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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Allele Biotechnology
 
Resource Report
Resource Website
1+ mentions
Allele Biotechnology (RRID:SCR_003164) Allele Biotech commercial organization A private company offering a wide variety of Molecular Biology reagents, fluorescent proteins, luciferase assay substrates, genotyping kits, and various custom services. The company isalso in the RNAi field with its recent patents in Pol III promoter-driven siRNA, shRNA, and miRNA. They introduced high titer lentivirus, camelid antibodies, and cell based assays and also offer Baculovirus protein expression and Gryphon retrovirus systems. molecular biology, reagent, fluorescent protein, luciferase assay substrate, genotyping kit, custom service is related to: Phoenix Free, Available for download, Freely available nlx_156865 SCR_003164 Allele Biotechnology and Pharmaceuticals Inc 2026-08-01 12:02:17 1
Solas
 
Resource Report
Resource Website
1+ mentions
Solas (RRID:SCR_003168) data analysis software, source code, software application, software resource, sequence analysis software, data processing software Software package for the statistical language R, devoted to the analysis of next generation short read data of RNA-seq transcripts. It provides predictions of alternative exons in a single condition/cell sample, predictions of differential alternative exons between two conditions/cell samples, and quantification of alternative splice forms in a single condition/cell sample. r statistical package, rna seq, exon prediction, exon splicing, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: R Project for Statistical Computing
has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany
Free, Available for download, Freely available biotools:solas, OMICS_01339 https://bio.tools/solas SCR_003168 2026-08-01 12:02:04 8
GenePattern
 
Resource Report
Resource Website
1000+ mentions
GenePattern (RRID:SCR_003201) GenePattern data processing software, data analysis software, software application, software resource A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. gene expression, analysis, genomic, pattern, proteomics, silico, snp, workflow, analysis pipeline, flow cytometry, rna-seq, data processing, bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is affiliated with: GenePattern Notebook
is related to: TIGRESS
has parent organization: Broad Institute
NCI ;
NIGMS
PMID:16642009 Free, Freely available biotools:genepattern, OMICS_01855, nif-0000-30654 https://bio.tools/genepattern SCR_003201 2026-08-01 12:02:28 1078
rDiff
 
Resource Report
Resource Website
1+ mentions
rDiff (RRID:SCR_003162) data analysis software, software application, software resource, sequence analysis software, data processing software Software tool for detecting differential RNA processing from RNA-Seq data. It implements two statistical tests, rDiff.parametric and rDiff.nonparametric, to detect changes of the RNA processing between two samples. differential rna processing, rna processing, rna seq is listed by: OMICtools PMID:23585274 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01338 SCR_003162 2026-08-01 12:02:04 6
American Association for the History of Medicine
 
Resource Report
Resource Website
American Association for the History of Medicine (RRID:SCR_003161) AAHM nonprofit organization A professional association of historians, physicians, nurses, archivists, curators, librarians, and others that promotes and encourages research, study, writing, and interest in the history of medicine and allied fields. history, medicine Free, Freely available nlx_156861, grid.486311.9 https://ror.org/04w1hax42 SCR_003161 2026-08-01 12:02:28 0
PIRSF
 
Resource Report
Resource Website
10+ mentions
PIRSF (RRID:SCR_003352) PIRSF narrative resource, data or information resource, database, standard specification A SuperFamily classification system, with rules for functional site and protein name, to facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors. The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. There are different PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network. The FTP site provides free download for PIRSF. protein annotation, classification, protein, superfamily, functional site, protein name, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: UniProtKB
has parent organization: Protein Information Resource
NHGRI U01-HG02712;
NSF DBI-0138188;
NSF ITR-0205470
PMID:19455212
PMID:14681371
Free, Freely available biotools:pirsf, nif-0000-03294, OMICS_01697 https://bio.tools/pirsf http://pir.georgetown.edu/pirsf/ SCR_003352 PIR SuperFamily, Protein Information Resource SuperFamily 2026-08-01 12:02:20 28
Emory University, Molecular and Systems Pharmacology
 
Resource Report
Resource Website
Emory University, Molecular and Systems Pharmacology (RRID:SCR_003351) data or information resource, portal, organization portal, graduate program resource, department portal The Molecular and Systems Pharmacology graduate program at Emory University offers broad training in the biomedical sciences for students interested in learning how the drugs of today work and how the novel therapeutics of tomorrow can be developed. The Program offers a specialization in toxicology. Emory University was recently rated by The Scientist magazine as the number 1 university in the world in terms of impact in pharmacology and toxicology research. Particular strengths within the MSP graduate school program at Emory include neuropharmacology, cancer biology, AIDS research, cardiovascular pharmacology, toxicology, and chemical biology. Ph.D. training in the Emory MSP program provides students with an ideal preparation for successful careers in the biotechnology and pharmaceutical industries as well as in academic research, teaching, government research, patent law and other disciplines that depend upon knowledge of fundamental pharmacological principles. has parent organization: Emory University; Georgia; USA Free, Freely available nif-0000-01944 http://www.pharm.emory.edu/MSP/ SCR_003351 EU MSP, Emory University Molecular and Systems Pharmacology Graduate Program, Emory MSP Graduate Program, Emory Molecular and Systems Pharmacology Graduate Program, Emory MSP 2026-08-01 12:02:09 0
George Washington University, Department of Pharmacology and Physiology
 
Resource Report
Resource Website
George Washington University, Department of Pharmacology and Physiology (RRID:SCR_003358) portal, organization portal, data or information resource, department portal The Department of Pharmacology & Physiology at the George Washington University provides unique research opportunities at the predoctoral and postdoctoral levels. They also offer courses in Pharmacology and Physiology for Medical and Health Sciences students, as well as a number of graduate-level courses. Our mission is to provide the highest quality of educational opportunities to our community, and to advance scientific knowledge and improve human health through leading-edge research in the biomedical sciences. has parent organization: George Washington University; Washington D.C.; USA Free, Freely available nif-0000-01952 SCR_003358 GWU Department of Pharmacology & Physiology, GWU Department of Pharmacology and Physiology, GWU Dept. of Pharmacology and Physiology 2026-08-01 12:02:09 0
MouseNET
 
Resource Report
Resource Website
1+ mentions
MouseNET (RRID:SCR_003357) mouseNet data analysis service, data or information resource, database, service resource, production service resource, analysis service resource A functional network for laboratory mouse based on integration of diverse genetic and genomic data. It allows the users to accurately predict novel functional assignments and network components. MouseNET uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the mouseNET algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. The graph may be explored further. As you move the mouse over genes in the network, interactions involving these genes are highlighted.If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. gene, network, mouse, protein function, visualization, open reading frame, graph is listed by: OMICtools
is related to: Gene Ontology
is related to: mouseMAP
has parent organization: Princeton University; New Jersey; USA
NSF DBI-0546275;
NIGMS R01 GM071966;
NSF IIS-0513552;
NIGMS P50 GM071508
PMID:18818725 Free, Freely available OMICS_01550, nif-0000-32003 SCR_003357 MouseNET 2026-08-01 12:02:29 3
Niftilib
 
Resource Report
Resource Website
1+ mentions
Niftilib (RRID:SCR_003355) Niftilib source code, software library, software toolkit, software resource Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. nifti-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. Niftilib currently has C, Java, MATLAB, and Python libraries; we plan to add some MATLAB/mex interfaces to the C library in the not too distant future. Niftilib has been developed by members of the NIFTI DFWG and volunteers in the neuroimaging community and serves as a reference implementation of the nifti-1 file format. In addition to being a reference implementation, we hope it is also a useful i/o library. Niftilib code is released into the public domain, developers are encouraged to incorporate niftilib code into their applications, and, to contribute changes and enhancements to niftilib. Please contact us if you would like to contribute additonal functionality to the i/o library. image data, mri, fmri, brain image, image, brain, neuroimaging is related to: NIfTI Data Format Working Group
has parent organization: SourceForge
Free, Available for download, Freely available nif-0000-32011 SCR_003355 The Nifti Libraries, Nifti Libraries 2026-08-01 12:02:09 3
East Tennessee State University, Department of Pharmacology
 
Resource Report
Resource Website
East Tennessee State University, Department of Pharmacology (RRID:SCR_003350) portal, organization portal, data or information resource, department portal Faculty members of our Department are actively engaged in delivering outstanding teaching to undergraduate students, graduate students, medical students, and residents. Our Doctor of Philosophy (graduate) students matriculate to Pharmacology through the Biomedical Sciences Graduate Program at the Quillen College of Medicine. Students pursuing Master of Science and Doctor of Philosophy degrees may pursue a focus in Toxicology. Our faculty members are trained in several medical disciplines and our research applies methodological approaches that span molecular biology, cellular biology, systems biology, and human biology and pathology. Through research, our department strives to understand human disease pathology and use this understanding to develop new therapeutic entities (e.g. drugs) for the treatment of major human diseases. The primary foci of department research efforts are cardiovascular and neuropsychiatric diseases, although other areas of interest and activity exist. Our laboratories are funded by the National Institutes of Health, American Heart Association, the American Foundation for Suicide Prevention and a variety of other agencies and sources. has parent organization: East Tennessee State University; Tennessee; USA nif-0000-01942 SCR_003350 ETSU COM Dept. of Pharmacology, East Tennessee State University Quillen College of Medicine Department of Pharmacology 2026-08-01 12:02:29 0
Lipid Ontology
 
Resource Report
Resource Website
Lipid Ontology (RRID:SCR_003349) LiPrO ontology, controlled vocabulary, data or information resource An ontology that describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. owl, lipid, ontology is listed by: BioPortal
is listed by: OBO
Free, Available for download, Freely available nlx_157458 http://www.lipidprofiles.com/LipidOntology SCR_003349 2026-08-01 12:02:20 0
Duke University Trinity College of Arts and Sciences Undergraduate Neuroscience
 
Resource Report
Resource Website
Duke University Trinity College of Arts and Sciences Undergraduate Neuroscience (RRID:SCR_003345) portal, organization portal, data or information resource, department portal The major and minor in Neuroscience at Duke University was approved by the Arts and Sciences Council of Trinity College of Arts and Sciences on April 9, 2009. The program offers three academic plans: Bachelor of Science (B.S.) degree in Neuroscience, Bachelor of Arts (A.B.) degree in Neuroscience, and a Minor in Neuroscience. Although Neuroscience is a new major/minor, there is a rich and long-standing tradition of excellence in undergraduate neuroscience research and education at Duke. Groups of faculty in the Department of Psychology and Neuroscience and the Department of Biology, as well as the Department of Neurobiology in the Duke University School of Medicine, have been especially engaged in teaching neuroscience in undergraduate classes and hosting independent study projects in their research laboratories. Building upon this broad foundation, the new Undergraduate Studies in Neuroscience program is a truly interdisciplinary experience reflecting the diverse sources of knowledge that advance our understanding of the brain sciences. Undergraduate Studies in Neuroscience is a unique collaboration among many Departments and Schools , with administrative support provided by Trinity College of Arts and Sciences and the Duke Institute for Brain Sciences. has parent organization: Duke University; North Carolina; USA Free, Freely available nif-0000-01936 SCR_003345 Duke Undergraduate Neuroscience, DU Trinity College of Arts and Sciences Undergraduate Neuroscience 2026-08-01 12:02:29 0
Allelic Variations of The XP Genes
 
Resource Report
Resource Website
1+ mentions
Allelic Variations of The XP Genes (RRID:SCR_003376) Allelic Variations of the XP Genes data or information resource, data repository, storage service resource, database, service resource Interactive repository of mutations and other allelic variations of the genes involved in the DNA repair disorders, Xeroderma Pigmentosum (XP), Cockayne Syndrome (CS), Trichothiodystrophy (TTD), and other UV-sensitivity disorders. Any omitted data or new data may be submitted by using the on-line data submission form. There is a message board system to support discussions amongst those interested in XP and DNA Repair. RESOURCES * Educational module of the molecular biology of Nucleotide Excision Repair * Introduction to the DNA Repair disorders (XP, CS, TTD, UVs) * Background on each of the XP genes * A searchable database of mutations and sequence variations for the XP genes * Contact point for the submission of new mutation data * Discussion Forums and a Guest Book * Web Links to Additional Resources nucleotide excision repair, dna, excision, function, gene, allele, cell, sensitivity, trichothiodystrophy, ultra violet, variation, xeroderma pigmentosum, pigment, mutation, allelic variation, dna repair has parent organization: University of California at San Francisco; California; USA DNA repair disorder, Xeroderma Pigmentosum, Cockayne Syndrome, Trichothiodystrophy, UV-sensitivity disorder Xeroderma Pigmentosum Society PMID:10447254 Free, Freely available nif-0000-32042 SCR_003376 xpmutations.org 2026-08-01 12:02:30 2
Fisher BioReagents
 
Resource Report
Resource Website
1000+ mentions
Fisher BioReagents (RRID:SCR_003374) commercial organization An Antibody supplier Free, Freely available nlx_152364 SCR_003374 2026-08-01 12:02:20 1474
Measurement Method Ontology
 
Resource Report
Resource Website
Measurement Method Ontology (RRID:SCR_003373) MMO ontology, controlled vocabulary, data or information resource An ontology designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms. obo, phenotype, clinical is listed by: SourceForge
is listed by: BioPortal
is listed by: OBO
PMID:22654893 Free, Available for download, Freely available nlx_157468 http://sourceforge.net/projects/phenoonto/, ftp://rgd.mcw.edu/pub/ontology/measurement_method/measurement_method.obo SCR_003373 2026-08-01 12:02:10 0
FMA
 
Resource Report
Resource Website
1+ mentions
FMA (RRID:SCR_003379) FMA data or information resource, ontology, controlled vocabulary, data analysis software, database, software application, software resource, data processing software A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model. anatomy, informatics, model, neuroanatomy, protg, reference, standard, structural, taxonomy, owl, phenotype is listed by: BioPortal
is related to: T3DB
is related to: HIV Brain Sequence Database
is related to: CELDA Ontology
has parent organization: University of Washington; Seattle; USA
RSNA-NIBIB ;
University of Washington; Washington; USA ;
Murdock Charitable Trust ;
Microsoft ;
Intel Corporation ;
NLM LM006822;
NLM LM06316;
NLM contract LM03528;
NHLBI HL08770
PMID:18688289
PMID:18360535
PMID:16779026
Free, Freely available nif-0000-00066 http://bioportal.bioontology.org/ontologies/FMA SCR_003379 Foundational Model of Anatomy Ontology, Foundational Model of Anatomy 2026-08-01 12:02:30 8
Statistics Online Computational Resource
 
Resource Report
Resource Website
10+ mentions
Statistics Online Computational Resource (RRID:SCR_003378) SOCR data or information resource, software toolkit, narrative resource, software application, software resource, training material A hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications. The tools and resources include a repository of interactive applets, computational and graphing tools, instructional and course materials. The core SOCR educational and computational components include the following suite of web-based Java applets: * Distributions (interactive graphs and calculators) * Experiments (virtual computer-generated games and processes) * Analyses (collection of common web-accessible tools for statistical data analysis) * Games (interfaces and simulations to real-life processes) * Modeler (tools for distribution, polynomial and spectral model-fitting and simulation) * Graphs, Plots and Charts (comprehensive web-based tools for exploratory data analysis), * Additional Tools (other statistical tools and resources) * SOCR Java-based Statistical Computing Libraries * SOCR Wiki (collaborative Wiki resource) * Educational Materials and Hands-on Activities (varieties of SOCR educational materials), * SOCR Statistical Consulting In addition, SOCR provides a suite of tools for volume-based statistical mapping (http://wiki.stat.ucla.edu/socr/index.php/SOCR_EduMaterials_AnalysesCommandLine) via command-line execution and via the LONI Pipeline workflows (http://www.nitrc.org/projects/pipeline). Course instructors and teachers will find the SOCR class notes and interactive tools useful for student motivation, concept demonstrations and for enhancing their technology based pedagogical approaches to any study of variation and uncertainty. Students and trainees may find the SOCR class notes, analyses, computational and graphing tools extremely useful in their learning/practicing pursuits. Model developers, software programmers and other engineering, biomedical and applied researchers may find the light-weight plug-in oriented SOCR computational libraries and infrastructure useful in their algorithm designs and research efforts. The three types of SOCR resources are: * Interactive Java applets: these include a number of different applets, simulations, demonstrations, virtual experiments, tools for data visualization and analysis, etc. All applets require a Java-enabled browser (if you see a blank screen, see the SOCR Feedback to find out how to configure your browser). * Instructional Resources: these include data, electronic textbooks, tutorials, etc. * Learning Activities: these include various interactive hands-on activities. * SOCR Video Tutorials (including general and tool-specific screencasts). probability, statistics, instruction, statistical computing, applet, computational tool, graphing tool, course material, computation, java, statistical mapping, graphing, computational neuroscience, java, loni pipeline, educator, student, tool developer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
has parent organization: University of California at Los Angeles; California; USA
NIH Roadmap for Medical Research ;
NSF 0442992;
NSF DUE 0716055;
NSF 1023115;
NCRR U54 RR021813
PMID:21451741
PMID:21297884
Free, Freely available nif-0000-32655 http://www.nitrc.org/projects/socr SCR_003378 2026-08-01 12:02:20 13
Syracuse University; Institute for Sensory Research
 
Resource Report
Resource Website
Syracuse University; Institute for Sensory Research (RRID:SCR_003377) ISR topical portal, data or information resource, portal The Institute for Sensory Research (ISR) defines itself as a world class research center dedicated to the discovery and application of knowledge of the sensory systems. Integration of engineering, life, and physical sciences, combining rigorous experimental methodology with mathematical analysis is stressed. Our multidisciplinary approach to bioengineering, sensory neuroscience, graduate, and undergraduate education, makes ISR a unique academic research center. At ISR, we study sensory systems, our gateways to the world. Our ears, eyes, skin, and mouth are channels through which we experience sound, light, texture, etc. These are functions that we usually take for granted until problems arise. Engineers, scientists, and students at ISR investigate both the basic sensory principles used by the brain, and also how the sensory systems can be best utilized, modified, and repaired if necessary to better communicate with our surroundings and with one another. In addition to basic research in hearing, touch, vision, and oro-facial biomechanics, recent projects include the design and testing of sensory-aid devices such as cochlear implants, hearing aids, ear protectors, and tactile aids for the visually and hearing impaired. Additional projects involve visual-depth perception, chewing and swallowing, oto-acoustic emissions, and personal care products such as oral rinses and skin lotions. Research * Auditory * Somatosensory * Vision cochlea model, auditory, somatosensory, vision, eye, ear, skin, mouth, sensory system Free, Freely available nif-0000-01969 https://library.syracuse.edu/digital/guides_sua/html/sua_sensory_research.htm SCR_003377 2026-08-01 12:02:10 0
Marquette University, Neuroscience
 
Resource Report
Resource Website
Marquette University, Neuroscience (RRID:SCR_003404) Marquette Neuroscience, Marquette Neuroscience Graduate Program portal, organization portal, data or information resource, department portal Neuroscience specialization in Graduate Program in Biological Sciences at Marquette University brings together researchers from Departments of Biological and Biomedical Sciences at Marquette to offer quality graduate education in the field of neuroscience with the goal of training students for careers as neuroscience researchers and educators. The specialization is for students who wish to pursue a Ph.D. degree. The collaborative and multi-disciplinary neuroscience research environment at Marquette is supported by the Integrative Neuroscience Research Center (INRC), a consortium of researchers committed to advancing neuroscience research and education at Marquette. The Neuroscience Graduate Program offers the opportunity to conduct research in a collaborative, intellectually rigorous environment, with access to the most modern research tools. has parent organization: Marquette University College of Health Sciences; Wisconsin; USA Free, Freely available nif-0000-01990 http://biology.marquette.edu/gradstudneuro/gettingstarted.htm, http://www.marquette.edu/chs/bisc/graduate.shtml SCR_003404 Marquette University Neuroscience Graduate Program, Marquette University College of Health Sciences Neuroscience Graduate Program, Marquette University College of Health Sciences Biomedical Sciences Neuroscience Graduate Program 2026-08-01 12:02:11 0

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