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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Sequencing Analysis Software Resource Report Resource Website 1+ mentions |
Sequencing Analysis Software (RRID:SCR_000718) | Sequencing Analysis Software | software resource | A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends. | basecall, capillary dna, quality control, low-quality sequence ends | is listed by: OMICtools | Restricted | OMICS_01814 | SCR_000718 | SciCrunch Registry | 2026-10-24 12:44:23 | 1 | ||||||||
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Stanford University Psychiatry and Behavioral Sciences Resource Report Resource Website |
Stanford University Psychiatry and Behavioral Sciences (RRID:SCR_000719) | university | A Stanford-affiliated organization which is primarily concerned with the study and treatment of sleep disorders, the treatment of psychological illnesses, and the training of medical students, residents and research fellows in psychiatry and sleep medicine. | stanford, sleep disorder, psychiatry, medical, psychological illness, research, medicine | nif-0000-02073 | SCR_000719 | SciCrunch Registry | Stanford | 2026-10-24 12:44:19 | 0 | ||||||||||
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Scripps Women's College, Neuroscience Department Resource Report Resource Website |
Scripps Women's College, Neuroscience Department (RRID:SCR_000717) | university | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A neuroscience program that prepares the student for graduate work in biology, psychology, neuroscience, or preparation for medical school or a career in the health services. | neuroscience, psychology, biology, health sciences, medical, services, graduate | has parent organization: Scripps College; California; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02059 | SCR_000717 | SciCrunch Registry | Scripps College Neuroscience | 2026-10-24 12:44:22 | 0 | ||||||||
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MRI Watcher Resource Report Resource Website |
MRI Watcher (RRID:SCR_000710) | data processing software, data visualization software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A visualization tool for MRI images which handles several formats (.gipl,.mha,.hdr). It uses integrated coupled cursors to show the differences between images. It can load an overlay image and make screenshots. | magnetic resonance imaging, 3d spatial image, correlated imaging | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00332 | SCR_000710 | SciCrunch Registry | MRI Watcher | 2026-10-24 12:44:23 | 0 | ||||||||
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clipcrop Resource Report Resource Website |
clipcrop (RRID:SCR_000678) | software resource | Software tool for detecting structural variations with single-base resolution using soft-clipping information from SAM files. | structural variation, detecting structural variations, soft-clipping information, SAM files, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22373054 | Free, Available for download, Freely available | biotools:clipcrop, OMICS_00310 | https://bio.tools/clipcrop | SCR_000678 | SciCrunch Registry | ClipCrop | 2026-10-24 12:44:18 | 0 | ||||||
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Americans for Medical Progress Resource Report Resource Website |
Americans for Medical Progress (RRID:SCR_000711) | AMP | nonprofit organization | A non-profit charity dedicated to providing education about animal research for the purpose of protecting medical and scientific progress. The organization seeks to provide accurate and incisive information to foster a balanced public debate on animal research issues. They work to do outreach by distributing timely and relevant news, information and analysis about animal rights extremism to the research community. | animal, research, issue, extremism, education, progress, debate | Crossref funder ID: 100005411, grid.468272.d, Wikidata: Q4745618, nif-0000-00456, ISNI: 0000 0004 4659 713X | https://ror.org/05xxn0r26 | SCR_000711 | SciCrunch Registry | 2026-10-24 12:44:19 | 0 | |||||||||
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TriageTools Resource Report Resource Website |
TriageTools (RRID:SCR_000675) | TriageTools | software resource | A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets. | matlab, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23408855 | Free, Available for download, Freely available | biotools:triagetools, nlx_156740 | https://bio.tools/triagetools | SCR_000675 | SciCrunch Registry | 2026-10-24 12:44:21 | 0 | ||||||
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Oregon State University College of Pharmacy Resource Report Resource Website |
Oregon State University College of Pharmacy (RRID:SCR_000715) | university | The college of pharmacy at Oregon State University that offers professional education in pharmacy. The foundational goals are to provide professional education, foster research to contribute to public health initiatives and promote safe and affordable medication access. | pharmacy, pharmaceutical, professional, education, public health, access, medication, drugs | nif-0000-02038 | SCR_000715 | SciCrunch Registry | Oregon State | 2026-10-24 12:44:19 | 0 | ||||||||||
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Clinical Trials Registry - India Resource Report Resource Website 10+ mentions |
Clinical Trials Registry - India (RRID:SCR_000679) | CTRI | clinical trial, data or information resource, data repository, database, service resource, storage service resource | Free, online public record system for registration of clinical trials being conducted in India. Initiated as a voluntary measure, trial registration in the CTRI has been made mandatory by the Drugs Controller General (India) (DCGI) (http://www.cdsco.nic.in/). Moreover, Editors of Biomedical Journals of 11 major journals of India declared that only registered trials would be considered for publication. Today, any researcher who plans to conduct a trial involving human participants, of any intervention such as drugs, surgical procedures, preventive measures, lifestyle modifications, devices, educational or behavioral treatment, rehabilitation strategies as well as trials being conducted in the purview of the Department of AYUSH (http://indianmedicine.nic.in/) is expected to register the trial in the CTRI before enrollment of the first participant. Trial registration involves public declaration and identification of trial investigators, sponsors, interventions, patient population etc before the enrollment of the first patient. Submission of Ethics approval and DCGI approval (if applicable) is essential for trial registration in the CTRI. Multi-country trials, where India is a participating country, which have been registered in an international registry, are also expected to be registered in the CTRI. In the CTRI, details of Indian investigators, trial sites, Indian target sample size and date of enrollment are captured. After a trial is registered, trialists are expected to regularly update the trial status or other aspects as the case may be. After a trial is registered, all updates and changes will be recorded and available for public display. The CTRI is working with the WHO ICTRP to ensure that results of all trials registered with the CTRI are adequately reported and publicly available. | clinical trial, registry, registration, trial, clinical, randomized, non-randomized, india |
is listed by: WHO International Clinical Trials Registry Platform has parent organization: National Institute of Medical Statistics; New Delhi; India |
PMID:18630235 | THIS RESOURCE IS NO LONGER IN SERVICE | r3d100010980, nlx_151507 | https://doi.org/10.17616/R3C61N | SCR_000679 | SciCrunch Registry | Clinical Trials Registry-India (CTRI), Clinical Trials Registry-India, Clinical Trials Registry - India (CTRI) | 2026-10-24 12:44:21 | 13 | |||||
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VarB Resource Report Resource Website |
VarB (RRID:SCR_000671) | VarB | software resource | A variation browsing and analysis tool for variants derived from next-generation sequencing data. | variant, next-generation sequencing, polymorphism, c++ | is listed by: OMICtools | PMID:22976080 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00898 | SCR_000671 | SciCrunch Registry | 2026-10-24 12:44:22 | 0 | |||||||
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BAMseek Resource Report Resource Website |
BAMseek (RRID:SCR_000672) | BAMseek | data processing software, data visualization software, software application, software resource | A Large File Viewer for BAM and SAM alignment files. | matlab, sam, bam, viewer, alignment, format, large file, vcf, sff, fastq, sequencing |
is listed by: OMICtools has parent organization: Google Code |
Free, Available for download, Freely available | OMICS_00877 | SCR_000672 | SciCrunch Registry | bamseek - Browse large BAM and SAM alignment files. | 2026-10-24 12:44:18 | 0 | |||||||
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Comprehensive Drug Self-administration and Discrimination Bibliographic Databases Resource Report Resource Website |
Comprehensive Drug Self-administration and Discrimination Bibliographic Databases (RRID:SCR_000707) | bibliography, data or information resource, database | Database of bibliographic details of over 9,000 references published between 1951 and the present day, and includes abstracts, journal articles, book chapters and books replacing the two former separate websites for Ian Stolerman's drug discrimination database and Dick Meisch's drug self-administration database. Lists of standardized keywords are used to index the citations. Most of the keywords are generic drug names but they also include methodological terms, species studied and drug classes. This index makes it possible to selectively retrieve references according to the drugs used as the training stimuli, drugs used as test stimuli, drugs used as pretreatments, species, etc. by entering your own terms or by using our comprehensive lists of search terms. Drug Discrimination Drug Discrimination is widely recognized as one of the major methods for studying the behavioral and neuropharmacological effects of drugs and plays an important role in drug discovery and investigations of drug abuse. In Drug Discrimination studies, effects of drugs serve as discriminative stimuli that indicate how reinforcers (e.g. food pellets) can be obtained. For example, animals can be trained to press one of two levers to obtain food after receiving injections of a drug, and to press the other lever to obtain food after injections of the vehicle. After the discrimination has been learned, the animal starts pressing the appropriate lever according to whether it has received the training drug or vehicle; accuracy is very good in most experiments (90 or more correct). Discriminative stimulus effects of drugs are readily distinguished from the effects of food alone by collecting data in brief test sessions where responses are not differentially reinforced. Thus, trained subjects can be used to determine whether test substances are identified as like or unlike the drug used for training. Drug Self-administration Drug Self-administration methodology is central to the experimental analysis of drug abuse and dependence (addiction). It constitutes a key technique in numerous investigations of drug intake and its neurobiological basis and has even been described by some as the gold standard among methods in the area. Self-administration occurs when, after a behavioral act or chain of acts, a feedback loop results in the introduction of a drug or drugs into a human or infra-human subject. The drug is usually conceptualized as serving the role of a positive reinforcer within a framework of operant conditioning. For example, animals can be given the opportunity to press a lever to obtain an infusion of a drug through a chronically-indwelling venous catheter. If the available dose of the drug serves as a positive reinforcer then the rate of lever-pressing will increase and a sustained pattern of responding at a high rate may develop. Reinforcing effects of drugs are distinguishable from other actions such as increases in general activity by means of one or more control procedures. Trained subjects can be used to investigate the behavioral and neuropharmacological basis of drug-taking and drug-seeking behaviors and the reinstatement of these behaviors in subjects with a previous history of drug intake (relapse models). Other applications include evaluating novel compounds for liability to produce abuse and dependence and for their value in the treatment of drug dependence and addiction. The bibliography is updated about four times per year. | drug, drug-seeking behavior, drug-taking behavior, abstract, behavior, behavioral neuropharmacology, discrimination, non-human vertebrate, publication, relapse, self-administration, substance-related disorder, book, journal article | has parent organization: University of Texas Health Science Center at Houston; Texas; USA | NIDA DA-04376 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00090 | http://www.drugrefs.org/ | SCR_000707 | SciCrunch Registry | Drug Self-administration and Discrimination Bibliographic Databases | 2026-10-24 12:44:22 | 0 | ||||||
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FlyBrain Resource Report Resource Website 1+ mentions |
FlyBrain (RRID:SCR_000706) | atlas, data or information resource, data processing software, narrative resource, software application, software resource, training material, training resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Interactive database of Drosophila melanogaster nervous system. Used by drosophila neuroscience community and by other researchers studying arthropod brain structure. | drosophila melanogaster, ganglion, gene, 3-dimensional, abdominal, anatomy, arthropod, autofluorescence, chemical, development, developmental, golgi, histology, immunocytology, impregnation, map, model, morphology, nervous system, neuroanatomical, neuroanatomy, neuron, neuropil, periphery, phenotype, structure, thoracic, visualization |
has parent organization: National Institute for Basic Biology; Okazaki; Japan has parent organization: University of Arizona; Arizona; USA has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
PMID:8592752 PMID:21280038 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00031 | SCR_000706 | SciCrunch Registry | FlyBrain | 2026-10-24 12:44:22 | 3 | |||||||
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Virginia Commonwealth University, Department of Pharmacology Resource Report Resource Website |
Virginia Commonwealth University, Department of Pharmacology (RRID:SCR_000666) | university | A graduate program for pharmacology and toxicology that is a component of the Virginia Commonwealth University. This organization also performs studies on medical disorders, and new pharmacology agents and their effects on human health. | pharmacology, toxicology, virginia commonwealth, medical disorders, graduate program, pharmacology agents | has parent organization: Virginia Commonwealth University; Virginia; USA | nif-0000-02004 | http://views.vcu.edu/pharmtox/ | SCR_000666 | SciCrunch Registry | VCU SOM Pharmacology and Toxicology, VCU Department of Pharmacology and Toxicology, VCU Pharmacology and Toxicology, VCU Department of Pharmacology Toxicology, VCU School of Medicine; Department of Pharmacology and Toxicology | 2026-10-24 12:44:22 | 0 | ||||||||
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NGS tools for the novice Resource Report Resource Website 1+ mentions |
NGS tools for the novice (RRID:SCR_000664) | NGS tools for the novice | software resource | A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution. | next generation sequencing, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01063 | SCR_000664 | SciCrunch Registry | NGS tools for the novice - Handy tools for processing of next generation sequencing (NGS) data | 2026-10-24 12:44:21 | 3 | |||||||
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Opera Resource Report Resource Website 1+ mentions |
Opera (RRID:SCR_000665) | software resource | A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads. | sequence assembly, paired-end, orient contigs, shotgun-sequencing, shotgun, software program, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:27169502 PMID:21929371 |
Free, Available for download, Freely available | biotools:opera, OMICS_00045 | https://bio.tools/opera | SCR_000665 | SciCrunch Registry | OPERA-LG, Optimal Paired-End Read Assembler | 2026-10-24 12:44:21 | 3 | ||||||
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MeGX Resource Report Resource Website 1+ mentions |
MeGX (RRID:SCR_000738) | data access protocol, data or information resource, database, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts.Includes geographic information system to systematically store and analyse marine genomic and metagenomic data in conjunction with contextual information; environmental genome browser with fast search functionalities; database with precomputed analyses for selected complete genomes; database and tool to classify metagenomic fragments based on oligonucleotide signatures. | functioning of marine ecosystems, marine bacterial, archaeal, phage, metagenome, marine microbe, megdb, analysis |
is listed by: 3DVC has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany |
PMID:16381894 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03109, nif-0000-21260, SCR_008204, r3d100011324 | https://doi.org/10.17616/R3B05S | SCR_000738 | SciCrunch Registry | Marine Ecological GenomiX, megx: marine ecological genomics, Megx.net | 2026-10-24 12:44:22 | 2 | ||||||
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Semantic Web Applications in Neuromedicine (SWAN) Ontology Resource Report Resource Website |
Semantic Web Applications in Neuromedicine (SWAN) Ontology (RRID:SCR_000697) | SWAN Ontology | controlled vocabulary, data or information resource, narrative resource, ontology | The SWAN (Semantic Web Applications in Neuromedicine) ontology is an ontology for modeling scientific discourse and has been developed in the context of building a series of applications for biomedical researchers, as well as extensive discussions and collaborations with the larger bio-ontologies community. Developing cures for highly complex diseases, such as neurodegenerative disorders, requires extensive interdisciplinary collaboration and exchange of biomedical information in context. Our ability to exchange such information across sub-specialties today is limited by the current scientific knowledge ecosystem's inability to properly contextualize and integrate data and discourse in machine-interpretable form. This inherently limits the productivity of research and the progress toward cures for devastating diseases such as Alzheimer's and Parkinson's. The SWAN ontology is organized in three types of modules: * basic: basic modules represent the ontology building blocks. They cover topics that are general enough to be included in every ontology distribution. The current basic modules are: ** collections ** provenance, authoring and versioning (PAV) ** discourse relationships ** FOAF (in OWL-DL) ** SKOS (in OWL-DL) ** qualifiers ** scientific discourse * extension: extensions modules are covering topics (a) that can be related only to some fields of science (b) for which there could be more than one implementation (c) for which a temporary solution has been provided and it is possible to forecast its substitution. The current extensions modules are: ** life science entities ** citations ** qualifiers extension modules * distribution: distributions are modules that are including all the basic modules and extensions necessary for serving a specific domain (i.e. the SWAN ontology for the Alzheimer knowledge base or the generic distribution that is not binded to any specific scientific domain). The current available distributions are: ** swan-scientific-discourse ** swan-alzheimer | scientific discourse, biomedical research, semantics, owl, semantic web, biomedicine, swan, alzheimer disease, knowledgebase, hypothesis/claim-based representation of the rhetorical structure of a scientific paper |
is listed by: FORCE11 is related to: AlzSWAN Knowledge Base has parent organization: Harvard Medical School; Massachusetts; USA |
Ellison Medical Foundation ; alz.org ; Eli Lilly and Company |
PMID:18583197 | nlx_149502 | SCR_000697 | SciCrunch Registry | Semantic Web Applications in Neuromedicine Ontology | 2026-10-24 12:44:22 | 0 | ||||||
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PiNGO Resource Report Resource Website |
PiNGO (RRID:SCR_000692) | PiNGO | software resource | A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, annotation, network, candidate gene, biological network, ontology or annotation search engine, statistical analysis, term enrichment, functional similarity, functional prediction, search engine, windows, mac os x, linux, unix |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Cytoscape has parent organization: Ghent University; Ghent; Belgium |
PMID:21278188 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149330, OMICS_02281 | SCR_000692 | SciCrunch Registry | 2026-10-24 12:44:22 | 0 | |||||||
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RMAP Resource Report Resource Website 1+ mentions |
RMAP (RRID:SCR_000695) | RMAP | software resource | Software for short-read mapping to accurately map reads from the next-generation sequencing technology. It can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches. | next-generation sequencing, solexa |
is listed by: OMICtools has parent organization: Cold Spring Harbor Laboratory |
PMID:19736251 | OMICS_00681 | SCR_000695 | SciCrunch Registry | 2026-10-24 12:44:18 | 2 |
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