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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.

(last updated: Aug 10, 2019)

Physical Resource or Software Tool Software

16,721 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Peer Review RadioResource, narrative resource, podcast, data or information resourcePeer Review Radio is a weekly radio show and podcast that portions the tastiest science and prepares it for public consumption. The end goal of this program is to provide an outlet where anyone and everyone can understand current scientific issues and generate their own informed opinions. In addition, Peer Review Radio promotes careers in research and science and serves as a training ground for future scientists to acquire invaluable communication skills. Peer Review Radio was established by a group of motivated graduate students with a desire to spread their love of science. By breaking down complicated concepts into bite-sized morcels, the ''Peers'' hope to spark the curiosity of their listeners with relevant, reliable information. Our producers determine content and coordinate the activities of the journalists. To ensure variety of content, graduate students are enlisted to act as advisers in their fields of expertise and direct literature research for necessary episode scripts. Then, we get together with professors, industrial scientists, post doctoral fellows and graduate students to talk about issues in science. Also, we supplement each episode with ''what if''-type questions, critiquing of science in film, profiles of alternative careers in science, book reviews and more! Our weekly radio show will air on CHUO 89.1 FM in Ottawa, Ontario, Canada starting this Fall 2010, and with each episode we hope to address another hot topic in science without frying your frontal, podcastSCR_004970(Peer Review Radio, RRID:SCR_004970)University of Ottawa; Ontario; Canada Last checked downnlx_93325
miRDeepFinderResource, software resourceProvides an comprehensive workflow of analyzing data from plant microRNA (miRNA) deep sequencing.SCR_004456(miRDeepFinder, RRID:SCR_004456)listed by: OMICtoolsPMID:22290409Last checked downOMICS_00362
ZFIN Antibody DatabaseResource, data or information resource, databaseThe ZFIN Antibody Database is a database of zebrafish gene expression antibodies.monoclonal, polyclonal, antibody, antigen, gene expressionSCR_004729(ZFIN Antibody Database, RRID:SCR_004729)ZFIN Last checked downnlx_74236
shortranResource, software resourceA pipeline for small RNA-seq data analysis.SCR_009636(shortran, RRID:SCR_009636)listed by: OMICtoolsPMID:22914220Last checked downOMICS_00368
Georgetown, NeuroscienceResource, organization portal, training resource, department portal, graduate program resource, medical school program resource, portal, degree granting program, data or information resourceFaculty of the Department of Neuroscience participate in the teaching of courses in the Interdisciplinary Program in Neuroscience and the School of Medicine. A Ph.D. in Neuroscience is offered through the Interdisciplinary Program in Neuroscience. Support for graduate training is offered through the Department, the research grants of individual faculty, as well as through three NIH training grants directed by Neuroscience faculty. * Training in Recovery of Function after CNS Injury. Program Director: Barbara S. Bregman, Ph.D. * Training Program in Drug Abuse. Program Director: Barbara S. Bayer, Ph.D. * Training in Neural Injury and Plasticity. Program Director: Jean R. Wrathall, Ph.D. Scientists in the Department of Neuroscience participate in a wide array of research activities with a focus on understanding both the normal and injured nervous system. The theme of neuroplasticity characterizes much of the research in the Department. We study neuroplasticity during normal development and in the adult in response to activity (e.g., learning) or drugs. Our research is also focused on studying the plasticity that ensues after traumatic (such as spinal cord injury) or ischemic damage to the nervous system and over the course of developmental or neurodegenerative diseases (such as Specific Language Impairment, autism, or Parkinson's and Alzheimer's Diseases). The specific research interests of each of the principal investigators falls under four broad subheadings: *CNS disorders ( Faden, Mocchetti, Rebeck, Riesenhuber,Ullman) *Cognitive/Computational (Riesenhuber, Ullman) *Development, Regeneration and recovery of function after injury (Bregman, Faden, Kromer, Ullman, Wrathall) *Neuroimmunology and Drugs of Abuse (Bayer, Faden, Kromer, Mocchetti) Under this common theme, a variety of diverse techniques and models are employed by the faculty. They range from molecular studies of gene function to studies on humans using Event-Related Potentials (ERPs) and functional MRI. Experimental models include cell culture systems, rodent genetic and experimental models of nervous system injury and disorders, as well as the use of computer simulations to understand higher cortical processing.SCR_003363(Georgetown, Neuroscience, RRID:SCR_003363)Last checked downnif-0000-01954
Medical Diagnostic Categories - Diagnosis Related GroupsResource, ontology, data or information resource, controlled vocabularyOntology of Medical Diagnostic Categories-Diagnosis Related GroupsowlSCR_003725(Medical Diagnostic Categories - Diagnosis Related Groups, RRID:SCR_003725)listed by: BioPortalLast checked downnlx_157470
Mosquito Gross Anatomy OntologyResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the anatomy of mosquitoes.oboSCR_003839(Mosquito Gross Anatomy Ontology, RRID:SCR_003839)listed by: BioPortalLast checked downnlx_157485
Beaumont Hospital; Dublin; IrelandResource, hospitalHospital in Dublin.SCR_011070(Beaumont Hospital; Dublin; Ireland, RRID:SCR_011070)Last checked downnlx_143741
PASTAResource, software resourceA complete pipeline for the analysis of alternative splicing using RNA-Sequencing data.SCR_008770(PASTA, RRID:SCR_008770)University of Florida; Florida; USA listed by: OMICtoolsLast checked downOMICS_01247
HAPLOVISUALResource, software resource, software applicationSoftware application (entry from Genetic Analysis Software)gene, genetic, genomic, javaSCR_009073(HAPLOVISUAL, RRID:SCR_009073)listed by: Genetic Analysis SoftwareLast checked downnlx_154068
Singapore Tissue NetworkResource, biomaterial supply resource, material resource, tissue bankTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016.SCR_010697(Singapore Tissue Network, RRID:SCR_010697)Last checked downnlx_81651
Project HaloResource, organization portal, portal, data or information resourceProject Halo is a staged, long-range research effort by Vulcan Inc. towards the development of a Digital Aristotlea reasoning system capable of answering novel questions and solving advanced problems in a broad range of scientific disciplines and related human affairs. The project focuses on creating two primary functions: a tutor capable of instructing and assessing students in those subjects, and a research assistant with broad, interdisciplinary skills to help scientists and others in their work. Vulcan began work towards this ambitious vision in 2003 with the Halo Pilot a six-month effort to investigate the feasibility of creating a scientific knowledge base capable of answering novel questions from the AP (1st year college level) chemistry test. Three teams SRI International, Cycorp, and Ontoprise developed knowledge bases, for a limited section of an AP-chemistry syllabus, that were able to correctly answer 40 to 50 percent of the associated questions from the AP test. Since 2004, Project Halo has worked to improve these systems, with an emphasis on enabling knowledge entry by domain experts, instead of specialists in artificial intelligence software. In 2004, Vulcan began the development of Automated User-Centered Reasoning and Acquisition System (AURA), by SRI, that enables domain experts (graduate students in Biology, Chemistry, and Physics) to enter knowledge from introductory science textbooks. In 2006, an evaluation of AURA showed that students could create AURA knowledge bases that correctly answered 40 percent of the questions on a limited AP exam. In 2008, the next evaluation demonstrated an improvement of that score to 70 percent correct. In parallel, Project Halo has sponsored Ontoprise to develop semantic extensions to MediaWiki, the software that Wikipedia runs on. Ontoprise has developed a set of Semantic MediaWiki (SMW)+ extensions to MediaWiki that provide a community-based environment for authoring ontologies and creating semantically enhanced wikis. SMW+ has been widely used and is being applied in project management, enterprise collaboration and knowledge management, business intelligence, and the management of large terminology sets. In 2007, Vulcan began a new effort, Halo Advanced Research (HalAR), to address the difficult knowledge representation and reasoning (KR) challenges that prevent the realization of Digital Aristotle. This effort has produced a new semantic rule language and reasoning system, Semantic Inferencing on Large Knowledge (SILK), which includes major advances, including for default and higher-order reasoning over the web.project, tutor, research assistant, science, knowledge-base, semantic mediawiki, ontology, textbook, book, training material, digital book, data mining, biologySCR_000136(Project Halo, RRID:SCR_000136)Stanford Research Institute International Last checked downnlx_144483
Mind HacksResource, blog, narrative resource, book, data or information resourceMind Hacks: Neuroscience and psychology tricks to find out what's going on inside your brain. Mind Hacks is also a book by Tom Stafford and Matt Webb.neuroscience, psychology, brainSCR_000170(Mind Hacks, RRID:SCR_000170)used by: NIF Data Federation, Integrated BlogsLast checked downnlx_48997
Duplicate reads removalResource, software resource, commercial organizationPlug-in tool to filter out duplicate reads that is specifically well-suited to handle those coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high numbers.pcr amplification, duplicate, readSCR_000231(Duplicate reads removal, RRID:SCR_000231)listed by: OMICtoolsLast checked downOMICS_02101
RNAmotifsResource, software resourceSoftware that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs.rna, motifSCR_000263(RNAmotifs, RRID:SCR_000263)Bitbucket listed by: OMICtoolsLast checked downOMICS_02287
Backyard BrainsResource, material resource, instrument supplierA commercial company that sells affordable brain recording kits geared for neuroscience education purposes. Their products are meant to mimic electroencephalograms, a tool that measures the electrical activity of neurons.neuron, eeg, electrophysiology, electroencephalogram, neuroscience, education, school, childrenSCR_000704(Backyard Brains, RRID:SCR_000704)Last checked downnif-0000-01870
Evidence-Based Medicine LibrarianResource, portal, data or information resourceA portal for developing a community of librarians that teach and support the practice of evidence-based medicine (EBM). The site offers a forum for sharing teaching materials, discussing issues and asking for advice from colleagues.evidence based medicine, library, community, teaching, librarySCR_000522(Evidence-Based Medicine Librarian, RRID:SCR_000522)Last checked downnlx_40990
UCSCinResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Beta software used to align and browse a genome.genomeSCR_000571(UCSCin, RRID:SCR_000571)University of Toronto; Ontario; Canada Last checked downnlx_144379
Bio Resource for Array Genes DatabaseResource, data or information resource, databaseBio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice a week from public databases. Search options offer capability to organize and cluster genes based on their Interactions in biological pathways, their association with Gene Ontology terms, Tissue/organ specific expression or any other user-chosen functional grouping of genes. A color coding scheme is used to highlight differential gene expression patterns against a background of gene functional information. Concept hierarchies (Anatomy and Diseases) of MESH (Medical Subject Heading) terms are used to organize and display the data related to Tissue specific expression and Diseases. Sponsors: BioRag database is maintained by the Bioinformatics group at Arizona Cancer Center. The material presented here is compiled from different public databases. BioRag is hosted by the Biotechnology Computing Facility of the University of Arizona. 2002,2003 University of Arizona.drug, experiment, expression, fly, functional, gene, array, biological, biology, c. elegans, cluster, database, disease, human, microarray, mouse, protein, rat, target, tissueSCR_000748(Bio Resource for Array Genes Database, RRID:SCR_000748)University of Arizona; Arizona; USA Last checked downnif-0000-10165
GVK Biosciences Labs and FacilitiesResource, service resource, portal, core facility, access service resource, data or information resourceA contract research organization based in India that provides services including Clinical Development, Contract Manufacturing and Informatics.contract research organization, India, informatics, commercialSCR_001044(GVK Biosciences Labs and Facilities, RRID:SCR_001044)related to: GVK BIO Chemistry Group, listed by: Science ExchangeLast checked downSciEx_4904
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