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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Entrez Utilities Resource Report Resource Website 10+ mentions |
Entrez Utilities (RRID:SCR_013249) | software resource |
Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment. Additional information is available in the NCBI Bookshelf Short Courses Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils) and the NCBI PowerScripting course. User Requirements: Please read for important information on scripting NCBI servers. EInfo: Provides field index term counts, last update, and available links for each database. ESearch: Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user''s environment. EPost: Posts a file containing a list of primary IDs for future use in the user''s environment to use with subsequent search strategies. ESummary: Retrieves document summaries from a list of primary IDs or from the user''s environment. EFetch: Retrieves records in the requested format from a list of one or more primary IDs or from the user''s environment. ELink: Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs. EGQuery: Provides Entrez database counts in XML for a single search using Global Query. ESpell: Retrieves spelling suggestions. SOAP Interface for Entrez Utilities PMID to PMC ID Converter Entrez DTDs Demonstration Program Announcement Mailing List Leasing Data from the National Library of Medicine Help Desk User Requirements Do not overload NCBI''s systems. Users intending to send numerous queries and/or retrieve large numbers of records from Entrez should comply with the following: Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests. Send E-utilities requests to http://eutils.ncbi.nlm.nih.gov, not the standard NCBI Web address. Make no more than 3 requests every 1 second. Use the URL parameter email, and tool for distributed software, so that we can track your project and contact you if there is a problem. NCBI''s Disclaimer and Copyright notice must be evident to users of your service. NLM does not claim the copyright on the abstracts in PubMed; however, journal publishers or authors may. NLM provides no legal advice concerning distribution of copyrighted materials, consult your legal counsel. |
has parent organization: National Library of Medicine | nif-0000-30519 | http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html | SCR_013249 | Entrez Utilities | 2026-08-08 12:00:20 | 21 | |||||||||
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BrainVisa Morphology extensions Resource Report Resource Website 1+ mentions |
BrainVisa Morphology extensions (RRID:SCR_013248) | BrainVisa Morphology extensions | software resource | An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa | analyze, c++, image display, linux, macos, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, shape analysis, software, visualization, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainVISA / Anatomist is related to: INCF Software Center |
Artistic License | nlx_155716 | http://www.nitrc.org/projects/brainvisa_ext | SCR_013248 | 2026-08-08 12:00:09 | 1 | |||||||
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BOOST Resource Report Resource Website 10+ mentions |
BOOST (RRID:SCR_013133) | BOOST | software resource, software application, data analysis software, data processing software | Software application (entry from Genetic Analysis Software) for a method for detecting gene-gene interactions. It allows examining all pairwise interactions in genome-wide case-control studies. | gene, genetic, genomic, logistic regression model, gene-gene interactions | is listed by: Genetic Analysis Software | Free, Available for download | nlx_154249 | SCR_013133 | BOolean Operation based Screening and Testing | 2026-08-08 12:00:19 | 33 | |||||||
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CSA - Catalytic Site Atlas Resource Report Resource Website 10+ mentions |
CSA - Catalytic Site Atlas (RRID:SCR_013099) | CSA | database, data or information resource, software resource | The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. We defined a classification of catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalyzed by an enzyme. The CSA contains 2 types of entry: 1. Original hand-annotated entries, derived from the primary literature. References for these entries are given. 2. Homologous entries, found by PSI-BLAST alignment (using an e value cut-off of 0.00005) to one of the original entries. The equivalent residues, which align in sequence to the catalytic residues found in the original entry are documented. Access to the CSA is via PDB code, SWISS-PROT entry or E.C. number. Accessing via PDB code takes you straight to the CSA entry for that PDB, while accessing via SWISS-PROT or E.C. number gives a list of all PDB codes for structures assigned that particular SWISS-PROT identifier or E.C. number. Structures with entries in the CSA are given as hyperlinks. Each CSA entry lists the catalytic residues found in that entry, using PDB residue numbering. Each site is also marked with an evidence tag, which is either Literature reference or PSI-BLAST hit. If the entry is a PSI-BLAST hit you can follow the link to the original entry. You may download the CSA. JESS, an algorithm for constraint-based structural template matching and its application to 3D templates used by the CSA, is available for download. | enzyme, enzyme 3d structure, enzyme catalysis, enzyme structure, catalysis, catalytic site, catalytic residue, gold standard |
has parent organization: European Bioinformatics Institute works with: MOLEonline |
PMID:14681376 | nif-0000-02699, r3d100010815 | SCR_013099 | Catalytic Site Atlas | 2026-08-08 12:00:07 | 14 | |||||||
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miRSeqNovel Resource Report Resource Website 1+ mentions |
miRSeqNovel (RRID:SCR_013257) | miRSeqNovel | software resource | An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
Free, Public, Non-commercial | OMICS_00381 | SCR_013257 | 2026-08-08 11:59:54 | 2 | |||||||||
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AutoMap Resource Report Resource Website 100+ mentions |
AutoMap (RRID:SCR_013095) | AutoMap | software resource | A tool for structural biology and drug design. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01596 | SCR_013095 | 2026-08-08 12:00:19 | 100 | ||||||||||
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DynamicProg Resource Report Resource Website 1+ mentions |
DynamicProg (RRID:SCR_013217) | DynamicProg | software resource | A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01150 | SCR_013217 | 2026-08-08 11:59:53 | 1 | ||||||||||
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A Catalogue of Illusions Resource Report Resource Website |
A Catalogue of Illusions (RRID:SCR_013186) | data or information resource, image collection | Set of different illusions, including color illusions, motion illusions, and optic illusions. Most illusions are from Professor Akiyoshi Kitaoka of the Ritsumeikan University in Kyoto, Japan. | color, illusion, motion, optical, vision | has parent organization: Ritsumeikan University; Kyoto; Japan | nif-0000-24679 | SCR_013186 | Catalogue of Illusions | 2026-08-08 12:00:08 | 0 | |||||||||
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muliAlignFree Resource Report Resource Website 1+ mentions |
muliAlignFree (RRID:SCR_013188) | muliAlignFree | software resource | R package intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
PMID:23990418 | Free | OMICS_00981 | SCR_013188 | muliAlignFree: Multiple Alignment-free Sequence Comparison | 2026-08-08 11:59:53 | 1 | |||||||
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Akiyoshis illusion pages Resource Report Resource Website 1+ mentions |
Akiyoshis illusion pages (RRID:SCR_013187) | data or information resource, portal, topical portal | This portal describes Professor Kitaoka Akiyoshi''s research in the science of visual illusions. Working as an associate professor at the Ritsumeiken University, Department of Psychology, he is one of the few researchers in Japan to be actively researching in this field of study. Professor Kitaoka defines an illusion as a misperception of a real object, adding that defining what is real is a difficult task that depends on recognition and epistemology. An illusion is formed when the perceived characteristics of the object differ from the physical characteristics. Professor Kitaoka first started studying visual illusions when working at the Tokyo Metropolitan Institute for Neuroscience, before coming to RU. He currently researches geometrical, color, lightness, and motion illusions and visual completion, and has become a prominent expert in the field, publishing a wide range of articles on the subject as well as the popular books Trick Eyes, Trick Eyes 2, Trick Eyes Graphics, and the Handbook of the Science of Illusion. To create his illusions, Professor Kitaoka uses graphic design software such as CorelDRAW, Adobe Illustrator, and the drawing software included in Microsoft Word in addition to making use of programming languages like Borland Delphi (Pascal). All of the images set out to test hypotheses that serve to advance his study of illusions and their applications for other visual functions. The goal of his research is to test visual mechanisms through visual illusions. | epistemology, eye, function, color, geometrical, graphic, illusion, lightness, mechanism, motion, neuroscience, object, perception, psychology, recognition, research, science, software, visual | has parent organization: Ritsumeikan University; Kyoto; Japan | nif-0000-24776 | SCR_013187 | Illusions Pages | 2026-08-08 12:00:20 | 7 | |||||||||
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U.S. Public Health Service Commissioned Corps Resource Report Resource Website 1+ mentions |
U.S. Public Health Service Commissioned Corps (RRID:SCR_013104) | USPHS | institution | Commissioned Corps of the United States Public Health Service, is the federal uniformed service of the U.S. Public Health Service, and is one of the eight uniformed services of the United States. | Government granting agency | nlx_152565, Crossref funder ID: 100007197, ISNI: 0000 0001 1554 5300, grid.417684.8, Wikidata: Q476322 | https://ror.org/05xf94514 | SCR_013104 | US Public Health Service Commissioned Corps, U.S. Public Health Service | 2026-08-08 11:59:52 | 7 | ||||||||
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Mean Machine Resource Report Resource Website |
Mean Machine (RRID:SCR_013103) | Mean Machine | software resource, software application, data analysis software, data processing software | This software can be used to analyze EEG data either using a graphical interface (GUI) or using Matlab scripts, which make use of the functions provided by the MeanMachine. As compared to other libraries, MeanMachine can handle even very large data sets like, for example, 256 channels recorded at 2KHz. | eeg, meg, electrocorticography, matlab | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License v2 | nlx_155808 | http://www.nitrc.org/projects/incf_mean-machi | SCR_013103 | 2026-08-08 12:00:19 | 0 | |||||||
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National Institute for Occupational Safety and Health Resource Report Resource Website 1+ mentions |
National Institute for Occupational Safety and Health (RRID:SCR_013180) | NIOSH, OH | institution | http://www.cdc.gov/niosh/oep/funding.html |
has parent organization: Centers for Disease Control and Prevention is parent organization of: Adult Blood Lead Epidemiology and Surveillance Interactive Database |
nlx_inv_1005099, grid.416809.2, ISNI: 0000 0004 0423 0663, Wikidata: Q60346, Crossref funder ID: 100000125 | https://ror.org/0502a2655 | SCR_013180 | 2026-08-08 11:59:53 | 2 | |||||||||
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CancerMutationAnalysis Resource Report Resource Website |
CancerMutationAnalysis (RRID:SCR_013181) | CancerMutationAnalysis | software resource | Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer. |
is listed by: OMICtools has parent organization: Bioconductor |
Cancer | OMICS_00141 | SCR_013181 | 2026-08-08 12:00:08 | 0 | |||||||||
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NCJDSU Resource Report Resource Website 1+ mentions |
NCJDSU (RRID:SCR_013183) | NCJDSU | data or information resource, portal, topical portal | The incidence of Creutzfeldt-Jakob disease (CJD) is monitored in the UK by the National CJD Surveillance Unit (NCJDSU) based at the Western General Hospital in Edinburgh, Scotland. The Unit brings together a team of clinical neurologists, neuropathologists and scientists specialising in the investigation of this disease. This document is intended to summarise the research in progress at the NCJDSU and also provide some background information about CJD and other human spongiform encephalopathies. We have also provided some links to other resources and contrary points of view available on the Web. | has parent organization: University of Edinburgh; Scotland; United Kingdom | nif-0000-32035 | http://www.cjd.ed.ac.uk/vcjdworld.htm | SCR_013183 | National Creutzfeldt-Jakob Disease Surveillance Unit, The National Creutzfeldt-Jakob Disease Surveillance Unit, National CJD Surveillance Unit | 2026-08-08 12:00:20 | 9 | ||||||||
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LiverSegm Resource Report Resource Website |
LiverSegm (RRID:SCR_013108) | LiverSegm | image processing software, segmentation software, image analysis software, software resource, software application, data processing software | Software tools for the processing of liver images. These tools consist of a level set based variational approach that incorporates shape priors and appearance models. It uses ITK-SNAP 1.4 as interface. The tools are capable of automatic liver segmentation and semi-automatic injury segmentation. | liver segmentation, image processing software, injury segmentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ITK-SNAP |
Free | nlx_155788 | https://zenodo.org/records/20089269 | SCR_013108 | 2026-08-08 12:00:07 | 0 | |||||||
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BEADS Resource Report Resource Website 10+ mentions |
BEADS (RRID:SCR_013229) | BEADS | software resource | Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21646344 | OMICS_00466, biotools:beads | https://bio.tools/beads | SCR_013229 | BEADS: Bias Elimination Algorithm for Deep Sequencing, Bias Elimination Algorithm for Deep Sequencing | 2026-08-08 12:00:20 | 38 | ||||||
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Expectation-Maximization Segmentation Resource Report Resource Website 1+ mentions |
Expectation-Maximization Segmentation (RRID:SCR_013228) | software resource, software application, data visualization software, data processing software | EMS is a freely available suite of Matlab functions and subroutines (with some externally compiled C routines) for fully-automated multi-spectral classification of brain tissues in Magnetic Resonance (MR) images. It uses a model based approach (including an explicit model for MR bias fields) in which all the model parameters are automatically estimated for each individual scan. This enables it to process large amounts of data from normal subjects and subjects suffering from Multiple Sclerosis without need for user intervention or preceeding manual training phase. | nif-0000-00295 | SCR_013228 | EMS | 2026-08-08 12:00:09 | 1 | |||||||||||
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AcroMine Resource Report Resource Website |
AcroMine (RRID:SCR_013196) | software resource, data access protocol, web service, service resource | An acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE. This freely available service can be used through your browser or by integrating it with your applications using the ReSTful service. Acromine identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. Applied to the whole MEDLINE (9,635,599 abstracts), the implemented system extracted 68,007 abbreviation candidates and recognized 467,402 expanded forms. The current Acromine achieves 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE. | acronym, abbreviation, disambiguation, computational linguistics, text mining |
is listed by: FORCE11 is listed by: OMICtools has parent organization: University of Manchester; Manchester; United Kingdom |
JISC ; BBSRC ; EPSRC |
PMID:20360059 PMID:17050571 |
Free, Public | OMICS_01169, nif-0000-10215 | SCR_013196 | Acromine | 2026-08-08 12:00:08 | 0 | ||||||
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Wake Forest University Pharmacology Resource Report Resource Website |
Wake Forest University Pharmacology (RRID:SCR_013111) | postdoctoral program resource, data or information resource, graduate program resource, training resource, people resource, portal, organization portal | The pursuit of the Department of Physiology & Pharmacology at Wake Forest University School of Medicine is excellence in research and education. Graduate education and training includes quality introductory and advanced courses in physiology, pharmacology and neuroscience, as well as seminars and journal clubs in several major research areas. Laboratory rotations encourage the graduate student to explore various experimental approaches and provide a diverse training experience. The department and Medical Center are frequented by distinguished visitors from other universities who further enrich the stimulating academic environment. Departmental faculty are active in the medical education as well as in residency training programs in Neurology, Psychiatry, Urology, and Surgery. | nif-0000-02297 | SCR_013111 | Wake Forest U | 2026-08-08 12:00:19 | 0 |
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