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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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George Washington University, Department of Pharmacology and Physiology Resource Report Resource Website |
George Washington University, Department of Pharmacology and Physiology (RRID:SCR_003358) | data or information resource, department portal, organization portal, 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 | SciCrunch Registry | GWU Department of Pharmacology & Physiology, GWU Department of Pharmacology and Physiology, GWU Dept. of Pharmacology and Physiology | 2026-09-26 02:13:27 | 0 | |||||||||
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MouseNET Resource Report Resource Website 1+ mentions |
MouseNET (RRID:SCR_003357) | mouseNet | analysis service resource, data analysis service, data or information resource, database, production service resource, 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 | SciCrunch Registry | MouseNET | 2026-09-26 02:13:28 | 3 | |||||
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NGSANE Resource Report Resource Website 10+ mentions |
NGSANE (RRID:SCR_003478) | NGSANE | software resource | Software providing a Linux-based High Performance Computing (HPC) enabled framework for high-throughput data analysis that minimizes overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing raw sequence data. | next generation sequencing | is listed by: OMICtools | PMID:24470576 | BSD License, v3 | OMICS_02298 | SCR_003478 | SciCrunch Registry | Next Generation Sequencing ANalysis for Enterprises | 2026-09-26 02:13:29 | 10 | ||||||
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Niftilib Resource Report Resource Website 1+ mentions |
Niftilib (RRID:SCR_003355) | Niftilib | software library, software resource, software toolkit, source code | 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 | SciCrunch Registry | The Nifti Libraries, Nifti Libraries | 2026-09-26 02:13:27 | 3 | |||||||
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SNAPE-pooled Resource Report Resource Website 1+ mentions |
SNAPE-pooled (RRID:SCR_003476) | software resource | Software that computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome. | standalone software |
is listed by: OMICtools has parent organization: Google Code |
PMID:22992255 | GNU General Public License, v3 | OMICS_05820 | SCR_003476 | SciCrunch Registry | snape-pooled: Computes the minor allele frequency spectrum in pooled DNA (sequenced) samples | 2026-09-26 02:13:29 | 8 | |||||||
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East Tennessee State University, Department of Pharmacology Resource Report Resource Website |
East Tennessee State University, Department of Pharmacology (RRID:SCR_003350) | data or information resource, department portal, organization portal, 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 | SciCrunch Registry | ETSU COM Dept. of Pharmacology, East Tennessee State University Quillen College of Medicine Department of Pharmacology | 2026-09-26 02:13:27 | 0 | ||||||||||
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Bpipe Resource Report Resource Website 10+ mentions |
Bpipe (RRID:SCR_003471) | Bpipe | software resource | Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments. | genetics, dna, analysis, cluster, workflow, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22500002 | Free, Available for download, Freely available | biotools:bpipe, OMICS_02301 | https://github.com/ssadedin/bpipe | SCR_003471 | SciCrunch Registry | bpipe - A tool for running and managing bioinformatics pipelines | 2026-09-26 02:13:31 | 13 | |||||
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Lipid Ontology Resource Report Resource Website |
Lipid Ontology (RRID:SCR_003349) | LiPrO | controlled vocabulary, data or information resource, ontology | 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 | SciCrunch Registry | 2026-09-26 02:13:27 | 0 | |||||||
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Parseq Resource Report Resource Website 1+ mentions |
Parseq (RRID:SCR_003464) | Parseq | software resource | Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders. | rna-seq, genome, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Sorbonne University; Paris; France |
PMID:24470570 | Free, Available for download, Freely available | biotools:parseq, OMICS_02302 | https://bio.tools/parseq | SCR_003464 | SciCrunch Registry | 2026-09-26 02:13:30 | 2 | ||||||
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Solstice Resource Report Resource Website 1+ mentions |
Solstice (RRID:SCR_003463) | Solstice | software application, software development environment, software development tool, software resource | A Web application development framework for Perl. Based on the MVC programming paradigm, it provides a sensible layout for Web applications that helps you write applications faster and with fewer mistakes. Solstice serves as the foundation for a suite of enterprise communication and collaboration tools used at the University of Washington. Many of these tools, such as the WebQ survey and quiz creation application, the UMail anonymous email form, and the CrowdControl module for managing groups of users, are available for download now. More are on the way. They will offer you rich starting points, examples, and solutions for your own applications. Solstice is designed to support large, complex applications that have a serious need for structured navigation. Its state-machine based navigation system ensures that users stay on the paths they need to follow within your Web application. With any mod_perl enabled Apache server, Solstice offers easy installation and proven scalability. Specifically, Solstice provides your application with: * a state-machine based navigation system, * integrated validation, * highly reusable and embeddable page elements, * session management, * user and group models for flexible, built-in authorization, * a development mode for realtime diagnostics, and * a focus on scalability. When you work with Solstice, you can also use Majere, a Web-based development tool that automates the creation of applications and manages their configuration. Majere frees you to focus on the more interesting parts of application development and is available along with Solstice on our Download page. Solstice provides support for RESTful development. | perl |
is listed by: Biositemaps has parent organization: University of Washington; Seattle; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33380 | SCR_003463 | SciCrunch Registry | 2026-09-26 02:13:29 | 2 | ||||||||
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Population and Community Ontology Resource Report Resource Website |
Population and Community Ontology (RRID:SCR_003462) | PCO | controlled vocabulary, data or information resource, ontology | An ontology that models material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies, such as the Gene Ontology (GO), which covers biological processes, and the Phenotypic Quality Ontology (PATO). | owl, community, population, biomedical, evolution, ecology |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
New BSD License, (Code) | nlx_157557 | http://purl.bioontology.org/ontology/PCO, http://purl.obolibrary.org/obo/pco.owl | SCR_003462 | SciCrunch Registry | 2026-09-26 02:13:29 | 0 | |||||||
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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) | data or information resource, department portal, organization portal, 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 | SciCrunch Registry | Duke Undergraduate Neuroscience, DU Trinity College of Arts and Sciences Undergraduate Neuroscience | 2026-09-26 02:13:27 | 0 | |||||||||
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Plant Environmental Conditions Resource Report Resource Website |
Plant Environmental Conditions (RRID:SCR_003460) | PECO, EO | controlled vocabulary, data or information resource | A structured controlled vocabulary for the representation of plant environmental conditions. | obo, environment, gene expression, phenotype |
is listed by: BioPortal is listed by: OBO has parent organization: Gramene |
nlx_157554 | http://purl.bioontology.org/ontology/PECO, http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_environment/environment_ontology.obo, http://www.gramene.org/plant_ontology/index.html#eo | SCR_003460 | SciCrunch Registry | 2026-09-26 02:13:30 | 0 | ||||||||
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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, database, service resource, storage 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 | SciCrunch Registry | xpmutations.org | 2026-09-26 02:13:29 | 2 | ||||
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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 | SciCrunch Registry | 2026-09-26 02:13:28 | 1475 | |||||||||||
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Measurement Method Ontology Resource Report Resource Website |
Measurement Method Ontology (RRID:SCR_003373) | MMO | controlled vocabulary, data or information resource, ontology | 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 | SciCrunch Registry | 2026-09-26 02:13:28 | 0 | ||||||
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FMA Resource Report Resource Website 1+ mentions |
FMA (RRID:SCR_003379) | FMA | controlled vocabulary, data analysis software, data or information resource, data processing software, database, ontology, software application, software resource | 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 | SciCrunch Registry | Foundational Model of Anatomy Ontology, Foundational Model of Anatomy | 2026-09-26 02:13:28 | 8 | ||||
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Statistics Online Computational Resource Resource Report Resource Website 10+ mentions |
Statistics Online Computational Resource (RRID:SCR_003378) | SOCR | data or information resource, narrative resource, software application, software resource, software toolkit, 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 | SciCrunch Registry | 2026-09-26 02:13:28 | 13 | |||||
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Syracuse University; Institute for Sensory Research Resource Report Resource Website |
Syracuse University; Institute for Sensory Research (RRID:SCR_003377) | ISR | data or information resource, portal, topical 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 | SciCrunch Registry | 2026-09-26 02:13:28 | 0 | ||||||||
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MultiPhen Resource Report Resource Website 10+ mentions |
MultiPhen (RRID:SCR_003498) | software resource | Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model). | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:22567092 | GNU General Public License, v2 | biotools:multiphen, OMICS_04397 | https://bio.tools/multiphen | SCR_003498 | SciCrunch Registry | MultiPhen: a package for the genetic association testing of multiple phenotypes | 2026-09-26 02:13:30 | 31 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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