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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
TheDataWeb and DataFerrett
 
Resource Report
Resource Website
1+ mentions
TheDataWeb and DataFerrett (RRID:SCR_003197) DataFerrett software application, text-mining software, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2025. A data analysis and extraction tool from the US Census Bureaus with recoding capabilities to customize federal, state, and local data to suit your requirements. DataFerret works with the DataWeb, a network of online data libraries and an infrastructure for intelligent browsing. TheDataweb provides easy access to data from disparate locations across the internet using DataFerrett as its interface. It brings together demographic, economic, environmental, health, and other datasets that are usually separated by geography and/or organization.Using DataFerrett, you can develop an unlimited array of customized spreadsheets that are as versatile and complex as your usage demands. For a listing/description of datasets available using the DataFerrett refer to the Datasets Available tab. DataFerrett helps you locate and retrieve the data you need across the Internet to your desktop or system, regardless of where the data resides. You can develop and customize tables and select the results to create a graph or map for a visual depiction of your data. You can also save your data in the databasket and save the table you have created for reuse. The DataFerrett tool can use a java applet through an internet browser or be installed as an application on your desktop. The DataFerrett Applet requires you to have popup windows enabled in your browser for this website to function properly. data mining, data extraction, data analysis, economics, health, demographics, education, census, statistics, employment, unemployment, federal, state, local, transportation, housing, economic, environment, demography has parent organization: U.S. Census Bureau THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00616 SCR_003197 Data Federated Electronic Research Review Extraction and Tabulation Tool, TheDataWeb/DataFerrett, TheDataWeb for the DataFerrett, DataFerrett for TheDataWeb 2026-08-14 09:24:47 3
NIH Toolbox - Assessment of Neurological and Behavioral Function
 
Resource Report
Resource Website
100+ mentions
NIH Toolbox - Assessment of Neurological and Behavioral Function (RRID:SCR_002423) NIH Toolbox assessment test provider, material resource An integrated set of tools for measuring cognitive, emotional, motor and sensory function. These tools are being validated for use in diverse cultures, ethnic and geographic groups, ages (3-85 years) and study types. The toolbox is expected to provide a more complete picture of neurological and behavioral health in large-scale longitudinal studies, epidemiological studies, and clinical trials; and to facilitate cross-study comparisons. Moreover, the toolbox will: * be minimally burdensome to subjects and investigators, * utilize state-of-the art psychometric approaches and technology, including computer-assisted evaluation, and * be dynamic and adaptable to changes in measurement and technology. * be available in English and Spanish Many clinical studies collect data on aspects of neurological and behavioral function. However, the neurological and behavioral tests currently available to researchers lack uniformity and often require specialized training to administer. These limitations make it difficult to compile data across the full range of normal neurological function, and to compare data across studies. The toolbox is royalty-free and is expected to be available online by summer 2012. cognitive, motor, emotional, sensory, epidemiology, prevention, computerized adaptive testing, disease, cognition, executive function, episodic memory, working memory, speed, language, attention, emotion, negative affect, positive affect, stress, coping, social, relationship, motor, locomotion, strength, non-vestibular, dexterity, endurance, sensation, vision, audition, vestibular, somatosensation, nneurological assessment, behavioral assessment, taste, olfaction, learning, memory, lexical retrieval, visuospatial ability, speed of processing, mood, adaptability, interpersonal relations, self-regulation, motor function, non-vestibular balance, hearing, vestibular balance, smell, touch, adult human, late adult human, child, psychometric test, measurement tool is related to: Pediatric Imaging Neurocognition and Genetics
has parent organization: Northwestern University; Illinois; USA
is parent organization of: NIH Toolbox Picture Vocabulary Test
is parent organization of: NIH Toolbox Words-in Noise Test
is parent organization of: NIH Toolbox Dimensional Change Card Sort Test
is parent organization of: NIH Toolbox Flanker Inhibitory Control and Attention Test
is parent organization of: NIH Toolbox Picture Sequence Memory Test
is parent organization of: NIH Toolbox Auditory Verbal Learning Test (Rey)
is parent organization of: NIH Toolbox 9-Hole Pegboard Dexterity Test
is parent organization of: NIH Toolbox Oral Reading Recognition Test
is parent organization of: NIH Toolbox Pattern Comparison Processing Speed Test
is parent organization of: NIH Toolbox Oral Symbol Digit Test
is parent organization of: NIH Toolbox List Sorting Working Memory Test
is parent organization of: NIH Toolbox Standing Balance Test
is parent organization of: NIH Toolbox 2-Minute Walk Endurance Test
is parent organization of: NIH Toolbox 4-Meter Walk Gait Speed Test
is parent organization of: NIH Toolbox Grip Strength Test
is parent organization of: NIH Toolbox Odor Identification Test
is parent organization of: NIH Toolbox Pain Interference Survey
is parent organization of: NIH Toolbox Pain Intensity Survey
is parent organization of: NIH Toolbox Regional Taste Intensity Test
is parent organization of: NIH Toolbox Dynamic Visual Acuity Test
is parent organization of: NIH Toolbox Visual Acuity Test
WO HHS-N-260-2006-00007-C Free, Available for download, Freely available nif-0000-00393 SCR_002423 NIH Toolbox - Assessment of Neurological Behavioral Function, NIH Toolbox for Assessment of Neurological and Behavioral Function, NIH Toolbox for the Assessment of Neurological and Behavioral Function 2026-08-14 09:24:37 105
Honey Bee Brain EST Project
 
Resource Report
Resource Website
1+ mentions
Honey Bee Brain EST Project (RRID:SCR_002389) Bee-ESTdb biomaterial supply resource, material resource A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu. expressed sequence tag, brain, behavior, cdna, blast, gene, annotation, microarray, gene expression, comparative genomics, cdna clone, resource:genbank is listed by: One Mind Biospecimen Bank Listing
is related to: One Mind Biospecimen Bank Listing
is related to: Gene Ontology
has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA
NSF ;
University of Illinois Critical Research Initiatives Program ;
Burroughs Wellcome Fund
PMID:11932240 Free nif-0000-00118 SCR_002389 Honeybee EST Project 2026-08-14 09:24:36 5
GERMLINE
 
Resource Report
Resource Website
100+ mentions
GERMLINE (RRID:SCR_001720) GERMLINE software application, software resource Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, genetic, genomic, c++, linux, bio.tools is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
has parent organization: Columbia University; New York; USA
PMID:18971310 Free, Available for download, Freely available biotools:germline, OMICS_00202, nlx_154080 https://bio.tools/germline http://www1.cs.columbia.edu/~gusev/germline/ SCR_001720 2026-08-14 09:24:23 451
MUMA
 
Resource Report
Resource Website
10+ mentions
MUMA (RRID:SCR_002412) MUMA software application, standalone software, software resource Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY). standalone software, mac os x, unix/linux, windows, r, metabolomics, univariate, multivariate, data analysis is listed by: OMICtools
has parent organization: CRAN
Free, Available for download, Freely available OMICS_03370 SCR_002412 Metabolomics Univariate and Multivariate Analysis (MUMA), Metabolomic Univariate and Multivariate Analysis 2026-08-14 09:24:36 28
RFT FDR
 
Resource Report
Resource Website
RFT FDR (RRID:SCR_002533) RFT_FDR software application, software resource So far there is a lack for Random Field Theory (RFT) -based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley?s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer?s matlab subdirectory in the Matlab?s search path. In addition, this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses (Neuroimage 52, 158-171). console (text based), gnome, kde, matlab, mgh/mgz, modeling, magnetic resonance, os independent, rendering, statistical operation, surface analysis, surface rendering, thickness, visualization, random field theory is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: FreeSurfer
Free, Available for download, Freely available nlx_155938 SCR_002533 RFT-FDR, RFT FDR 2026-08-14 09:24:32 0
OLORIN
 
Resource Report
Resource Website
OLORIN (RRID:SCR_002015) OLORIN software application, software resource An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software) gene, genetic, genomic, java, any platform with java 1.6 or later, next generation sequencing, variant, haplotype, allele frequency, java swing is listed by: OMICtools
is listed by: Genetic Analysis Software
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
has parent organization: SourceForge
PMID:23052039 Free, Available for download, Freely available nlx_154503, OMICS_01556 http://sourceforge.net/p/olorin/ SCR_002015 2026-08-14 09:24:25 0
NIRx2nirs: A NIRx to .nirs data converter
 
Resource Report
Resource Website
1+ mentions
NIRx2nirs: A NIRx to .nirs data converter (RRID:SCR_002492) NIRx2nirs software application, software resource A matlab script which takes near-infrared spectroscopy data recorded by NIRx system(s) and converts it to a .nirs file format for use with the HOMER2 NIRS processing pacakge. hardware, nirs, fnir, optical imaging, optical imaging, physiological recording is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Homer2
Free, Available for download, Freely available nlx_155887 SCR_002492 2026-08-14 09:24:33 1
SIMIBD
 
Resource Report
Resource Website
SIMIBD (RRID:SCR_002094) SIMIBD software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software) gene, genetic, genomic, c, unix, (sunos/solaris/hp/dec-unix) is listed by: Genetic Analysis Software PMID:9002040 Free, Available for download, Freely available nlx_154622 http://watson.hgen.pitt.edu/register/soft_doc.html, http://watson.hgen.pitt.edu/~davis/ SCR_002094 2026-08-14 09:24:30 0
BREAKDANCER
 
Resource Report
Resource Website
100+ mentions
BREAKDANCER (RRID:SCR_001799) BreakDancer software application, software resource A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software) gene, genetic, genomic, perl, c++, next generation sequencing, structural variant, insertion, deletion, inversion, inter-chromosomal translocation, intra-chromosomal translocation, chromosomal translocation, indel, bio.tools is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA
PMID:19668202 Free, Available for download, Freely available biotools:breakdancer, nlx_154253, OMICS_00307 https://bio.tools/breakdancer SCR_001799 2026-08-14 09:24:22 390
MBF BioScience: Stereo Investigator
 
Resource Report
Resource Website
100+ mentions
MBF BioScience: Stereo Investigator (RRID:SCR_002526) instrument resource, software resource Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology. stereology, MBF Bioscience, number, length, area, volume cells, biological structures, tissue specimen is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: SoftCite
Restricted SciRes_000114, SCR_024705, SCR_018948 http://www.nitrc.org/projects/si_stereology SCR_002526 Stereo Investigator system 2026-08-14 09:24:34 162
HAPLOPAINTER
 
Resource Report
Resource Website
10+ mentions
HAPLOPAINTER (RRID:SCR_001710) HaploPainter software application, software resource A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software) gene, genetic, genomic, perl, pedigree, haplotype, draw, bio.tools is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
has parent organization: SourceForge
PMID:15377505 Free, Freely Available nlx_154062, OMICS_00209, biotools:haplopainter https://bio.tools/haplopainter http://haplopainter.sourceforge.net/html/ManualIndex.htm SCR_001710 2026-08-14 09:24:23 48
Primate Embryo Gene Expression Resource
 
Resource Report
Resource Website
1+ mentions
Primate Embryo Gene Expression Resource (RRID:SCR_002765) PREGER biomaterial supply resource, material resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods. primate, embryo, gene, expression, embryologist, microarray, rhesus, monkey, oocyte, embryo, cdna, library, molecular, analysis, stem cell, oocyte quality, preimplantation development, transcription is listed by: One Mind Biospecimen Bank Listing
has parent organization: Temple University School of Medicine; Pennsylvania; USA
NIH Office of the Director R24 OD012221;
NCRR RR15253
PMID:14724133
PMID:17147927
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-24366 https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources SCR_002765 PREGER Online, Preger.org 2026-08-14 09:24:37 6
RightField
 
Resource Report
Resource Website
1+ mentions
RightField (RRID:SCR_002649) RightField software application, software resource An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies. annotation, semantic, ontology, term selection, excel, java, bio.tools is listed by: BioPortal
is listed by: FORCE11
is listed by: bio.tools
is listed by: Debian
is related to: SEEK
is related to: Workflow4Ever
has parent organization: University of Manchester; Manchester; United Kingdom
has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany
PMID:21622664 Free, Available for download, Freely available biotools:rightfield, nlx_156077 https://bio.tools/rightfield SCR_002649 2026-08-14 09:24:35 3
GenomeSmasher
 
Resource Report
Resource Website
GenomeSmasher (RRID:SCR_002406) software application, software resource Software repository for tools used to create diploid FASTA files with containing snps, indels, duplications, deletions, and translocations. They can be used to create artificial genomes for next-gen sequencing simulations. fasta file creation, file creation, artificial genome creator, diploid fasta files, sequencing simulations is listed by: OMICtools
is hosted by: Google Code
Open source OMICS_00251 SCR_002406 2026-08-14 09:24:31 0
CERAD - Consortium to Establish a Registry for Alzheimer's Disease
 
Resource Report
Resource Website
1000+ mentions
CERAD - Consortium to Establish a Registry for Alzheimer's Disease (RRID:SCR_003016) CERAD assessment test provider, material resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Consortium that developed brief, standardized and reliable procedures for the evaluation and diagnosis of patients with Alzheimer's disease (AD) and other dementias of the elderly. These procedures included data forms, flipbooks, guidebooks, brochures, instruction manuals and demonstration tapes, which are now available for purchase. The CERAD assessment material can be used for research purposes as well as for patient care. CERAD has developed several basic standardized instruments, each consisting of brief forms designed to gather data on normal persons as well as on cognitively impaired or behaviorally disturbed individuals. Such data permit the identification of dementia based on clinical, neuropsychological, behavioral or neuropathological criteria. Staff at participating CERAD sites were trained and certified to administer the assessment instruments and to evaluate the subjects enrolled in the study. Cases and controls were evaluated at entry and annually thereafter including (when possible) autopsy examination of the brain to track the natural progression of AD and to obtain neuropathological confirmation of the clinical diagnosis. The CERAD database has become a major resource for research in Alzheimer's disease. It contains longitudinal data for periods as long as seven years on the natural progression of the disorder as well as information on clinical and neuropsychological changes and neuropathological manifestations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. clinical, behavior, late adult human, male, female, caucasian, african-american, autopsy, longitudinal, neuropsychology, neuropathology, FASEB list has parent organization: Duke University; North Carolina; USA Aging, Alzheimer's disease, Dementia, Cognitive impairment, Neurodegenerative disorder, Systemic illness, Cerebrovascular disease, Parkinson's disease, Depressive Disorder NIA THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00523 SCR_003016 Consortium to Establish a Registry for Alzheimer's Disease 2026-08-14 09:24:43 2337
Slicer3 Example Modules
 
Resource Report
Resource Website
Slicer3 Example Modules (RRID:SCR_002559) Slicer3 Example Modules software application, software development tool, software resource Example Slicer3 plugins that can be built against a Slicer3 build or a Slicer3 installation. Note: these are for 3D Slicer version 3. There is now a version 4 of 3D Slicer available. Information about extensions for version 4 can be found at the following links: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/ExtensionsManager http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/BuildTestPackageDistributeExtensions analyze, c++, console (text based), computed tomography, dicom, linux, macos, microsoft, magnetic resonance, nifti, pet, spect, platform or development environment, posix/unix-like, win32 (ms windows), windows, windows nt/2000, windows vista is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: 3D Slicer
is related to: INCF Software Center
Free, Available for download, Freely available nlx_155965 SCR_002559 2026-08-14 09:24:33 0
PEDHUNTER
 
Resource Report
Resource Website
1+ mentions
PEDHUNTER (RRID:SCR_002031) PedHunter software application, software resource Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot. gene, genetic, genomic, genealogy, pedigree, bio.tools is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
has parent organization: NCBI
PMID:20433770
PMID:9521925
THIS RESOURCE IS NO LONGER IN SERVICE biotools:pedhunter, OMICS_00211, nlx_154518 https://bio.tools/pedhunter SCR_002031 2026-08-14 09:24:26 2
TherMos
 
Resource Report
Resource Website
100+ mentions
TherMos (RRID:SCR_002790) algorithm resource, software resource Software used for estimating protein-DNA binding energies from in vivo binding profiles. It is a de novo motif discovery algorithm that exploits the information in transcription factor ChIP-seq or ChIP-exo datasets based on a more natural thermodynamic formalism., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. protein dna binding energy, in vivo binding profiles, motif discovery uses: MATLAB
is listed by: OMICtools
PMID:23595148 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00498 SCR_002790 2026-08-14 09:24:39 208
LAMP
 
Resource Report
Resource Website
1000+ mentions
LAMP (RRID:SCR_001740) LAMP software application, software resource Software for linkage and association modeling in pedigrees that uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern. gene, genetic, genomic, c++, unix, linux, windows, macos, linkage, association, modeling, pedigree is listed by: Genetic Analysis Software
has parent organization: University of Michigan; Ann Arbor; USA
PMID:16642434 Free, Available for download, Freely available nlx_154103 SCR_001740 Linkage and Association Modeling in Pedigrees 2026-08-14 09:24:21 1166

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