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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Parallel-META Resource Report Resource Website 1+ mentions |
Parallel-META (RRID:SCR_000121) | data processing software, data analysis software, software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis. | data mining, microbial community data, comparative taxonomics, metagenomic analysis, parallel algorithms | is listed by: OMICtools | PMID:23046922 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01519 | SCR_000121 | Parallel META, Parallel Meta | 2026-08-12 10:48:10 | 4 | |||||||
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Adaptively Sampled Particle Fluids Resource Report Resource Website |
Adaptively Sampled Particle Fluids (RRID:SCR_000083) | ASPF | simulation software, software application, software resource, source code | Scalable particle fluid simulation code for Lagrangian particle-based fluid simulation. This adaptive sampling strategy allows using smaller (and thus more) particles in geometrically complex regions, while less particles are used for thick flat fluid volumes. Additionally, a novel distance-based particle surface definition is implemented which hides the particle granularity and allows dynamic resampling near the fluid-air interface. The code is implemented in C++ and should compile on Linux. | fluid simulation, lagrangian particle fluid, linux |
is listed by: Biositemaps is listed by: Simtk.org |
Free, Available for download, Freely available | nif-0000-23328 | SCR_000083 | 2026-08-12 10:48:10 | 0 | ||||||||
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BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | data visualization software, software application, data processing software, software resource, data analysis software | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | BAIT - Software to help analyse Strand-Seq data | 2026-08-12 10:48:14 | 1 | |||||
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RefFinder Resource Report Resource Website 10+ mentions |
RefFinder (RRID:SCR_000472) | RefFinder | service resource, production service resource, software resource, data access protocol, analysis service resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, gene expression, reference gene, web based tool |
uses: BestKeeper uses: NormFinder uses: geNORM is listed by: OMICtools has parent organization: East Carolina University; Carolina; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02321 | http://www.leonxie.com/referencegene.php | SCR_000472 | 2026-08-12 10:48:13 | 45 | |||||||
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Human Disease Ontology Resource Report Resource Website 1+ mentions |
Human Disease Ontology (RRID:SCR_000476) | DO | data or information resource, controlled vocabulary, database, ontology | Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases. | obo, pathological, organismal, cellular, disease, biomedical, health, neurologic disease, neurological disorder, phenotype, bio.tools, |
is used by: DOAF is listed by: BioPortal is listed by: OBO is listed by: bio.tools is listed by: Debian is related to: PharmGKB Ontology is related to: GWASdb is related to: NUgene Project is related to: FunDO is related to: Neurocarta has parent organization: University of Maryland School of Medicine; Maryland; USA |
NHGRI U24 HG012557 | PMID:22080554 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-35926, nlx_157432, SCR_003491, biotools:disease_ontology | http://disease-ontology.org/, https://bio.tools/disease_ontology, http://purl.obolibrary.org/obo/doid.obo, | http://do-wiki.nubic.northwestern.edu/index.php/Main_Page | SCR_000476 | Human Disease Ontology Knowledgebase, Disease Ontology | 2026-08-12 10:48:13 | 5 | |||
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Gazetteer Resource Report Resource Website 1+ mentions |
Gazetteer (RRID:SCR_000473) | GAZ | data or information resource, topical portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available. | obo, owl |
is listed by: BioPortal is listed by: OBO has parent organization: Genomic Standards Consortium |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157412 | http://purl.obolibrary.org/obo/gaz.owl, http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/gaz.obo | http://gensc.org/gc_wiki/index.php/GAZ_Project | SCR_000473 | 2026-08-12 10:48:13 | 1 | ||||||
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AETIONOMY Resource Report Resource Website 1+ mentions |
AETIONOMY (RRID:SCR_000232) | AETIONOMY | data or information resource, portal, consortium, organization portal | Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery. | drug development, drug, taxonomy, biomarker, etiology, epidemiology, neuroimaging, mechanism, clinical, clinical trial, database, classification, biological pathway, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Fraunhofer Institute for Algorithms and Scientific Computing SCAI; North Rhine-Westphalia; Germany |
IMI ; EFPIA |
nlx_157972, biotools:AETIONOMY | https://bio.tools/AETIONOMY | SCR_000232 | 2026-08-12 10:48:11 | 3 | |||||||
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Denver University Department of Psychology Resource Report Resource Website |
Denver University Department of Psychology (RRID:SCR_000474) | data or information resource, department portal, portal, organization portal | The department of psychology at Denver University that offers degrees at the undergraduate, graduate and doctoral level. The doctoral programs have specializations such as Affect/Social, Child Clinical, Cognitive, and Developmental. | psychology, graduate, doctoral, affect, social, child, clinical, cognitive, developmental, neuroscience | has parent organization: University of Denver; Colorado; USA | nif-0000-01928 | SCR_000474 | DU Dept. of Psychology, University of Denver Department of Psychology | 2026-08-12 10:48:13 | 0 | |||||||||
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ECNP Resource Report Resource Website 1+ mentions |
ECNP (RRID:SCR_000501) | ECNP | data or information resource, community building portal, portal | A pan-European scientific association to encourage research across the neurosciences and to translate new knowledge on fundamental disease mechanisms into new medicines and clinical applications. As an interdisciplinary forum for the science and treatment of disorders of the brain, they promote the communication and cross- fertilization of high-quality experimental and clinical research across the field of neuroscience. ECNP is a non-profit member-based association, independently governed and self-funded. ECNP is a public-interest-serving entity. | brain, neuroscience, disease mechanism, medicine, clinical, disease | is parent organization of: Preclinical Data Forum Network | Brain disorder | nlx_158605 | SCR_000501 | European College of Neuropsychopharmacology, ECNP - neuroscience applied | 2026-08-12 10:48:14 | 1 | |||||||
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National MS Society Resource Report Resource Website 10+ mentions |
National MS Society (RRID:SCR_000104) | National MS Society | portal, data or information resource, funding resource, disease-related portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Society helps people affected by Multiple Sclerosis by funding cutting-edge research, driving change through advocacy, facilitating professional education, and providing programs and services that help people with MS and their families move their lives forward. | multiple sclerosis, award, grant, postdoctoral fellowship | Multiple Sclerosis | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143693 | SCR_000104 | National Multiple Sclerosis Society | 2026-08-12 10:48:10 | 34 | |||||||
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RSEM Resource Report Resource Website 100+ mentions |
RSEM (RRID:SCR_000262) | data processing software, data analysis software, software resource, software application | Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. | quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:21816040 | Free, Available for download, Freely available | OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 | https://github.com/deweylab/RSEM, https://github.com/deweylab/RSEM/releases, https://bio.tools/rsem, https://sources.debian.org/src/rsem/ | SCR_000262 | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-08-12 10:48:11 | 115 | ||||||
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TEDDY Resource Report Resource Website 1+ mentions |
TEDDY (RRID:SCR_000383) | TEDDY | portal, data or information resource, database, clinical trial, organization portal, consortium | International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes. | consortium, gene, infectious agent, dietary factor, environmental factor, young human, insulin, child, pediatric, autoantibody, blood, stool, biomaterial supply resource, longitudinal, neonate, parent, genetic risk, genetic factor, observation, prospective, serum, plasma, peripheral blood mononuclear cell, saliva, nasal swab, nail clipping, water, dna, virus, nutrition, toxic agent, socioeconomic, psychosocial, male, female, environment, exposure, diet, toxin, infectious agent, bacterial, viral, immunization |
is listed by: One Mind Biospecimen Bank Listing is listed by: ClinicalTrials.gov is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Central Repository is related to: Teddy study IA prediction has parent organization: University of South Florida; Florida; USA |
Type 1 diabetes, Diabetes | NIDDK 2UC4DK063829 | PMID:21564455 | nlx_152857 | SCR_000383 | The Environmental Determinants of Diabetes in the Young, TEDDY study | 2026-08-12 10:48:12 | 3 | |||||
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Trans-Institute Angiogenesis Research Program Resource Report Resource Website |
Trans-Institute Angiogenesis Research Program (RRID:SCR_000384) | TARP | data or information resource, topical portal, resource, portal | Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests. | blood vessel, growth, development, target, therapeutic, vascularization, angiogenesis, lymphangiogenesis |
is listed by: NIDDK Information Network (dkNET) has parent organization: National Institutes of Health |
Angiogenesis, Lymphangiogenesis | JDRF ; NEI ; NHLBI ; NCI ; NICHD ; NIDDK ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152866 | SCR_000384 | Trans-Institute Angiogenesis Research Program (TARP) | 2026-08-12 10:48:12 | 0 | |||||
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M(at)CBETH Resource Report Resource Website |
M(at)CBETH (RRID:SCR_000265) | M(at)CBETH | software resource, data access protocol, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. Web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset. | microarray, classification, performing microarray classification, |
is listed by: OMICtools has parent organization: Catholic University of Leuven; Flemish Brabant; Belgium |
PMID:15890742 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02292 | SCR_000265 | MicroArray Classification BEnchmarking Tool on Host server | 2026-08-12 10:48:11 | 0 | ||||||
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Local Binary Pattern Analysis Tools for MR Brain Images Resource Report Resource Website 1+ mentions |
Local Binary Pattern Analysis Tools for MR Brain Images (RRID:SCR_000412) | LBP Analysis Tools for MR Brain Images | image analysis software, image processing software, software application, data processing software, software resource | The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology. | free for non-commercial use only, mr | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155652 | SCR_000412 | 2026-08-12 10:48:13 | 1 | ||||||||
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PSCBS Resource Report Resource Website |
PSCBS (RRID:SCR_000417) | sequence analysis software, software application, data processing software, software resource, data analysis software | Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported. | abnormal copy number regions detection, allele specific DNA copy number data segmentation, |
is listed by: OMICtools is listed by: Debian is related to: CRAN has parent organization: University of California at San Francisco; California; USA |
PMID:21666266 DOI:10.1093/bioinformatics/btr329 |
Free, Available for download, Freely available | OMICS_05545 | https://sources.debian.org/src/r-cran-pscbs/ | SCR_000417 | PSCBS: Analysis of Parent-Specific DNA Copy Numbers | 2026-08-12 10:48:13 | 0 | ||||||
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Open Colleges Resource Report Resource Website |
Open Colleges (RRID:SCR_000418) | Open Colleges | online course, training resource | A resource for online accredited courses in a wide variety of areas, including accounting, animal care, beauty, building and construction, business, education, design and writing. This resource is based in Australia. | open source, accredited, accounting, beauty, animal care, writing, journalism, education, business, building, real estate |
is parent organization of: Open Colleges Interactive Brain is parent organization of: Open Colleges Group |
nlx_155866 | SCR_000418 | 2026-08-12 10:48:13 | 0 | |||||||||
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uManager Resource Report Resource Website 100+ mentions |
uManager (RRID:SCR_000415) | software toolkit, data acquisition software, software application, data processing software, software resource | Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories. | microscopy, plugin, data acquisition, automated microscope control, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ImageJ has parent organization: University of California at San Francisco; California; USA |
Free, Available for download, Freely available | SCR_016865, nlx_155812 | https://micro-manager.org/wiki/Download_Micro-Manager_Latest_Release, https://sources.debian.org/src/micromanager/, http://www.nitrc.org/projects/micromanager | SCR_000415 | Micro-Manager, Micro Manager | 2026-08-12 10:48:13 | 285 | |||||||
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BSmooth-align Resource Report Resource Website 1+ mentions |
BSmooth-align (RRID:SCR_000013) | image analysis software, software application, data processing software, alignment software, software resource, data analysis software | Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements. | bisulfite sequence, read-level methylation, bisulfite sequence reads alignment, | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01846 | SCR_000013 | 2026-08-12 10:48:08 | 1 | |||||||||
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Sequence Read Format Resource Report Resource Website 1+ mentions |
Sequence Read Format (RRID:SCR_000132) | SRF | data or information resource, narrative resource, standard specification, interchange format | A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology. | dna sequence, dna sequencing, interchange format |
is listed by: OMICtools has parent organization: SourceForge |
Public, A C++ implementation of Sequence Read Format is available | OMICS_05130 | SCR_000132 | Sequence Read Format (SRF) | 2026-08-12 10:48:10 | 1 |
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