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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: Sep 14, 2019)

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1,038 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
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
Primate Resource Referral ServiceResource, service resource, database, production service resource, data or information resource, material service resourceIt provides the communications/database network needed for efficient acquisition and sharing of existing captive primates and primate-related resources by investigators and institutions both nationally and internationally. The overall goal of this service is to maximize the use of existing captive primates, thereby reducing the total number of primates needed for research, and in turn, helping to promote the conservation of primate populations in the wild. Services Provided PRRS services include 1) Referral Service, an immediate, staff-operated service designed to match investigator inquiries/requests to the available resource listings maintained in the PRRS master database; 2) CURRENT LISTINGS, a twice-monthly newsletter listing current availability of, as well as needs for, primates, tissues, equipment, and services; 3) ANNUAL RESOURCE GUIDE (ARG), an annual publication that lists subscribing suppliers of primates, laboratories, equipment, and commercial services such as transportation and quarantine facilities; and 4) Web site, an interactive site that includes the full text of CURRENT LISTINGS as well as online forms for posting resource availabilities/needs and listing updates, the current ARG, a diagram of primate taxonomy with illustrative photographs, online renewal and feedback forms, general service information, and links to other sites of interest to the primate research community. The PRRS also maintains a database of colonies, primates, and primate materials to which notices of availability and need can be referred. Services are available without charge to government-supported researchers and other scientists in the United States and abroad using primates in their work. Sponsors: The PRRS is made possible by grant RR-01240 from the National Center for Research Resources, National Institutes of, colony, communication, institution, investigator, network, primate, research, tissueSCR_002828(Primate Resource Referral Service, RRID:SCR_002828)University of Washington; Seattle; USA Last checked downnif-0000-24969
cpnDB: A Chaperonin DatabaseResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceA curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.chaperonin sequence, microbial ecology, phylogenetics, chaperonin, plastid, mitochondria, cytoplasm, sequence, blast, fastaSCR_002263(cpnDB: A Chaperonin Database, RRID:SCR_002263)Canadian Biotechnology Strategy, National Research Council Genomics and Health Initiativelisted by: OMICtoolsPMID:15289485Last checked downnif-0000-02694, OMICS_01511
ImpactStoryResource, software resource, source code, service resource, production service resourceA web application which provides altmetrics to help researchers measure and share the impacts of their research outputs. After making a profile, scientists can track which of their publications are most popular through number of citations, frequency of PDF downloads, etc. Information from research outputs such as journal articles, blog posts, datasets, and software contribute to a user's impact, which is viewable in their profile.altmetrics, metric, citeulike, crossref, scienceseeker, scopus, slideshare, topsy, twitter, vimeo,, plos, youtubeSCR_002632(ImpactStory, RRID:SCR_002632)Alfred P. Sloan Foundation, NSF, Open Society Foundationrelated to: PubMed, GitHub, FigShare, Dryad, Wikipedia, Mendeley, used by: Publons, listed by: FORCE11, Connected Researchers, PLOS Article-Level MetricsLast checked downnlx_156056
ISFinderResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, data repository, data or information resourceDatabase of a list of insertion sequences isolated from eubacteria and archaea. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences. Although most of the entries have been identified as individual elements, a growing number are included from their description in sequenced bacterial genomes. The search engine permits the retrieval and display of individual and groups of ISs based on a combination of their general features. Two levels of search are available. The simple search option enables the user to sort elements using a limited number of basic items whereas the extensive search offers an additional set of possibilities such as comparisons of the sequences of terminal inverted repeats and a variety of different layout displays. Built in links are provided to: the EMBL sequence database, the NCBI taxonomy database and to the ESF plasmid database. At present, only individual sequences can be downloaded one by one for comparison. An on-line BLAST facility is available and in future versions direct access to additional analytical tools will be provided on line. Direct submission of ISs is encouraged using the on-line form provided.insertion sequence, insertion, sequence, blast, dna, protein sequenceSCR_003020(ISFinder, RRID:SCR_003020)Paul Sabatier University - Toulouse III; Toulouse; France CNRSLast checked downnif-0000-03050
Radiotracer Chemistry Instrumentation and Biological ImagingResource, organization portal, instrument supplier, production service resource, instrument manufacture, material service resource, laboratory portal, service resource, portal, material resource, data or information resourceDevelop new scientific tools to image the movement of molecules in energy-relevant and environmentally-sensitive contexts in response to BER's call to explore the potential of radiotracer imaging in energy and environmentally-responsive contexts. Their goal is to visualize metabolic networks and regulatory systems underlying cellular communication in the living organism including plants and microbial communities. This has broad implications to DOE missions in energy and the environment and is very relevant to improvements in plant biomass for biofuel.neuroimaging, imaging instrumentation, radiotracer chemistry, plant scienceSCR_003258(Radiotracer Chemistry Instrumentation and Biological Imaging, RRID:SCR_003258)DOE, Office of ScienceLast checked downnif-0000-31420
GOtchaResource, analysis service resource, data analysis service, service resource, production service resourceGOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online toolfunction, protein, prediction, genome, annotation, gene, statistical analysisSCR_005790(GOtcha, RRID:SCR_005790)University of Dundee; Scotland; United Kingdom European Union fifth framework, Wellcome Trustrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15550167Last checked downnlx_149269
ERICResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceERIC is a resource of annotated enterobacterial genomes. Information is available and accessed through a open web portal uniting biological data and analysis tools. ERIC contains information on Escherichia, Shigella, Salmonella, Yersinia, and other microorgansims. ERIC has recently been moved over to PATRIC: The PATRIC BRC is now responsible for all bacterial species in the NIAID Category A-C Priority Pathogen lists for biodefense research, and pathogens causing emerging/reemerging infectious diseases. For ERIC users, we understand that the resource was valuable to your work. As such, we will be doing our very best to create a useful PATRIC resource to continue supporting your work. We realize that the transition will cause disruptions. However, it is a priority for us to work with established BRC users and communities to identify and prioritize our transition efforts. We have concentrated on the transfer of genomic data for this initial release. We anticipate adding new data, tools, and website features over the next several months. We look forward to working with you during the next 5 years.enterobacteria, enterobacteria pathogen, biodefense, disease bioinformatics, human disease, pathogen, pathogenic bacteria, cronobacter, enterobacter, erwinia, klebsiella, pectobacterium, photorhabdus, proteus, serratia, escherichia, shigella, salmonella, yersinia, citrobacterSCR_007644(ERIC, RRID:SCR_007644)Virginia Polytechnic Institute and State University; Virginia; USA NIAIDLast checked downnif-0000-02813
PROTOTYPE - Suspected Overlap Among OBO Foundry Candidate OntologiesResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Service that determines the Suspected Overlap Among OBO Foundry Candidate Ontologies.SCR_008834(PROTOTYPE - Suspected Overlap Among OBO Foundry Candidate Ontologies, RRID:SCR_008834)National Center for Biomedical Ontology Last checked downnlx_144632
isomiRexResource, analysis service resource, data analysis service, service resource, production service resourceA web tool for the identification of microRNAs and their isomiRs, as well as differential expression from NGS datasets.SCR_009521(isomiRex, RRID:SCR_009521)listed by: OMICtoolsPMID:23831580Last checked downOMICS_00359
EcoCyte BioscienceResource, service resource, material service resource, production service resourceSupplier and servicer of products for experiments involving Xenopus laevis. Their products include laboratory equipment, media, and oocytes, and their services for pharmacological studies include heterologous expression and in vitro electrophysiology.supplier, commercial, xenopus, xenopus laevis, laboratory equipment, oocyte, pharmacology, heterologous expression, electrophysiologySCR_014773(EcoCyte Bioscience, RRID:SCR_014773)submitted by: Resource Identification PortalLast checked down
HologicOrganization, service resource, production service resource, material service resourceCommercial organization that provides services and products in global healthcare and service, healthcare products, diagnostic services, diagnostic productsSCR_015529(Hologic, RRID:SCR_015529)related to: Gen-ProbeLast checked down
OrpheliaResource, software resource, analysis service resource, data analysis service, service resource, production service resourceA metagenomic open reading frame (ORF) finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin. The resource is based on a two-stage machine learning approach that uses linear discriminants to extract features from the ORFs. An artificial neural network then combines the features and computes a gene probability for each ORF fragment.metagenomic open reading frame, tool, resource, protein, genes, DNA, phyologenetic origin, machine learning, linear discriminates, artificial neural network, computation, scientific computing, fragmentSCR_000119(Orphelia, RRID:SCR_000119)listed by: OMICtoolsLast checked downOMICS_01492
GenNavResource, analysis service resource, data analysis service, service resource, production service resourceGenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG. Platform: Online toolimage, gene, ontology or annotation browserSCR_000147(GenNav, RRID:SCR_000147)National Library of Medicine related to: Gene Ontology, listed by: Gene Ontology ToolsLast checked downnlx_149123
Core Life SciencesResource, instrument supplier, production service resource, core facility, material service resource, instrument manufacture, service resource, access service resource, reagent supplier, material resourceA commercial organization that supplies researchers with life science instruments, reagents and consumables, and lab services.commercial, lab procedures, affymetrix DNA microarray, microRNA, methylation analysis, peptide microarray, quantitative PCR, reagent supplier, instrument supplierSCR_000138(Core Life Sciences, RRID:SCR_000138)listed by: Science ExchangeLast checked downSciEx_10652
Mining On-Line Expert on MedLineResource, data analysis service, production service resource, analysis service resource, software application, text-mining software, service resource, software resourceMedMOLE improves the comprehension of microarray experimental results by grouping co-regulated genes on the basis of the informational content of MEDLINE documents. The tool relies on two components: a gene name extractor and a mining algorithm. The name extractor is based on existing dictionaries of gene names and aliases. The mining algorithm analyses the co-occurrences of words in the selected documents in order to automatically interpret the context, identify where the gene names appear, and map documents/genes into functional classes. DNA microarray technology is a high throughput method for gaining information on gene function. This large amount of data can be analyzed to identify groups of genes that share common expression characteristics, but the obtained results provide little information regarding the presence of functional biological correlations of genes within clusters. The published literature, on the other hand, provides a potential source of information to assist in interpretation of clustering results. We have developed a tool (MedMOLE) that improves the comprehension of microarray experimental results by grouping co-regulated genes on the basis of the informational content of MEDLINE documents. The tool relies on two components: a gene name extractor and a mining algorithm. The name extractor is based on existing dictionaries of gene names and aliases. The mining algorithm analyses the co-occurrences of words in the selected documents in order to automatically interpret the context, identify where the gene names appear, and map documents/genes into functional classes. Microarray transcriptional profiling is a powerful tool used in the study of transcriptional control mechanisms. An important point in the analysis of microarray data is the identification of hidden correlations between the differentially expressed genes generated upon some kind of cell stimulus. Functional annotation is an important topic for microarray data mining, however this is quite limited for complex organisms (e.g. H. sapiens, M. musculus) where a limited number of genes are well characterized and annotated. However, functional data are rapidly accumulating in the scientific literature and most of them are collected by MEDLINE, a database that contains over 11,000,000 biomedical journal citations. A microarray analysis usually generates few hundred of differentially expressed genes and, after statistical validation of the data and transcription profiles clustering, biologists try to identify genes functionally correlated by scientific literature analysis. Even if some tools have been recently developed to simplify information extraction on the MEDLINE database, reading every article requires too much time and labor. Therefore, it is necessary to have some kind of intelligent information extracting system that recognizes gene names inside the texts. The analysis of text documents (e.g. MEDLINE abstracts) can be approached by two different points of view: text mining and information extraction (I.E.). The former aims at the automatic identification of groups of documents that share the same patterns of words, and thus refer to the same topic or theme. The latter aims at providing a structured representation of the textual information and requires a pre-definition of entities and relationships to be looked for inside texts. Thus while the text mining algorithms are general purpose, the information extraction algorithms are specific to the application. Furthermore, the text mining approach is explorative and enables the discovery of new concepts and relations while information extraction only extracts those elements that have already been defined. These two approaches can be integrated: information extraction tools generate databases that can be analyzed using data mining techniques, and, on the other side, text mining tools might take advantage of specific domain information extracted using I.E. techniques. MedMOLE takes advantage of text mining techniques, and simplifies the extraction of functional knowledge by literature abstracts directly/indirectly related to differentially expressed genes identified by microarray technology. Sponsors: This work was partially supported by PRIN 2001 and FIRB 2002 grants.experimental, extractor, function, functional, gene, algorithm, cell, characteristic, class, dna, informational, literature, mechanism, medline, medline interfaces, microarray, mining, organism, stimulus, technology, transcriptionalSCR_001848(Mining On-Line Expert on MedLine, RRID:SCR_001848)Last checked downnif-0000-21258
RefFinderResource, analysis service resource, data analysis service, service resource, production service resourceA web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking.gene, gene expression, reference gene, web based toolSCR_000472(RefFinder, RRID:SCR_000472)East Carolina University; Carolina; USA uses: BestKeeper, NormFinder, GENORM, listed by: OMICtoolsLast checked downOMICS_02321
PhyloPythiaResource, analysis service resource, data analysis service, service resource, production service resourceData analysis service for accurate phylogenetic classification of variable-length DNA fragments.classification, phyolgenetic, dna fragment, dna, metagenome, sequenceSCR_000540(PhyloPythia, RRID:SCR_000540)listed by: OMICtoolsPMID:17179938Last checked downOMICS_01459
Onto-DesignResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceMany Laboratories chose to design and print their own microarrays. At present, the choice of the genes to include on a certain microarray is a very laborious process requiring a high level of expertise. Onto-Design database is able to assist the designers of custom microarrays by providing the means to select genes based on their experiment. Design custom microarrays based on GO terms of interest. User account required. Platform: Online toolmicroarray, gene, biological process, molecular function, cellular component, data-mining, browser, visualization, analysis, design, search engine, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, other analysis, design custom microarrays based on go terms of interestSCR_000601(Onto-Design, RRID:SCR_000601)Wayne State University; Michigan; USA related to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15215428Last checked downnlx_149109
PredSLResource, data analysis service, data analysis software, data processing software, production service resource, analysis service resource, software application, service resource, software resourceA web tool using an algorithm that exploits neural networks, Markov Chains, and HMMs for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence and aims to classify proteins into five groups: Chloroplast, Thylakoid, Mitochondrion, Secreted proteins, and Other. Analysis of a non-redundant test set, consisting of plant protein sequences provides a ~90% accuracy, whereas analysis of a similar set of nonplant protein sequences provides a ~92% accuracy. As input PredSL requires the protein's sequence in fasta format. The algorithm cosists of 11 steps: # Initially the 100 N-terminal residues of the sequence are coded (see supplementary material-neural network training) and fed to a first layer of 2 neural networks which determine whether a residue belongs or not to a chloroplast transit peptide (cTP) or a mitochondrial transit peptide (mTP). From this step we get 100 scores (one per residue) from each network. # We have set a cutoff where the residues do not belong to a transit peptide any longer, and thus we calculate two approximate cleavage sites from the 100 scores we calculated in step 1.(One from each network) # We take a window of 40 positions around the approximate cleavage site we estimated in step 2, and we use a set of neural networks to predict the cleavage site. Therefore we have one prediction of the cleavage site of the hypothetical cTP and one for the mTP. # We calculate the average of the scores of the hypothetical peptides predicted from each network, and this results to two scores. # We feed the 100 scores from step 1 to two neural networks (one for the cTP and one for the mTP), and we get two more scores. These scores represent the probability that the sequence has an mTP or a cTP. # We use PrediSi to calculate one more score for each sequence. This score represents the probability of a sequence belonging to a secreted protein. # We use a program that uses Markov chains to discriminate between two categories to get 6 more scores for the plant proteins and 3 more for the nonplant. (See supplementary material-Markov chains) # We use HMMER to get two additional scores for each protein. One that shows the existence or not of a cTP and one that shows the existence or not of an mTP. # We feed all the scores we gathered (13 for the plant and 7 for the non-plant proteins) to a neural network that does the final prediction. # Finally, if a sequence is predicted to belong to a chloroplast protein, we use HMMER to determine the existence of a lumenal-transit peptide (lTP) # If the user requires it, PredSL provides the possibility to make a graph for each case. The graphs for the chloroplast and mitochondrial sequences are created using the scores from Step 1 and taking a window around the predicted cleavage site from Step 3. For the secreted proteins, the graphs are created usind the hydrophobicity index (Kytte-Doolittle, 1982) for a window around the predicted cleavage site from PrediSi.fasta, neural network, markov chain, hidden markov model, predict, subcellular localization, eukaryote, cell, n-terminal, amino acid sequence, classification, protein, chloroplast, thylakoid, mitochondrion, secreted protein, localization, secretory pathway, protein sequence, target peptide, transit peptide, signal peptideSCR_000626(PredSL, RRID:SCR_000626)University of Athens Biophysics and Bioinformatics Laboratory PMID:16689702Last checked downnlx_151739
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