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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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UNAFold Resource Report Resource Website 100+ mentions |
UNAFold (RRID:SCR_001360) | software application, software resource, 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 | 2026-08-10 09:31:24 | 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 application, portal, topical portal, software resource | 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 | 2026-08-10 09:31:25 | 1 | ||||||
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Happy Resource Report Resource Website 10+ mentions |
Happy (RRID:SCR_001395) | HAPPY | source code, data analysis software, software application, software resource, 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 | 2026-08-10 09:31:24 | 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, data repository, database, service resource, storage service resource | 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 | 2026-08-10 09:31:25 | 1 | ||||||
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CenterWatch Resource Report Resource Website 1+ mentions |
CenterWatch (RRID:SCR_001158) | data or information resource, topical portal, portal | CenterWatch is an online resource for news, directories, analysis, and proprietary market research for clinical research professionals and patients. For patients, CenterWatch is committed to providing information on clinical trials, specific drugs, as well as other essential health and educational resources. On this website, patients can search clinical trials, receive e-mail notifications about specific clinical trials, review results from completed clinical trials, search drug information, learn about volunteering for a clinical trial, read an overview of the clinical trials process and find other health and educational resources. For researchers, CenterWatch offers a wide range of tools and resources to improve patient and investigator recruitment, remain current with industry trends and business practices, and strengthen organizational procedures. CenterWatch also offers information on grant opportunities, and a variety of educational books and publications. Researchers can provide the public with information about their clinical trials by using the Clinical Trials Listing Serviceprovided through CenterWatch, or look up more specific information on medicines and equipment using Drug and Device Pipeline News. Overall, the mission of CenterWatch is to be the leading source of news, directories, analysis, and proprietary market research for clinical research professionals and patients. It is located in Boston, MA. :NIF thanks the :Parkinson's Disease Foundation : :for their referral of this resource to us. | drug information, drug study, clinical research, clinical study, clinical trial, medicine, patient, health, medical | nif-0000-11641 | SCR_001158 | CenterWatch | 2026-08-10 09:31:22 | 9 | ||||||||||
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CGHbase Resource Report Resource Website 1+ mentions |
CGHbase (RRID:SCR_001279) | CGHbase | software application, software resource, data analysis software, data processing software | Software package that contains functions and classes that are needed by arrayCGH packages. | copy number variation, infrastructure, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02057 | SCR_001279 | CGHbase: Base functions and classes for arrayCGH data analysis | 2026-08-10 09:31:23 | 1 | |||||||
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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 | access service resource, analysis service resource, production service resource, biomaterial analysis service, service resource, biomedical technology research center, material analysis service, training resource | 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 | 2026-08-10 09:31:25 | 1 | ||||||
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MRI Studio Resource Report Resource Website 100+ mentions |
MRI Studio (RRID:SCR_001398) | software application, data visualization software, software resource, image analysis software, image processing 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 | 2026-08-10 09:31:25 | 180 | ||||||
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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, narrative resource, common data element, 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 | 2026-08-10 09:31:24 | 8 | ||||||
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Simpleaffy Resource Report Resource Website 50+ mentions |
Simpleaffy (RRID:SCR_001302) | Simpleaffy | software application, software resource, 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 | 2026-08-10 09:31:23 | 85 | ||||||
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Open Colleges Interactive Brain Resource Report Resource Website 1+ mentions |
Open Colleges Interactive Brain (RRID:SCR_001427) | Open Colleges Interactive Brain | data or information resource, training material, narrative resource, atlas | Interactive infographic of a brain exploring more than 100,000 chemical reactions, highlighted by areas and explanations of what that area is known to do. | brain, chemical reaction | has parent organization: Open Colleges | Restricted | nlx_155867 | SCR_001427 | 2026-08-10 09:31:25 | 1 | ||||||||
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CODR: C PATH On Line Data Repository Resource Report Resource Website 1+ mentions |
CODR: C PATH On Line Data Repository (RRID:SCR_001388) | CODR | data or information resource, analysis service resource, data repository, production service resource, database, service resource, data analysis service, storage service resource | A repository of de-identified control arm data of patients from clinical studies of Alzheimer's disease and Mild Cognitive Impairment. It provides the ability to analyze the data online with the R statistical analysis program, create and download standard reports, run complex queries, or download data to a desktop for further analysis. Additional data will be added to the database over time. Critical Path Institute consortia members and qualified researchers may upload and work on scientific data relevant to biomarkers of drug toxicity, neurodegenerative diseases, and patient-reported outcomes. | clinical data, alzheimer's disease, camd, biomarker, drug toxicity, neurodegenerative disease, patient-reported outcome, patient outcome, metadata standard, data repository | has parent organization: CAMD | Neurodegenerative disease, Drug toxicity, Alzheimer's disease, Mild Cognitive Impairment | Free, Freely Available | nlx_152562 | SCR_001388 | C-Path Online Data Repository (CODR), CPATH online data repository, C-PATH Online Data Repository, C PATH On Line Data Repository | 2026-08-10 09:31:25 | 2 | ||||||
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CAMD Resource Report Resource Website 1+ mentions |
CAMD (RRID:SCR_001389) | CAMD | data or information resource, organization portal, consortium, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 8, 2022. Consortium developing new technologies and methods to accelerate the development and review of medical products for neurodegenerative diseases. It is focused on accelerating drug development for patients with chronic neurodegenerative disease, namely, Alzheimer's disease (AD) and Parkinson's disease (PD), by advancing drug development tools for evaluating drug efficacy, conducting clinical trials, and streamlining the process of regulatory review. The consortium focuses on sharing precompetitive patient-level data from the control arms of legacy clinical trials, developing new tools to be submitted to the regulatory agencies, and developing consensus data standards. CAMD has the following areas of focus: (1) qualification of biomarkers, (2) development of common data standards, (3) creation of integrated databases for clinical trials data, and (4) development of quantitative model-based tools for drug development. Regulatory milestones include a qualification opinion with EMA for the use of low baseline hippocampal volume for patient enrichment in pre-dementia trials, and most recently, positive regulatory decisions from the FDA and EMA for the use of a clinical trial simulation tool to aid in trials for mild to moderate stages of AD., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data set, clinical trial, mild cognitive impairment, clinical, biomarker, metadata standard, disease progression model, consortium, drug, data sharing, disease modeling, drug development, disease model, imaging, cerebral spinal fluid |
is listed by: Consortia-pedia has parent organization: Critical Path Institute; Arizona; USA is parent organization of: CODR: C PATH On Line Data Repository |
Publicly funded | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152563 | SCR_001389 | Coalition Against Major Diseases | 2026-08-10 09:31:24 | 6 | ||||||
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Mutascope Resource Report Resource Website 1+ mentions |
Mutascope (RRID:SCR_001265) | Mutascope | software application, software resource, data analysis software, data processing software | Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations. | high throughput sequencing, pcr amplicon, pcr, mutation, amplicon, sequencing, somatic variant |
is listed by: OMICtools has parent organization: SourceForge |
Tumor, Normal | PMID:23712659 | Free, Public | OMICS_02074 | SCR_001265 | Mutascope - Analysis software designed for PCR-amplicon sequencing data | 2026-08-10 09:31:23 | 4 | |||||
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Mugsy Resource Report Resource Website 50+ mentions |
Mugsy (RRID:SCR_001414) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy. | software, genome, genome alignment, segmentation, pairwise alignment, sequence analysis software |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:21148543 DOI:10.1093/bioinformatics/btq665 |
Free, Available for download, Freely available | OMICS_03606 | https://sources.debian.org/src/mugsy/ | SCR_001414 | 2026-08-10 09:31:25 | 75 | |||||||
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Phred Resource Report Resource Website 10+ mentions |
Phred (RRID:SCR_001017) | Phred | data analysis software, software application, software resource, sequence analysis software, data processing software | A base calling program for DNA sequence traces. | base calling, sequence analysis software, dna, trace | is listed by: OMICtools | PMID:9521922 | Restricted | OMICS_01809 | SCR_001017 | 2026-08-10 09:31:19 | 13 | |||||||
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Enrichr Resource Report Resource Website 5000+ mentions |
Enrichr (RRID:SCR_001575) | Enrichr | analysis service resource, production service resource, software application, service resource, software resource, data analysis service | A web-based gene list enrichment analysis tool that provides various types of visualization summaries of collective functions of gene lists. It includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes / proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. | bed, gene, software as a service, rna-seq, analyze, protein, function, gene list, visualization, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:23586463 | Free, Freely available | biotools:enrichr, SciRes_000171 | https://bio.tools/enrichr | SCR_001575 | 2026-08-10 09:31:28 | 5047 | ||||||
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EEGbase Resource Report Resource Website 1+ mentions |
EEGbase (RRID:SCR_001452) | data or information resource, data repository, database, service resource, storage service resource | EEG base is a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments. EEG base advances electrophysiology research by enabling access to public data, tools and results of research groups. The system essentially offers the following set of features (the set of accessible features depends on a specific user role): * User authentication * Storage, update, and download of EEG/ERP data and metadata * Storage, update and download of EEG/ERP experimental design (experimental scenarios) * Storage, update and download of data related to testing subjects * Fulltext search * Sharing of knowledge and working in groups The system is based on tree layer architecture (MVC pattern) consisting of persistent layer (relational database), application layer (object oriented code, object relational mapping from persistence layer) and presentation layer (JSP). The persistence layer uses Hibernate framework; Oracle 11g database server is used to ensure the processing of large data files. Application and presentation layers are designed and implemented using Spring technology. This framework supports MVC architecture, Dependency injection and Aspect Oriented Programming. There were no significant difficulties with integration of both frameworks, Hibernate and Spring MVC. Spring Security framework is used to ensure management of authentication and user roles. Since the system is thought to be finally open to the whole EEG/ERP community it is necessary to protect EEG/ERP data and metadata, and especially personal data of testing subjects stored in the database from an unauthorized access. Then a restricted user policy is applied and user roles are introduced. The complete overview of the system features and user roles (use case diagram) is available in (Pergler 2009). Concerning the architectural layers there is a question which layer is more feasible for mapping of its structure into ontology. Currently we have studied two possibilities: * Mapping from the persistence layer (relational database) * Mapping from the application layer (object oriented code) The mapping from the application layer to an ontology includes the precedent object relational mapping provided by Hibernate framework. | eeg, erp, experiments, data storage and management, EEG/ERP data, EEG/ERP experiments, |
uses: NIX uses: Open metadata mark up language is used by: NIF Data Federation has parent organization: University of West Bohemia; Pilsen; Czech Republic |
Ministry of Education Czech Science Foundation | Free, Freely Available | nif-0000-08190 | http://eegdatabase.kiv.zcu.cz/ | SCR_001452 | 2026-08-10 09:31:26 | 7 | |||||||
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GlyTorsion Resource Report Resource Website 1+ mentions |
GlyTorsion (RRID:SCR_001568) | GlyTorsion | data or information resource, analysis service resource, production service resource, data set, service resource, data analysis service | Service that performs a statistical analysis of carbohydrate torsion angles derived from the Protein Data Bank. Such as protein conformation can be described by the backbone torsion angles, a carbohydrate structure is mainly characterised by its linkage torsions. With the aid of pdb2linucs, a dataset of carbohydrate torsion angles was derived from from carbohydrate structures found in the PDB. This weekly updated dataset contains, besides linkage torsions, also ring torsions, omega torsions, N-acetyle group torsions and sidechain torsions of Asn residues involved in Glycan bonds. It can be queried by GlyTorsion. | carbohydrate, torsion angle, torsion, angle, linkage torsion, ring torsion, omega torsion, n-acetyle group torsion, sidechain torsion, asn residue, glycan bond, statistical analysis |
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: pdb2linucs is related to: CARP has parent organization: glycosciences.de |
DFG | PMID:15608187 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152881 | SCR_001568 | GlyTorsion: Analysis of Carbohydrate Torsion Angles found in the Protein Data Bank (PDB) | 2026-08-10 09:31:27 | 4 | |||||
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Functional Image Processing software Computational Olio Resource Report Resource Website 1+ mentions |
Functional Image Processing software Computational Olio (RRID:SCR_001689) | FIASCO | software application, software resource, image analysis software, image processing software, data processing software | Collection of software designed to analyze fMRI data using a series of processing steps. The input is the raw data, and the outputs are statistical brain maps showing regions of neural activation. Corrections for different systematic variations in the k-space (raw) data obtained from an fMRI session (head motion, ghosting, etc) are performed first. The image is then reconstructed (using the Fast Fourier Transform) and statistical analyses run. The user has a great deal of flexibility in choosing which corrections and statistics are executed. FIASCO emphasizes correct statistical models, for example for group comparisons. | fmri, brain, neural activation, neuroimaging, function | has parent organization: Carnegie Mellon University; Pennsylvania; USA | PMID:22348882 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00298 | SCR_001689 | 2026-08-10 09:31:30 | 5 |
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