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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: Oct 12, 2019)

Physical Resource or Software Tool Software

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
SplitSeekResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationTHIS RESOURCE IS NO LONGER SUPPORTED, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data.bioinformatics alignment, sequence analysis software, de novo, prediction, rna seq, rna, splice junctionSCR_001012(SplitSeek, RRID:SCR_001012)listed by: OMICtoolsPMID:20236510Last checked downOMICS_01253http://www.uppmax.uu.se/software/splitseek
Pathology DiagnosticsResource, service resource, core facility, access service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented September 15, 2016. Pathology Diagnostics Ltd is an independent GCLP accredited histopathology research organisation delivering tissue, laboratory, and diagnostics services to industry Research and Development scientists engaged in drug and biomarker development.diagnostics, histopathology, commercial, research organization, drug development, biomarker developmentSCR_001033(Pathology Diagnostics, RRID:SCR_001033)listed by: Science ExchangeLast checked downSciEx_11698http://www.scienceexchange.com/facilities/pathology-diagnostics
Seoul Cord Blood BankResource, biomaterial supply resource, material resource, tissue bankTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. An umbilical cord blood bank located in Seoul, South Korea.SCR_010514(Seoul Cord Blood Bank, RRID:SCR_010514)Last checked downnlx_17209
Genetic Alterations in CancerResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The NIEHS Genetic Alterations in Cancer (GAC) knowledgebase is a comprehensive collection of data compiled from studies reported in the published literature on genetic alterations in tumors associated with exposure to specific chemical, physical, or biological agents that can be linked to genes implicated in the development of cancers. GAC provides access to data from peer reviewed journals for hundreds of studies of gene mutations, loss of heterozygosity, and/or chromosome changes in tumors from humans, mice, or rats. Results are summarized in tables and graphic profiles that show the incidence (percent) of tumors with alterations in each gene that has been studied. Detailed data tables display results for each subject studied in the cited reference and the reference ID is hyperlinked to its PubMed abstract for more information. A mutation spectrum for individual genes and links to gene information from The Cancer Genome Anatomy Project and the Rat Genome Database are also provided.SCR_010533(Genetic Alterations in Cancer, RRID:SCR_010533)National Institute of Environmental Health Sciences PMID:16410370Last checked downnlx_23898http://www.niehs.nih.gov/research/resources/databases/gac/index.cfm
New York University Specialty Tissue BanksResource, biomaterial supply resource, material resource, tissue bankTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016.SCR_010540(New York University Specialty Tissue Banks, RRID:SCR_010540)Last checked downnlx_26476http://ci.med.nyu.edu/research/facilities/tissue-acquisition-and-banking-services-tabs/contact-information
Evidence-Based Health Care Search StrategiesResource, wiki, narrative resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. This wiki focuses on the process, techniques and tools of high quality searching in the context of evidence-based health care. Information collected in the wiki is primarily intended for medical librarians, but may be of interest to others. Please keep in mind that search strategies and tools here are intended for use by trained professionals in the course of their professional duties, and are not intended for use by the general public. If they are helpful or useful to others that is a plus, but not the primary purpose of the site.ebhc, ebm, evidence-based, health, healthcare, medicine, medline, pubmed searchingSCR_010606(Evidence-Based Health Care Search Strategies, RRID:SCR_010606)Last checked downnlx_51340
UC Davis Alzheimers Disease Center - ResourcesResource, training service resource, database, biomaterial supply resource, tissue bank, service resource, brain bank, material resource, funding resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Support research in Alzheimer's disease (AD) offering pilot grants, recruitment of research subjects, access to database, tissue samples, and statistical and research study design consultation for investigators. The scientific effort of the program seeks to: promote research directed at understanding factors that influence the expression and progression of Alzheimer's disease; develop and maintain cohorts of carefully diagnosed and well characterized research subjects available for research studies on Alzheimer's disease and dementia; provide support to investigators in subject recruitment, clinical research, experimental design, and statistical analysis of data; and maintain a variety of samples (brain, DNA, serum) and an extensive electronic database suitable for developing new research and supporting existing programs.brain, dna, serum, brain tissue, tissueSCR_010699(UC Davis Alzheimers Disease Center - Resources, RRID:SCR_010699)UC Davis Alzheimer's Disease Center Alzheimer's disease, AgingMartinez Veterans Health Administration, NIA, State of California's Department of Public Healthlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_82710
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_81651http://www.stn.org.sg/
Precision Allograft SolutionsResource, biomaterial supply resource, material resource, tissue bankTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. A commercial tissue bank focusing on human tissue.SCR_010702(Precision Allograft Solutions, RRID:SCR_010702)Last checked downnlx_88227
eVOCResource, ontology, data or information resource, controlled vocabularyTHIS RESOURCE IS NO LONGER SUPPORTED, documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information.mouse, mapping, cdna, development, microarray, expression, expressed sequence, anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation, treatment, gene expression, genome sequence, expression phenotype, genome, sequence, phenotype, anatomical system, cell type, pathology, anatomySCR_010704(eVOC, RRID:SCR_010704)University of the Western Cape; Bellville; South Africa European Union, South African Department of Arts Culture Science and Technology, South African National Research Foundation, Wellcome Trustrelated to: OBO, Bgee: a dataBase for Gene Expression EvolutionPMID:12799354Last checked downnlx_84448
SRSResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. Features include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in ''Nice views'', SRSQuickSearch bookmarklets. Quick Searches allow users to make a number of searches without needing to learn how to use SRS in depth. The searches query some of the common databanks without having to go and select them explicitly and without the need to understand the SRS Query Forms. Quick Searches can be performed from either the Start page (when you first open SRS) or the SRS Quick Search page (when you are already in a project). SRS also has the ability to search for links between your current results and related information in other databanks. Additionally, it is able to analyze the results of your search using many bioinformatics analysis tools or applications. This enables you to seek out further information that may be relevant to your initial search.data set, gold standardSCR_010736(SRS, RRID:SCR_010736)European Bioinformatics Institute listed by: 3DVCReferences (3)Last checked downnlx_95251
CASVMResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER AVAILABLE, documented December 12, 2016. CASVM is a web server for predicting caspase cleavage sites on protein sequences based on the SVM algorithms. It can also be used for predicting non-canonical caspase substrate cleavage sites. The server has a relational database containing experimentally verified caspase substrates retrievable using accession IDs, keywords or sequence similarity.caspase cleavage sites, protein sequences, svm algorithms, cleavage, databaseSCR_001121(CASVM, RRID:SCR_001121)listed by: OMICtoolsPMID:17599937Last checked downOMICS_01671http://www.casbase.org/casvm/index.html
Earlier versus Later Levodopa Therapy in Parkinson DiseaseResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from the ELLDOPA study: a multicenter, placebo-controlled, randomized, dose-ranging, double-blind clinical trial of 361 early, mild Parkinson's disease (PD) subjects, not requiring symptomatic medications with a duration from time of diagnosis less than 2 years. A NINDS funded study. The multicenter, placebo-controlled, randomized, dose-ranging, double-blind clinical trial, called the Earlier versus Later Levodopa Therapy in Parkinson Disease (ELLDOPA) study was run by the Parkinson Study Group and sponsored by the National Institute of Neurological Disorders and Stroke (NINDS). The subjects (n=361) were enrolled between September 1998 and August 2001 at 33 sites in the United States and 5 sites in Canada. Despite the known benefit of levodopa in reducing the symptoms of Parkinsons disease, concern has been expressed that its use might hasten neurodegeneration. This study assessed the effect of levodopa on the rate of progression of Parkinsons disease.The primary analysis assessed the doseresponse relationship between the assigned doses and the worsening of parkinsonism, as indicated by the changes in the total score on the UPDRS between the baseline visit and week 42. Washout of study drug occurred during weeks 40-42.ClinicalTrials.Gov: NCT00004733SCR_001150(Earlier versus Later Levodopa Therapy in Parkinson Disease, RRID:SCR_001150)Parkinson's DiseaseNational Institute of Neurological Disorders and StrokeLast checked downnif-0000-11249http://www.pd-doc.org/Databases/LinkedDatabases/PSGDatabases/ELLDOPAStudy/tabid/161/Default.aspx
NET-PD (Neuroprotection Exploratory Trials in PD): Futility Study IResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from a multicenter, double-blind, futility study of minocycline and creatine in subjects with early untreated Parkinson's Disease (PD) or FS-I (Futility Study I). There were 65 subjects/treatment arm with 195 total randomized subjects from approximately 42 sites in the US and Canada. A NINDS funded study. A Multicenter, Double-Blind, Futility Study of Minocycline and Creatine in subjects with early untreated Parkinson's Disease (PD) (FS-1).The primary objective of the study was to assess the impact of minocycline and creatine on the progression of PD in order to assess whether it was non-futile to proceed with further study of these agents. The progression of PD was measured by the change in total UPDRS score between the baseline visit and month 12 or the time of sufficient disability to require symptomatic therapy (last visit before subject goes on dopaminergic therapy), whichever occurs first. The additional follow-up of subjects until 18 months addressed the secondary objectives. The FS-1 study was conducted by the NINDS funded Neuroprotection Exploratory Trials in PD (NET-PD).SCR_001153(NET-PD (Neuroprotection Exploratory Trials in PD): Futility Study I, RRID:SCR_001153)Last checked downnif-0000-11251http://www.pd-doc.org/Databases/LinkedDatabases/NETPDDatabases/FS1Study/tabid/198/Default.aspx
NET-PD (Neuroprotection Exploratory Trials in PD): Futility Study IIResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from a multicenter, double-blind, pilot study of CoQ10 and GPI 1485 in subjects with early untreated Parkinson's Disease (PD) or FS-TOO (Futility Study II). There were 65 subjects/treatment arm with 195 total randomized subjects from approximately 42 sites in the US and Canada. A NINDS funded study. Multicenter, double-blind, pilot study of outpatients with early, untreated PD. De novo subjects were equally randomized to one of the three study arms: (1) active CoQ10 and placebo for GPI 1485, (2) active GPI 1485 and placebo for CoQ10 and (3) placebo for CoQ10 and GPI 1485. Subjects remained on blinded study drug for 12 months. The primary comparison of each drug was to historical control data, but a placebo group was included in order to ascertain concurrent control rates. The FS-TOO study was conducted by the NINDS funded Neuroprotection Exploratory Trials in PD (NET-PD).SCR_001154(NET-PD (Neuroprotection Exploratory Trials in PD): Futility Study II, RRID:SCR_001154)Last checked downnif-0000-11252
icyou Health VideosResource, topical portal, portal, video resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. icyou is an internet resource of health-related video clips submitted by users. Health topics covered in videos can range anywhere from infectious diseases to fitness and exercise, with videos generally being shorter than 10 minutes in length. Videos also contain information on treatment and procedures, medical fields, and health politics and policy. These videos may or may not be authored by licensed medical personnel. All videos are searchable, and users can also choose to upload their own healthcare-related videos. In addition to gathering healthcare video from the best sources on the Web and beyond, icyou.com can call on its own award-winning health reporting team to cover the latest issues and trends. Through its parent company Benefitfocus, icyou.com has full access to the Benefitfocus Media Studio, a state-of-the-art HD facility located in Charleston, South Carolina. This studio is the only one of its kind devoted solely to creating healthcare-oriented video content. In it, the Benefitfocus Media team creates up-to-the-minute reports, tutorials, features and more that help illuminate its users about the complexities of the many facets of healthcare.exercise, fitness, healthcare, health policy, health politics, health topic, medical fields, medical procedure, treatmentSCR_001167(icyou Health Videos, RRID:SCR_001167)Last checked downnif-0000-11652http://www.icyou.com
UCLA High-Throughput Clinical Proteomics CoreResource, service resource, core facility, access service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. The High-Throughput Clinical Proteomics (HTCP) core laboratory is a mass spectrometry core facility designed to profile large numbers of clinical samples for changes in protein content. We use small amounts (micrograms) of protein from samples such as urine, plasma, CSF, and cell lysates and incubate them with magnetic beads that bind different subsets of the total proteome. We then examine the different subsets of small proteins and peptides by high-resolution MALDI-TOF mass spectrometry. We measure the amounts and intact masses of the proteins in the samples and determine which have the greatest statistical relevance in defining clinical groupings before moving to physically isolate those peptides/proteins and identify them. The method works best for peptides and small proteins below 25 kDa and is an excellent complement to gel-based methods such as DIGE.SCR_012205(UCLA High-Throughput Clinical Proteomics Core, RRID:SCR_012205)University of California at Los Angeles; California; USA related to: University of California Los Angeles Labs and Facilities, listed by: Science ExchangeLast checked downSciEx_10613
ANFF CharacterisationResource, service resource, core facility, access service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Network of laboratories which provides leading-edge research capability and supports excellence in science. The capability provided by ANFF enables users to process hard materials (metals, composites and ceramics) and soft materials (polymers and polymer-biological materials) and transform these into structures that have various applications.atomic force microscopy, auger electron spectroscopy, chromatography, confocal microscopy, differential scanning calorimetry, electrochemical impedance spectroscopy, electron spin resonance spectroscopy, ellipsometry, film stress measurement, fluorescence microscopy, gas chromatography-mass spectrometry, holographic microscopy, ion beam microscopy, matrix-assisted laser desorption ionization time-of-flight, mass spectrometry, metallographic service, nuclear magnetic resonance spectroscopy, nuclear magnetic resonance, spectroscopy, phase contrast microscopy, raman spectroscopy, rutherford backscattering spectrometry, scanning electron microscopy, scanning near field microscopy, optical imaging, spectrofluorimetry, surface charge measurement, transmission electron microscopy, ultra violet visible spectrophotometry, x-ray diffraction, x-ray photoelectron spectrometry, x-ray tomographySCR_012687(ANFF Characterisation, RRID:SCR_012687)Australian National Fabrication Facility related to: Australian National Fabrication Facility Labs and Facilities, listed by: Science ExchangeLast checked downSciEx_8884
ANFF Specialist Device FabricationResource, service resource, core facility, access service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. The ANFF provides leading-edge research capability and supports excellence in science. The capability provided by ANFF enables users to process hard materials (metals, composites and ceramics) and soft materials (polymers and polymer-biological moieties) and transform these into structures that have application in sensors, medical devices, nanophotonics and nanoelectronics. It has a strong emphasis on service provision to the research community. ANFF seeks to enhance national and international collaborations and enable world-class-research.SCR_012689(ANFF Specialist Device Fabrication, RRID:SCR_012689)Australian National Fabrication Facility related to: Australian National Fabrication Facility Labs and Facilities, listed by: Science ExchangeLast checked downSciEx_8880
Symptom Score for Benign Prostatic HyperplasiaResource, material resource, assessment test providerTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Adapted from the American Urology Association Symptom Score for Benign Prostatic Hyperplasia, this chart will assist physicians, researchers, and patients in assessing the severity of the problem.severity, symptom, prostateSCR_000127(Symptom Score for Benign Prostatic Hyperplasia, RRID:SCR_000127)NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases Benign Prostatic Hyperplasialisted by: NIDDK Information Network, submitted by: NIDDK Information NetworkLast checked downnlx_152737https://www.niddk.nih.gov/health-information/health-topics/urologic-disease/benign-prostatic-hyperplasia-bph/pages/facts.aspx
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