mapping |
is listed by: Genetic Analysis Software is listed by: Debian has parent organization: Wellcome Trust Centre for Human Genetics |
Wellcome Trust | PMID:11050180 DOI:10.1073/pnas.230304397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152594 | http://www.well.ox.ac.uk/~rmott/happy.html | https://sources.debian.org/src/r-other-mott-happy.hbrem/ | SCR_001395 | reconstructing HAPlotYpes | 2026-08-08 11:57:41 | 46 | |||
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Retinal Topography Maps Database Resource Report Resource Website 1+ mentions |
Retinal Topography Maps Database (RRID:SCR_001399) | Retinal Topography Maps Database | data or information resource, database, service resource, storage service resource, data repository | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A database of over 700 retinal topography maps of a wide variety of species published in a diversity of journals. It has been assembled to assist vision and neuroscience researchers to locate and compare the distribution of retinal neurons within and across species. The maps can be searched by taxonomic or common name classification, cell type sampled, type of retinal specialization and staining/visualization method. Maps can be compared by selecting multiple maps and clicking the Compare Selected button. An interactive spreadsheet can be also downloaded. | retinal map, retina, vision, retinal neuron, topography, eye | has parent organization: University of Western Australia; Perth; Australia | PMID:26230981 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152606 | SCR_001399 | Retinal topography maps, retinalmaps.org | 2026-08-08 11:57:41 | 1 | ||||||
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aroma.light Resource Report Resource Website 1+ mentions |
aroma.light (RRID:SCR_001312) | aroma.light | software resource | Light-weight software package for normalization and visualization of microarray data using only basic R data types. Software can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. | infrastructure, microarray, preprocessing, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
DOI:10.1186/1471-2105-11-245 | Free, Available for download, Freely available | OMICS_01998, biotools:aroma.light | https://bio.tools/aroma.light, https://sources.debian.org/src/r-bioc-aroma.light/ | SCR_001312 | 2026-08-08 11:57:28 | 1 | ||||||
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Online Neuroscience Lectures - Maintained by the Kilgard Lab Resource Report Resource Website |
Online Neuroscience Lectures - Maintained by the Kilgard Lab (RRID:SCR_001397) | video resource, data or information resource, topical portal, slide, portal | List of lectures, slides and videos concerning neuroscience and neurophysiology. | neuroscience, neurophysiology, lecture, slide, video | Free, Freely Available | nif-0000-08126 | SCR_001397 | Online Neuroscience Lectures | 2026-08-08 11:57:29 | 0 | |||||||||
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National ESCA and Surface Analysis Center for Biomedical Problems Resource Report Resource Website 1+ mentions |
National ESCA and Surface Analysis Center for Biomedical Problems (RRID:SCR_001430) | NESAC/BIO | biomedical technology research center, material analysis service, access service resource, production service resource, training resource, analysis service resource, service resource, biomaterial analysis service | Biomedical technology research center that provides state-of-the-art surface analysis expertise, instrumentation, experimental protocols, and data analysis methods to address surface-related biomedical problems. NESAC/BIO develops and applies surface science methodologies that produce a full understanding of the surface composition, structure, spatial distribution, and orientation of biomaterials and adsorbed biomolecules. The NESAC/BIO program identifies areas where surface science must evolve to keep pace with the growth in biochemical knowledge and biomaterial fabrication technology, and develops instrumentation, experimental protocols, and data analysis methods to achieve this evolution. NESAC/BIO provides state-of-the-art surface analysis tools to researchers in the biomedical community. You can gain access to the NESAC/BIO facilities in one of the following ways: * Collaborative: Propose a project to collaborate on with NESAC/BIO. The project should be rewarding for both groups, and the results should reflect the utility of surface analysis for biomedical research * Service: Ask NESAC/BIO to analyze your biomaterial specimens. The spectra obtained from the analyses will be interpreted for you. * Training: Visit the University of Washington to receive training in surface analysis and personally run experiments for your individual research projects. These experiments should have a high probability for yielding useful information and should not involve the development of new ESCA techniques or methodologies. | surface, composition, structure, spatial distribution, orientation, biomaterial, biomolecule, surface science, biochemical, biomaterial fabrication, surface analysis | has parent organization: University of Washington; Seattle; USA | NIBIB 5P41RR001296-11 | Free, Freely Available | nlx_152654 | SCR_001430 | NESAC/BIO - National ESCA and Surface Analysis Center for Biomedical Problems | 2026-08-08 11:57:29 | 1 | ||||||
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BeadDataPackR Resource Report Resource Website |
BeadDataPackR (RRID:SCR_001310) | BeadDataPackR | software resource | Software that provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform. | microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:20981138 | Free, Available for download, Freely available | biotools:beaddatapackr, OMICS_02023 | https://bio.tools/beaddatapackr | SCR_001310 | BeadDataPackR - Compression of Illumina BeadArray data | 2026-08-08 11:57:40 | 0 | |||||
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MRI Studio Resource Report Resource Website 100+ mentions |
MRI Studio (RRID:SCR_001398) | image processing software, image analysis software, software resource, software application, data visualization software, data processing software | An image processing program running under Windows suitable for such tasks as tensor calculation, color mapping, fiber tracking, and 3D visualization. Most of operations can be done with only a few clicks. This tool evolved from DTI Studio. Tools in the program can be grouped in the following way: * Image Viewer * Diffusion Tensor Calculations * Fiber Tracking and Editing * 3D Visualization * Image File Management * Region of Interesting (ROI) Drawing and Statistics * Image Registration | tensor calculation, color mapping, fiber tracking, 3d visualization, dti, image registration, mri, diffusion mr fiber tracking, microsoft, c++, analyze |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion Tensor Imaging ToolKit has parent organization: Johns Hopkins University; Maryland; USA works with: UManitoba - JHU Functionally Defined Human White Matter Atlas |
NCRR ; Biomedical Informatics Research Network ; NIBIB |
Free, Freely Available | nif-0000-00291 | http://www.nitrc.org/projects/mri_studio | SCR_001398 | dtiStudio, DTI Studio | 2026-08-08 11:57:27 | 180 | ||||||
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PNEUMA Resource Report Resource Website 1+ mentions |
PNEUMA (RRID:SCR_001391) | PNEUMA | software application, software resource, software toolkit, simulation software | A set of modules that are used to simulate the autoregulation of the cardiovascular and respiratory systems under conditions of changing sleep-wake state and a variety of physiological and pharmacological interventions. It models the dynamic interactions that take place among the various component mechanisms, including those involved in the chemical control of breathing, heart rate, and blood pressure, as well as the effects of changes in the sleep-wake state and arousal from sleep. PNEUMA includes the autonomic control of the cardiovascular system, chemoreflex and state-related control of breath-to-breath ventilation, state-related and chemoreflex control of upper airway potency, as well as respiratory and circulatory mechanics. The model is capable of simulating the cardiorespiratory responses to sleep onset, arousal, continuous positive airway pressure, the administration of inhaled carbon dioxide and oxygen, Valsalva and Mueller maneuvers, and Cheyne-Stokes respiration during sleep. In PNEUMA 3.0, we have extended the existing integrative model of respiratory, cardiovascular, and sleepwake state control, to incorporate a sub-model of glucoseinsulinfatty acid regulation. The extended model is capable of simulating the metabolic control of glucoseinsulin dynamics and its interactions with the autonomic nervous system. The interactions between autonomic and metabolic control include the circadian regulation of epinephrine secretion, epinephrine regulation on dynamic fluctuations in glucose and free fatty acids in plasma, metabolic coupling among tissues and organs mediated by insulin and epinephrine, as well as the effect of insulin on peripheral vascular sympathetic activity. This extended model represents a starting point from which further in silico investigations into the interaction between the autonomic nervous system and the metabolic control system can proceed. Features in PNEUMA 3.0 * Incorporates metabolic component based on prior models of glucose-insulin regulation and free fatty acid (FFA) regulation. * Changes in sympathetic activity from the autonomic portion of PNEUMA produce changes in epinephrine output, which in turn affects the metabolic sub-model. * Inputs from the dietary intake of glucose and external interventions, such as insulin injections, have also been incorporated. * Also incorporated is autonomic feedback from the metabolic component to the rest of PNEUMA: changes in insulin level lead to changes in sympathetic tone. System Requirements: PNEUMA requires Matlab R2007b or higher with the accompanying version of Simulink to be installed on your computer. | matlab, simulate, autoregulation, cardiovascular system, respiratory system, sleep-wake state, physiological intervention, pharmacological intervention, drug, breathing, heart rate, blood pressure, respiration, glucose, insulin, fatty acid, regulation, autonomic nervous system, chemoreflex, ventilation, circulation, cardiorespiratory, metabolic control system, circadian, regulation, epinephrine | has parent organization: Biomedical Simulations Resource | NIBIB P41-EB001978; NCRR P41-RR01861 |
PMID:17271149 | Free, Freely Available | nlx_152572 | SCR_001391 | 2026-08-08 11:57:29 | 3 | ||||||
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NIH Common Data Element Repository Resource Report Resource Website 1+ mentions |
NIH Common Data Element Repository (RRID:SCR_001390) | NIH CDE Resource Portal, CDE Resource Portal | data or information resource, common data element, narrative resource, standard specification | A repository of Common Data Elements (CDE). The CDE is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. Forms in the Repository might be original, or might recreate the format of real-world data collection instruments or case report forms. NIH has endorsed collections of CDEs that meet established criteria. NIH-endorsed CDEs are designated with a gold ribbon. Users can Browse NIH-Endorsed CDEs, Browse All CDEs, or Browse Forms. | clinical research, clinical, patient registry, human subject research, human subject, data element, case report form, interoperability, data sharing | has parent organization: National Library of Medicine | Free, Freely Available | nlx_152564 | https://cde.nlm.nih.gov/home, http://www.nlm.nih.gov/cde/ | SCR_001390 | NIH Common Data Element (CDE) Resource Portal, Common Data Element (CDE) Resource Portal | 2026-08-08 11:57:41 | 8 | ||||||
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OLIN Resource Report Resource Website 10+ mentions |
OLIN (RRID:SCR_001304) | OLIN | software resource | Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data. | r, normalization, visualization, quality control, two-channel, microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:15585527 | Free, Available for download, Freely available | biotools:olin, OMICS_02029 | http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html | SCR_001304 | Optimised Local Intensity-dependent Normalisation | 2026-08-08 11:57:40 | 18 | |||||
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Simpleaffy Resource Report Resource Website 50+ mentions |
Simpleaffy (RRID:SCR_001302) | Simpleaffy | software resource, software application, data analysis software, data processing software | Software package that provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures. | affymetrix, annotation, data import, differential expression, microarray, one channel, preprocessing, quality control, report writing, transcription, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16076888 | GNU General Public License, v2 or newer | OMICS_02034 | SCR_001302 | Simpleaffy - Very simple high level analysis of Affymetrix data | 2026-08-08 11:57:28 | 85 |
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