Curator Dashboard

An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

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• SciCrunch
• 12 years ago - by Anonymous

A web-based analysis service for identifying exonic splicing enhancers in eukaryotic genes. ESEfinder accept sequences in the FASTA format. A typical mammalian gene is composed of several relatively short exons that are interrupted by much longer introns. To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently, in a process that requires the coordinated action of five small nuclear (sn)RNAs (U1, U2, U4, U5 and U6) and more than 60 polypeptides. The inaccurate recognition of exon/intron boundaries or the failure to remove an intron generates aberrant mRNAs that are either unstable or code for defective or deleterious protein isoforms. Exonic enhancers are thought to serve as binding sites for specific serine/arginine-rich (SR) proteins, a family of structurally related and highly conserved splicing factors characterized by one or two RNA-recognition motifs (RRM) and by a distinctive C-terminal domain highly enriched in RS dipeptides (the RS domain). The RRMs mediate sequence-specific binding to the RNA, and so determine substrate specificity, whereas the RS domain appears to be involved mainly in protein-protein interactions. SR proteins bound to ESEs can promote exon definition by directly recruiting the splicing machinery through their RS domain and/or by antagonizing the action of nearby silencer elements. Sponsors: ESEfinder is supported by the Cold Spring Harbor Laboratory.

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• SciCrunch
• 17 years ago - by Anonymous

A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs.

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• SciCrunch
• 17 years ago - by Anonymous

Public research university in Ohio that offers degree programs in a variety of fields such as business, music and arts, and medical and human service.

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• SciCrunch
• 13 years ago - submitted by Stephen Larson

Private research university in Chicago, Illinois.

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• SciCrunch
• 17 years ago - submitted by Stephen Larson

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. LOC3d is a database of predicted subcellular localization for eukaryotic proteins of known 3-D structure taken from the Protein Databank. Subcellular localization is currently predicted using four different methods: predictNLS (nuclear localization signal), LOChom (using homology), LOCkey (using keywords) and LOC3d (neural network based prediction). The reported localization is based on the method which predicts localization of a given protein with the highest confidence. LOCtree is a novel system of support vector machines (SVMs) that predict the subcellular localization of proteins, and DNA-binding propensity for nuclear proteins, by incorporating a hierarchical ontology of localization classes modeled onto biological processing pathways. Biological similarities are incorporated from the description of cellular components provided by the gene ontology consortium (GO). GO definitions have been simplified and tailored to the problem of protein sorting. Technically the ontology has been implemented using a decision tree with SVMs as the nodes. LOCtree, was extremely successful at learning evolutionary similarities among subcellular localization classes and was significantly more accurate than other traditional networks at predicting subcellular localization. Whenever available, LOCtree also reports predictions based on the following: 1) Nuclear localization signals found by PredictNLS, 2) Localization inferred using Prosite motifs and Pfam domains found in the protein, and 3) SWISS-PROT keywords associated with a protein. Localization is inferred in the last two cases using the entropy-based LOCkey algorithm. Additional information can be found in the LOCtree manuscript and associated PredictNLS and LOCkey publications.

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• SciCrunch
• 17 years ago - by Anonymous

Database that provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. The 16S rRNA gene database provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ARB users can use Greengenes to update local databases., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

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• SciCrunch
• 17 years ago - by Anonymous

It 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 Health.

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• SciCrunch
• 17 years ago - by Anonymous

Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs.

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• SciCrunch
• 16 years ago - by Anonymous

A nonprofit devoted to fostering education, scientific research, and dissemination of information in the physiological sciences. Founded in 1887 with 28 members, the APS now has over 10,500 members. Most members have doctoral degrees in physiology and/or medicine (or other health professions). APS is governed by an elected Council consisting of a President, President-Elect, Past President, and nine Councillors. The National headquarters of the Society is based in Bethesda, Maryland, on the campus of the Federation of American Societies for Experimental Biology (FASEB). The American Physiological Society Awards program demonstrates the Society's dedication to its members and biomedical research by recognizing the research efforts of outstanding APS members. Awards are offered by the Society and the various APS Sections. For questions regarding the Society awards (including Student awards), please send an email to awards_at_the-aps.org. For questions regarding the Section awards please contact the individual Sections directly www.the-aps.org/sections/.

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• SciCrunch
• 14 years ago - by Anonymous

Private, non-profit university in Utah. The university is a part of the Latter-day Saints Church Educational System.

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• SciCrunch
• 17 years ago - submitted by Andrea Stagg

Center to provide global research, training, and resources that will lead to the discovery of medically important toxins found in venoms. The Viper Resource Center (VRC) is located in the Natural Toxins Research Center at Texas A&M University-Kingsville.

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• SciCrunch
• 17 years ago - by Anonymous

Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas.

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• SciCrunch
• 15 years ago - by Anonymous

Marginalia is an open source Javascript web annotation system that allows users of web applications to highlight text and write margin notes. Marginalia has been integrated into several web applications: * An extension to Moodle adds annotation to Moodle discussion forums. * A plug-in for Open Journal Systems allows readers to annotate journal articles. * Marginalia is part of the Bungeni parliamentary and legislative information system. * A stand-alone demo implementation provides a minimal sample implementation as a demonstration of how to integrate Marginalia with other web applications. The annotation feature supports recent versions of major browsers (Firefox, Safari, and IE), but works best and fastest in Firefox. The features are integrated into and work with a host web application with no need for special browser or other client software. Marginalia is the 2008 winner of the British Columbia Innovation Award in Educational Technology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

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• SciCrunch
• 16 years ago - by Anonymous

Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26.

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• SciCrunch
• 17 years ago - by Anonymous

Automated software program for image analysis based on microarray based image application. Various output styles are available, including image overlay with warping and registration and scattered correlation plot with 2D or 3D spot profile. Outputs can be formatted in text, xml, excel, or custom format.

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• SciCrunch
• 13 years ago - by Anonymous

Core facility that provides metals analytical capabilities to biomedical and non-biomedical researchers and serves as a source for study design consultation and sample QA/QC requirements. The transport, fate, exposure, and toxic effects of heavy metals is a primary focus of research at the Center. It operates as a modified fee-for-service laboratory. Researchers have the option of having the samples run by the Service staff, or of receiving instruction (for themselves or a doctoral or post doctoral trainee) on how to operate the analytical equipment and analyze their own samples. Both options have associated fees and, as with other services, facility access funds can be requested internal or external services when individual grant support is not yet available.

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• SciCrunch
• 13 years ago - by Anonymous

The 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.

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• SciCrunch
• 17 years ago - by Anonymous

Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data.

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• SciCrunch
• 17 years ago - by Anonymous