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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

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Drug Information PortalResource, topical portal, database, portal, data or information resourceThe NLM Drug Information Portal gives users a gateway to selected drug information from the U.S. National Library of Medicine and other key U.S. Government agencies. At the top of the page are links to individual resources with potential drug information, including summaries tailored to various audiences. Resources include the NLM search systems useful in searching for a drug, NLM research resources, resources organized by audience and class, and other NIH and government resources such as FDA and CDC. The search box in the middle of the page lets you search many of these resources simultaneously. More than 34,000 drugs can be searched using this facility. The portal covers drugs from the time they are entered into clinical trials (Clinicaltrials.gov) through their entry in the U.S. market place (Drugs@FDA). Many drugs in other countries are covered, but not as thoroughly as U.S. drugs. The PubMed link provides medical literature describing research, and TOXLINE provides toxicology literature. Resources such as MedlinePlus provide easy to read summaries of the uses and efficacy of a drug. You may search by a drug's trade name or generic name. For example, the trade name Advil and the generic name ibuprofen will retrieve the same drug record. As you type in a name, suggestions are given beneath the search box. A spell checker gives suggestions if the name is not found. You can find embedded portions of names by using an asterisk at the beginning and/or end of a search term. You can also search by the general Category of usage of a drug by checking that radio button. Suggestions are given as you type here too. Once a drug is found, a summary of the drug's type and usage is given, as well as links leading to further information at one of the portal's resources. Outside links open in a new window. Within a given drug record, you may click on the drug category and retrieve drugs with the same or similar uses. * View drug category descriptions. * View top By Name searches (previous seven days). * View top By Category searches (previous seven days). * View top dispensed prescriptions in the US Market, 2010. * View common drug name list. * View category name list. * View list of resources searched. JavaScript must be enabled in your browser for the NLM Drug Information Portal to work properly.drug, catalog, medicine, prescriptionSCR_002818(Drug Information Portal, RRID:SCR_002818)National Library of Medicine NLMLast checked upnif-0000-24913
FLASHResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationOpen source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.SCR_005531(FLASH, RRID:SCR_005531)Johns Hopkins University; Maryland; USA NHGRI, NIGMS, NLMrelated to: shovill, listed by: OMICtoolsPMID:21903629Last checked upOMICS_01047https://sourceforge.net/projects/flashpage/files/
OligoGenome Resource, data or information resource, resource, databaseThe Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets.oligonucleotide, genome, probe, coding region, oligonucleotide sequence, chromosomeSCR_006025( OligoGenome , RRID:SCR_006025)Stanford University; Stanford; California Doris Duke Clinical Foundation, Howard Hughes Medical Foundation, Liu Bie Ju Cha and Family Fellowship in Cancer, NCI, NHGRI, NIDDK, NLM, Reddere Foundation, Wang Family FoundationPMID:22102592Last checked downnlx_151422
MedGenResource, data or information resource, databaseA database of organized information related to human medical genetics, such as attributes of conditions with a genetic contribution.medical genetics, medical, genetics, disease, clinicalSCR_000111(MedGen, RRID:SCR_000111)NCBI NLMlisted by: OMICtools, Genetic Testing RegistryLast checked upnlx_156941, OMICS_01549
ROSTLABResource, groupA lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research.protein, structure, function, dna, rna, gene, machine learning, statistics, analysis, protein, biomedicalSCR_000792(ROSTLAB, RRID:SCR_000792)Columbia University; New York; USA NLMLast checked upnif-0000-31417http://cubic.bioc.columbia.edu/services/disis
HanalyzerResource, software resource, software application, source codeAn open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download.genomic, visualization, reading, reasoning, reporting, throughput analyzer, data networkSCR_000923(Hanalyzer, RRID:SCR_000923) SourceForge , University of Colorado Denver; Colorado; USA NHGRI, NIDCR, NIGMS, NLMPMID:19325874Last checked upnlx_48287
Automated Microarray PipelineResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis.microarray, normalizationSCR_001219(Automated Microarray Pipeline, RRID:SCR_001219)TM4 NLMrelated to: Gene Ontology, listed by: OMICtoolsLast checked upOMICS_02125http://www.tm4.org/amp.html
pRESTOResource, software resource, software toolkitSoftware toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires.lymphocyte, high throughput sequencing, processing, raw readsSCR_001782(pRESTO, RRID:SCR_001782)Yale School of Medicine; Connecticut; USA EMD/Merck/Serono, NCRR, NIAAA, NLM, United States-Israel Binational Science Foundationlisted by: OMICtoolsPMID:24618469Last checked upOMICS_03443
Alignable Tight Genomic ClusterResource, data or information resource, databaseATGC stands for Alignable Tight Genomic Cluster, which is cluster of closely related prokaryotic genomes. ATGC is the principal notion of this web resource. The purpose of this web resource is to prepare ATGC-derived data sets for a variety of research projects in functional and evolutionary genomics. Unique features of ATGC include: * Reliable identification of orthologs (high degree of similarity between the genomes in the set allow an extensive use of synteny in ortholog identification); * Fine granularity of protein classification (in comparisons of more distant genomes, proteins belonging to families of paralogs are often lumped into a singlegroup; under the ATGC approach, comparison of genomic sequences from highly similar genomes allows one to track each set of orthologs separately); * Relative rarity of changes of any kind (in sequence, genome organization and gene content) allows the use of parsimony-related methods of analysis.gene, genomic cluster, genomic sequence, ortholog, paralog, prokaryotic genomic, protein, protein classificationSCR_001894(Alignable Tight Genomic Cluster, RRID:SCR_001894)Lawrence Berkeley National Laboratory Department of Energy Joint Genome Institute, DOE, NLMLast checked upnif-0000-02581
Directory of Health Organizations OnlineResource, data or information resource, databaseTHIS RESOURCE HAS BEEN DISCONTINUED, documented July 15, 2016. Database containing location and descriptive information about a wide variety of information resources including organizations, research resources, projects, and databases concerned with health and biomedicine. This information may not be readily available in bibliographic databases. Each record may contain information on the publications, holdings, and services provided. These information resources fall into many categories including federal, state, and local government agencies; information and referral centers; professional societies; self-help groups and voluntary associations; academic and research institutions and their programs; information systems and research facilities. Topics include HIV/AIDS, maternal and child health, most diseases and conditions including genetic and other rare diseases, health services research and technology assessment. DIRLINE can be searched using subject words (such as disease or condition) including Medical Subject Headings (MeSH) or for the name or location of a resource. It now offers an A to Z list of over 8,500 organizations.genetic, aids, biomedicine, child, condition, disease, health, hiv, maternal, medicine, public healthSCR_002331(Directory of Health Organizations Online, RRID:SCR_002331)National Library of Medicine NLMLast checked upnif-0000-21122
Midas PlatformResource, software resource, software toolkit, data management software, software applicationOpen-source toolkit that enables the rapid creation of tailored, web-enabled data storage and provides a cohesive system for data management, visualization, and processing. At its core, Midas Platform is implemented as a PHP modular framework with a backend database (PostGreSQL, MySQL and non-relational databases). While the Midas Platform system can be installed and deployed without any customization, the framework has been designed with customization in mind. As building one system to fit all is not optimal, the framework has been extended to support plugins and layouts. Through integration with a range of other open-source toolkits, applications, or internal proprietary workflows, Midas Platform offers a solid foundation to meet the needs of data-centric computing. Midas Platform provides a variety of data access methods, including web, file system and DICOM server interfaces, and facilitates extending the methods in which data is stored to other relational and non-relational databases.data storage, data analysis, visualization, multimedia, digital archiving, processingSCR_002186(Midas Platform, RRID:SCR_002186)Kitware NCI, NIH, NLMLast checked upnlx_154696
Developmental and Reproductive Toxicology DatabaseResource, data or information resource, databaseBibliographic database providing references to developmental and reproductive toxicology literature on the National Library of Medicine's Toxicology Data Network. It covers teratology and other aspects of developmental and reproductive toxicology. It contains over 200,000 references to literature published since 1965. DART/ETIC is easily accessible and free of charge. Search by subject terms, title words, chemical name, Chemical Abstracts Service Registry Number (RN), and author. Search results can easily be viewed, printed or downloaded. Search results are displayed in relevancy ranked order, but may be sorted by publication date, author or title.chemical, developmental, medicine, reproductive, teratology, toxicology, developmentSCR_002326(Developmental and Reproductive Toxicology Database, RRID:SCR_002326)National Library of Medicine National Center for Toxicological Research, NIEHS, NLM, U.S. Environmental Protection AgencyLast checked upnif-0000-21110
dbSNPResource, service resource, data or information resource, data repository, storage service resource, databaseDatabase as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.insertion, polymorphism, short, deletion, single, nucleotide, genetic, variation, genomics, genotype, disease, allele, microsatellite, marker, multinucleotide, heterozygous, sequence, gold standardSCR_002338(dbSNP, RRID:SCR_002338)NCBI , National Human Genome Research Institute NLMrelated to: Ensembl Variation, Monarch Initiative, GWAS Central, TopoSNP, Human Genome Variation database of Genotype-to-Phenotype information, used by: ExAc, GEMINI, listed by: OMICtools, re3data.orgLast checked upnif-0000-02734, OMICS_00264http://www.ncbi.nlm.nih.gov/projects/SNP/
GlimmerHMMResource, software resource, source codeA gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).gene, hidden markov modelSCR_002654(GlimmerHMM, RRID:SCR_002654)Johns Hopkins University; Maryland; USA NIH, NLMrelated to: GlimmerPMID:15145805Last checked upnlx_156092
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteinsResource, analysis service resource, data analysis service, service resource, production service resourceThis web-server takes a user-supplied sequence of a DNA-binding protein and predicts residue positions involved in interactions with DNA. Prediction can be performed using a profile of evolutionary conservation of the input sequence automatically generated by the web-server or the input sequence alone. Three prediction methods are run for each input sequence and consensus prediction is generated.dna bindingSCR_003039(DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins, RRID:SCR_003039)University at Albany; New York; USA NLMReferences (2)Last checked downnif-0000-30426
Distant Regulatory ElementsResource, analysis service resource, data analysis service, service resource, production service resourceWeb server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.regulatory element, enhancer identification, genome, prediction, transcription factor binding site, gene, co-expression, co-function, function, transcription factor, comparative genomics, regulatory function, gene locus, chromosomeSCR_003058(Distant Regulatory Elements, RRID:SCR_003058)NCBI Intramural Research Program, NLMPMID:18487623Last checked upnif-0000-30448
ProtegeResource, software resource, software application, authoring toolProtege is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protege implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protege can be customized to provide domain-friendly support for creating knowledge models and entering data. Further, Protege can be extended by way of a plug-in architecture and a Java-based Application Programming Interface (API) for building knowledge-based tools and applications. An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary. Ontologies range from taxonomies and classifications, database schemas, to fully axiomatized theories. In recent years, ontologies have been adopted in many business and scientific communities as a way to share, reuse and process domain knowledge. Ontologies are now central to many applications such as scientific knowledge portals, information management and integration systems, electronic commerce, and semantic web services. The Protege platform supports two main ways of modeling ontologies: * The Protege-Frames editor enables users to build and populate ontologies that are frame-based, in accordance with the Open Knowledge Base Connectivity protocol (OKBC). In this model, an ontology consists of a set of classes organized in a subsumption hierarchy to represent a domain's salient concepts, a set of slots associated to classes to describe their properties and relationships, and a set of instances of those classes - individual exemplars of the concepts that hold specific values for their properties. * The Protege-OWL editor enables users to build ontologies for the Semantic Web, in particular in the W3C's Web Ontology Language (OWL). An OWL ontology may include descriptions of classes, properties and their instances. Given such an ontology, the OWL formal semantics specifies how to derive its logical consequences, i.e. facts not literally present in the ontology, but entailed by the semantics. These entailments may be based on a single document or multiple distributed documents that have been combined using defined OWL mechanisms (see the OWL Web Ontology Language Guide). Protege is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development.ontology, java, develop, manage, edit, plug-inSCR_003299(Protege, RRID:SCR_003299)Stanford University School of Medicine; California; USA Defense Advanced Research Projects Agency, eBay, National Centers for Biomedical Computing, NCI, Neural ElectroMagnetic Ontologies NEMO, NIST - National Institute of Standards and Technology, NLM, NSF, Pfizerrelated to: National Center for Biomedical Ontology, Jambalaya, listed by: BiositemapsLast checked upnif-0000-31708
MiMI Plugin for CytoscapeResource, data visualization software, software application, data processing software, software resourceThe Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways.protein interaction, network visualization, xquery, interactive database, information refining, molecular interaction, bioinformatics tool, java, protein-protein interaction, interaction network, biological effect, bimolecular, interaction, molecular, network, pathway, protein, visualization, pluginSCR_003424(MiMI Plugin for Cytoscape, RRID:SCR_003424) National Center for Integrative Biomedical Informatics , University of Michigan; Michigan; USA NCRR, NIDA, NIH, NLMrelated to: Cytoscape, Michigan Molecular Interactions, listed by: BiositemapsPMID:18812364Last checked downnif-0000-33090http://mimiplugin.ncibi.org/index.html
Protein ClustersResource, data or information resource, databaseDatabase of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTPbacteriophage, mitochondrial organelle, chloroplast organelle, plasmid, phylogeny, nucleotide sequence, chloroplast, dna, virus, genome, organelle, gold standardSCR_003459(Protein Clusters, RRID:SCR_003459)NCBI Intramural Research Program, NIH, NLMlisted by: re3data.orgPMID:18940865Last checked upnif-0000-03354
Phymm and PhymmBLResource, software resourceSoftware for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy.metagenome, sequence, taxonomy, classification, phylogenetic classification, genome, short readSCR_004751(Phymm and PhymmBL, RRID:SCR_004751)University of Maryland; Maryland; USA NLMlisted by: OMICtoolsReferences (2)Last checked upOMICS_01461
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