Software
Displaying all 688 matches
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10 year CVD risk calculator CalculatorThis risk assessment tool uses information from the Framingham Heart Study to predict a person's chance of having a heart attack in the next 10 years. This tool is designed for adults aged 20 and older who do not have heart disease or diabetes. The calculation is based on age, gender, total and HDL cholesterol, smoker status, systolic blood pressure, and whether current medications are involved.
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3D Domains NCBI
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3DID, 3D interacting domains Database
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A-a gradient STAT!Ref
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Abcam DatabaseAn extensive repository of antibodies available for purchase. It provides information and purchase information for antibodies.
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ABG Mobile Application, iPhone/iPod touch/iPadMultipurpose medical calculator. Includes functionality to analyze arterial blood gasses and to determine drip rate from desired dosing for an infusion (or vice-versa).
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AbMiner DatabaseAbMiner is a tool that allows users to search for appropriate, commercially available antibodies (>600) for research purposes, and to match each antibody to its respective genomic identifiers. The unique feature of this antibody collection is that all antibodies are screened by Western blot. The sample used for antibody screening was a pool of the NCI-60 cancer cell lines, comprised of 60 different cell lines from 9 different tissues of origin. Besides results, AbMiner also includes the dilutions used and pertinent vendor information for all antibodies. The target antigen for each antibody was translated to the encoding gene symbol using MatchMiner. Other identifiers include gene name, HUGO status, UniGene Cluster ID, RefSeq for protein and mRNA, and Entrez Gene Ids. These identifiers are updated periodically as new information becomes available. Users can search AbMIner by any of the identifiers and easily navigate between antibody, protein, mRNA, and gene.
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Absolute Neutrophil count STAT!Ref
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Absolute Reticulocyte count STAT!Ref
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Adobe Acrobat Product DescriptionStudent Computing Version X (10.1.4) (Windows & Macintosh)M051 Version X (10.1.4) (Windows & Macintosh)Duck Room Version X (10.1.4) (Windows)Redwood Room Version X (10.1.4) (Windows)Stone Room Version X (10.1.4) (Windows)
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Adobe Flash Player Product DescriptionStudent Computing Version 11 (Windows)M051 Version 11 (Windows & Macintosh)Duck Room Version 11 (Windows)Redwood Room Version 11 (Windows)Stone Room Version 11 (Windows)
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Adobe Photoshop Product DescriptionRedwood Room, on computers Scan 1 & Scan 2, only. Version CS5.1 (Windows)
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AffinDB DatabaseA database of affinity data for structurally resolved protein-ligand complexes from the Protein Data Bank (PDB).
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Age calculator Calculator
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AHRQ Inpatient quality indicators IQI Download
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AHRQ Patient safety indicators PSI Download
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AHRQ Pediatric quality indicators PDI Download
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AHRQ Prevention quality indicators PQI Download
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AIDSinfo Mobile Application, iPhone/iPod touch/iPad"This app is designed as a resource to help health care providers, caseworkers, community-based organization professionals, and people living with HIV/AIDS and their families understand complex HIV/AIDS terminology. AIDSinfo, a service of the U.S. Department of Health and Human Services (HHS), is a trusted source for information about HIV/AIDS treatment, clinical trials, and medical practice guidelines for consumers and health care providers. AIDSinfo is collectively sponsored by the National Institutes of Health (NIH), Centers for Medicare and Medicaid Services (CMS), Health Resources and Services Administration (HRSA), and the Centers for Disease Control and Prevention (CDC)"--Website.
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Alcoholic liver disease STAT!Ref
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Allen brain atlas DatabaseThe Allen Brain Atlas (ABA) is a genome-wide image database of gene expression in the mouse brain. RNA in situ hybridization data, detailed Reference Atlases and analysis tools combine to provide a searchable digital atlas of gene expression. Presents a comprehensive online platform for exploration of the brain at the cellular and molecular level.
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Alvarado appendicitis score Calculator
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Alveolar-arterial gradient calculator Calculator
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Aminoglycoside clearance estimate STAT!Ref
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Anatomy hangman Palm
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Anion gap STAT!Ref
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Anion gap delta Multicalc STAT!Ref
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AntiJen database Database"AntiJen is a database of kinetic, thermodynamic and cellular properties for immune system proteins (MHCs, T cell receptors, B cell epitopes). It stores quantitative binding data for peptides binding to MHC Ligand, TCR-MHC Complexes, T Cell Epitope, TAP, B Cell Epitope molecules and immunological Protein-Protein interactions. AntiJen also includes a Peptide Library, Copy Numbers and Diffusion Coefficient data. All entries are from published experimentally determined data. The database currently holds over 24,000 entries. No data in AntiJen is from prediction experiments."
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Apache II Web version
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Apgar score STAT!Ref
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APMIS. Supplementum no. 106-, 2003-, Acad Search Prem, Full text delayed 12 monthsv. 119-, 2006- Wiley
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Maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.
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ARDS severity score Calculator, Use Internet Explorer only
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Artemis Analytical ToolA DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence and of its six-frame translation. It reads EMBL-format sequences and feature tables, and can work on sequences ranging from a few kb to entire genomes of 5 Mb or more.
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Ascites Albumin gradient STAT!Ref
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Atlas of Gene Expression in Mouse Aging Project (AGEMAP) Database (Product Information)The Atlas of Gene Expression in Mouse Aging Project ( AGEMAP ) is a database that catalogs changes in gene expression as a function of the aging process in Mus musculus.
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Available chemicals directory (ACD) Fulltext
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Axon Video Game"In this fast-paced game, you must click on protein targets to grow your neuron, connecting new brain regions. Climb through the tissue, outcompeting rival neurons to form the longest connection you can"--Website.
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Basic unit conversions STAT!Ref
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Bassett interactive, annotated Atlas of human anatomy Download software, Stanford users must down load software to view fulltextInteractive digital atlas eHuman
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Bayesian analysis model Calculator
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Bayesian statistics I multiCalc STAT!Ref
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Bayesian statistics II MultiCalc STAT!Ref
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Beginning MySQL 2005, ebrary
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Bicarbonate deficit STAT!Ref
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BiliTool Calculator
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BIND Database, Users need to register for a free accountOne of the main repositories for the storage of curated descriptions of protein interactions, molecular complexes and pathways.
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Binding interface database Database
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Binding-site estimation suite of tools Analytical ToolMetasearching sequence motif finding tool that enables easy comparison of outputs from AlignACE, BioProspector, CONSENSUS and MEME for transcription factor binding site prediction.
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BindingDB DatabaseDatabase of experimentally-determined binding affinities of protein-ligand complexes, including small molecule ligands.
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BIOBASE Knowledge Library (Formerly called Proteome)BIOBASE knowledge(R) library is a suite of databases updated weekly and focused on protein information in the published biological literature. The suite of databases focuses on mammalian species, model organisms, and human fungal pathogens in: HumanPSD - Proteome Survey DB for information on human, mouse, and rat proteins. GPCR-PD - G Protein-coupled Receptors DB for human, mouse & rat proteins, their ligands & downstream signaling molecules. YPD - Model organism S. cerevisiae. PombePD - Model organism S. pombe. WormPD - Model organism C. elegans. MycoPathPD - Human fungal pathogen DB.
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BioCyc database collection Database ListBioCyc is a collection of hundreds of Pathway/Genome Databases covering mostly prokaryotes, each of which describing the genome and metabolic pathways of a single organism. Most of these databases are computationally generated, but two are generated by an extensive curation process
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Biology Workbench Analytical ToolThe Biology WorkBench is a web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.
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BioMart FulltextBioMart is a query-oriented data management system developed jointly by the Ontario Institute for Cancer Research (OICR) and the European Bioinformatics Institute (EBI) that enables scientists to perform advanced querying of biological data sources through a single web interface. It offers access to major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase and PRIDE.
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Biomolecular interaction network database (BIND) Database, Users need to register for a free accountOne of the main repositories for the storage of curated descriptions of protein interactions, molecular complexes and pathways.
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BioPerl Analytical ToolBioPerl is a vast collection of Perl packages for performing typical analytical and management tasks for biological data
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BioProspector Analytical ToolA powerful tool for identifying DNA and protein motifs.
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BIOSIS 1926-, Thomson
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Biostatistics : Video, SUNet ID login required
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BioToolKit DatabaseA web-accessible annotated database of over 1200 online resources of interest to molecular biologists and neurobiologists.
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BioWarehouse Database SystemBioWarehouse is a relational database system for the integration of multiple bioinformatics databases. It provides a central data repository in a common representational framework within a single DB management system.
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BLAST (NCBI) NLMNucleotide or protein sequence similarity using the BLAST algorithm. BLAST compares a nucleotide sequence against the GenBank nucleotide sequence database.
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BLAST Output Visualization Tool (BOV) Analytical ToolBOV enables users to interactively visualize BLAST high-scoring segment pairs to understand matching patterns between a query and a subject sequence.
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Bleeding probability after TPA for MI Calculator
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Blood alcohol concentration estimation Calculator
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Blood oxygen content calculator Calculator
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Download Pocket PC version Pocket PC
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Body mass index (Quetelet's index) STAT!Ref
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Body surface area (Du Bois method) STAT!Ref
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Body surface area, body mass index Calculator
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Body surface area, body mass index (BMI) Calculator
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BodyMap DatabaseA repository of expression data for tissues and cell types of Homo sapiens and Mus musculus. BioMap attempts to reflect accurately the abundance of transcripts in the original source.
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Bradycardia treatment algorithm Calculator
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BrainNavigator Database, Users must registerBrainNavigator, a 3D brain interactive software tool for research in the rodent brain, combines atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science. It provides imaging for research, education and structure analysis to allow researchers to know exactly where they are when working with the rodent brain. Login is required for every user to access personalized workspace annotation, calibration, notes sharing, 3D slice configuration, saving of 3D model configurations and planning injection or electrode implants. BrainNavigator combines atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science.
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Breast cancer diagnostic algorithms Assessment of riskTo aid primary care clinicians with the work-up of breast abnormalities and to promote an understanding of the breast cancer risk assessment process.
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Breast cancer risk assessment tool Calculator
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BRENDA Univ CologneLogin Univ CologneBRENDA is the main collection of enzyme functional data available to the scientific community. It is the comprehensive enzyme database of data from primary literature sources, and includes links to literature citations, two-dimensional images, and other databases.
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BSA/BMI Calculator
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Candida genome database (CGD) Stanf UnivStores and organizes highly curated data for the yeast Candida albicans.
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Step 1. Physical Exam - Step 2. Co-existing Conditions - Step 3. Lab and Radiology Findings.
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Cardiac output STAT!Ref
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Cardiac output MultiCalc STAT!Ref
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Cardiac risk index for noncardiac surgical procedures Calculator, Use Internet Explorer only
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The Catalogue of somatic mutations In cancer (COSMIC) is a specialized database that stores data about somatic mutations related to human cancers.
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Catalyst Product DescriptionIntegrated software environment for pharmacophore modeling and three-dimensional modeling, with applications for rational drug design.
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CATH DatabaseThe Class Architecture Topology and Homologous superfamily protein structure classification (CATH) is one of the main databases providing hierarchical classification of protein domain structures. It clusters proteins at four major levels: Class(C), Architecture(A), Topology(T) and Homologous superfamily (H).
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CDTree Analytical ToolD igiFreeA system for studying the the classification of protein sequences and investigate their evolutionary relationships based on protein domains; includes a suite of analysis methods to visualize the structure of domains and align new domains against exist sequences.
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Cerius2 Product DescriptionPackage of molecular modeling and simulations programs, with applications in rational drug design and structure-based drug design.
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ChemBio3D Analytical Tool (Product Information)Molecular modeling and protein visualization software.
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Chi square analysis STAT!Ref
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CisGenome Analytical ToolAn integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
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Closing capacity STAT!Ref
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CMGM Computing resource Analytical Tool, CMGM/PMGM registration requiredThe Oligo program is likely the best tool for creating oligonucleotides ("oligos"), i.e., determining the sequence of oligos so that they can be synthesized and used in e.g., polymerase chain reaction (PCR).
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Cn3D Windows & Macintosh
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Collaborative Drug Discovery Database (Product Information)The Collaborative Drug Discovery (CDD) database is a system that enables scientists to archive, mine, and collaborate around pre-clinical chemical and biological drug discovery data using a web-based interface.
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COMBOSA3D Analytical ToolA popular DNA motif finder applicable to finding candidates for regulatory factor binding sites by searching for statistically overrepresented motifs. It enumerates all motifs in the search space and is guaranteed to produce those motifs with greatest z-scores
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Comorbidity Index and Score of Charlson et al Calculators, Use Internet Explorer only
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CompareProspector Analytical ToolGibbs sampling search tool biased to search in promoter regions that are conserved across species to identify motifs for transcription factors.
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The Comprehensive microbial resource (CMR) is a repository of data covering all microbial genomes whose genome has been sequenced to completion.
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Comprehensive unit conversions STAT!Ref
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Confidence interval of a survey STAT!Ref
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Consed Download software
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ContigExpress Analytical ToolA module of Vector NTI for generating and analyzing biomolecular sequence contigs.
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Convert celsius to fahrenheit Calculator
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Coremine DatabaseDatabase that presents search results as a graphic network that describes relationships discovered through text-mining. Relationship networks cluster important terms and act as a navigational tool. This approach is used to show relationships between a wide range of biomedical terms, including Medical Subject Heading, Gene Ontology, Pharmaceutical, Herbal medicine and Chemical as well as Gene and Protein terms.
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Coronary disease probability Calculator
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Coronary Heart Disease Risk Calculator CalculatorPredicts the risk of heart disease within 10 years. The results are applicable only for the ages of 30 to 74. Risk factors include: sex, age, smoker, diabetes, blood pressure, and cholesterol.
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Corrected CSF white count calculator Calculator
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Corrected serum Na+ Calculator
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Creatinine clearance (measured) STAT!Ref
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Creatinine clearance by mass STAT!Ref
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Crotalid snakebite severity score Calculator
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Croup score (pediatric) Calculator
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CSF IgG index STAT!Ref
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CSS mastery Lane Catalog record
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Cytoscape Analytical ToolVisualization, modeling and analysis tool for molecular and genetic interaction networks.
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A web-based suite of tools for analyzing microarray gene expression results using the annotations of a list of genes and their cognate proteins.tools for analyzing microarray data.
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Database of interacting proteins (DIP) Database, Login requiredDatabase of experimentally observed protein-protein interactions
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DataFerrett Analytical ToolA data mining and extraction tool for statistical data from US and international government agencies, including US Census and the National Center for Health Statistics.
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dbEST (NCBI) NLMdbEST (Nature Genetics 4:332-3;1993) is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or Expressed Sequence Tags, from a number of organisms.
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dbSNP database NLMA database of human genetic variation.
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DeepView Swiss-PdbViewer Windows & MacintoshPowerful biomolecular structure and analysis program that interacts with SWISS-MODEL.
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DeltaGraph Product Description
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DeltaOne Knockout database DatabaseDatabase of commercially available, highly characterized knockout mice.
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Derwent Innovations Index Inst Sci InfScope and coverage of Derwent innovations index Inst Sci Inf
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Devers OHTN to glaucoma risk calculator Web version, Users must register
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Diabetes screening TreeCalc STAT!Ref
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Diabetes type predictor TreeCalc STAT!Ref
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Diagnostic test calculator Calculator
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Dictionary of natural products DatabaseComprehensive database of natural products organised according to product chemical and physical properties.
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Digitalis body load STAT!Ref
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Discovery Studio visualizer Analytical Tool
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Compilation of data derived from the literature regarding therapeutic proteins and nucleic acids that are known drug targets.
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DrugBank DatabaseA bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
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Duke criteria for infective endocarditis Calculator
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DVT probability, Kahn score system STAT!Ref
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DVT probability, Wells score sSystem STAT!Ref
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EBI XEMBL Analytical Tool
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EBM calculator (University of Toronto) Web versionCalculates the Sensitivity, Specificity, PPV, NPV, LR+, and LR-, Relative Risk (RR), Absolute Relative Risk (ARR), Number Needed to Treat (NNT), Odds Ratio (OR), Relative Risk Reduction (RRR).
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ECR Browser DatabaseA navigation tool for visualizing pre-computed evolutionary relationships in vertebrates and non-vertebrates based on whole-genome primary sequence alignment.
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Based on the current, evidence-based recommendations of the U.S. Preventive Services Task Force (USPSTF)
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EMBOSS Analytical ToolEMBOSS is a high-quality package of free, Open Source software for molecular biology. It performs all of the classical molecular biological analytical tasks.
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Embryo Mobile Application, iPhone/iPod touch/iPad"Scientists and educators have used the Carnegie Embryo Collection, housed at the National Museum of Health and Medicine, to define normal human embryo development for decades. A database, called the Virtual Human Embryo, has been created to provide digital serial sections of human embryos from the collection. The Embryo App uses mobile telecommunication and multimedia technologies to add interactive capabilities to the digital information, enhancing our understanding of embryo development. This App is part of the National Library of Medicine's program to fulfill the NLM's role as a provider of medical, science and health care information using mobile technologies. The Eunice Kennedy Shriver National Institute of Child Health & Human Development has provided support for two components of the imaging project. Scientists at Louisiana State University Health Sciences Center has supported the 3D-reconstruction of the collection to add visual dynamics to the images"--Website.
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Endnote Product DescriptionDuck Room Version X4 (Windows)Redwood Room Version X4 (Windows)Stone Room Version X4 (Windows)Student Computing Version X4 (Windows & Macintosh)M051 Version X4 (Windows & Macintosh)
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Ensembl DatabaseEnsembl is a comprehensive database of the genomes of metazoans species ranging from primitive chordates to mammals, whose genomes have been sequenced to completion.
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Entrez (NCBI) NLMIncludes information cited in MEDLINE. GenBank, EMBL, DDBJ, SWISS-PROT, PIR, PDB, PRF, dbEST and U.S. and European patents.
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Entrez Programming utilities Analytical Tool
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EPConDB DatabaseProvides access to gene expression and sequences for genes active in mouse and human beta cells.
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Epworth sleepiness scale (ESS) STAT!Ref
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Esophageal varices STAT!Ref
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Estimated blood level calculations Calculator
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EteRNA Video Game"By playing EteRNA, you will participate in creating the first large-scale library of synthetic RNA designs. Your efforts will help reveal new principles for designing RNA-based switches and nanomachines -- new systems for seeking and eventually controlling living cells and disease-causing viruses. By interacting with thousands of players and learning from real experimental feedback, you will be pioneering a completely new way to do science. Join the global laboratory!"--Website.
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Eukaryotic promoter database (EPD) DatabaseAnnotated non-redundant collection of data on eukaryotic POL II promoters for which the transcription start site has been determined experimentally.
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European system for cardiac operative risk evaluation (EuroSCORE) Calculator, Use Internet Explorer only
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Evaluating patients for smallpox Calculator
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ExactAntigen DatabaseCurated database of commercial monoclonal antibodies.
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Expanded disability status scale Calculator
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ExPASy Proteomics server EXPASyExPASy provides integrated access to a variety of databases and analytical tools dedicated to understanding proteins.
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FirstConsult [mobile] MD Consult (Firm), Users must create a personal account in the MDConsult database using a desktop or laptop, download from the App store, click the account option, and login with their MDConsult username and password.The app includes the Medical Topics section of the Web version.
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FirstGlance Analytical ToolA simple applet-based tool for macromolecular visualization.
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Foldit Video Game"Foldit is a revolutionary new computer game enabling you to contribute to important scientific research ... With all the things proteins do to keep our bodies functioning and healthy, they can be involved in disease in many different ways. The more we know about how certain proteins fold, the better new proteins we can design to combat the disease-related proteins and cure the diseases ... We're collecting data to find out if humans' pattern-recognition and puzzle-solving abilities make them more efficient than existing computer programs at pattern-folding tasks. If this turns out to be true, we can then teach human strategies to computers and fold proteins faster than ever!"--Website.
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FoldMiner Analytical Tool
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Fractional excretion of sodium Calculator
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Fractional excretion of sodium STAT!Ref
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FRACTURE, Osteoporosis prediction tools Calculator
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Free water deficit Calculator
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Functional residual capacity STAT!Ref
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Galaxy DatabaseGalaxy combines genome annotation databases with a set of highly-integrated analytical tools to enable users to easily search remote resources, combine data from independent queries and analyses, and visualize the results.
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Gene expression atlas DatabaseA repository of microarray gene expression measurements maintained by the Genomics Institute of the Novartis Research Foundation . The atlas is aimed at profiling gene expression in a large number of tissues from Mus musculus and Homo sapiens .
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A gene expression and hybridization array data repository, as well as a curated, online resource for gene expression data browsing, query and retrieval.
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Gene ontology DatabaseThe Gene Ontology project provides a set of controlled vocabularies to describe gene and gene product attributes in any organism.
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Gene ontology Video
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Gene ontology term finder (SGD) Stanf UnivAnalyzes a list of gene IDs provided by e.g. gene expression data to find GO terms (or their parents) that occur at unexpectedly high frequency to identify commonalities between genes.
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GeneCards Weizmann InstituteStanford mirror site Weizmann Institute
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GeneCruiser Database
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GeneSifter Analytical ToolOverview SUNet ID login and CMGM/PMGM computer account are required for web usage of this softwareWeb-based gene expression microarray analysis environment.
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GeneSpring Analytical Tool, SUNet ID login and CMGM/PMGM computer account are required to download the softwareA microarray expression data analysis tool sold by Agilent, and something of a standard for such tasks.
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Genetics computer group Analytical ToolHelp Page Login requiredThe package is a vast collection of high-quality biological analysis tools and databases
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GENEVAR DatabaseProvides a microarray-based genome-wide gene expression measurements in the HapMap samples.
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GenMAPP, gene map annotator and pathway profile Analytical Tool
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GEO NCBIA gene expression and hybridization array data repository, as well as a curated, online resource for gene expression data browsing, query and retrieval.
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Geriatric depression scale STAT!Ref
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Geriatric functional rating scale (GFRS) Calculator, Use Internet Explorer only
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GFR calculator (with SI units) Calculator
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Gibbs Motif sampler Analytical ToolA powerful, well-documented DNA and protein motif finder program.
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GibbsILR Analytical ToolA DNA motif finder that is optimized for the identification of relatively weak motifs.
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Glasgow Coma Scale NCEMI
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Glasgow Coma Scale (MedCalc3000) STAT!Ref
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Glaucoma 5-year risk estimator Calculator
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Glaucoma risk calculator Web version, Users must register
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GoMiner Analytical ToolTool for biological interpretation of 'omic' data; can process large gene or protein lists.
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Google Chart Analytical ToolFree, simple charting service provided by Google. Suitable for charting simple to moderately complex biomedical data types. Large number of chart types and options.
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Google Chrome Product DescriptionDuck Room Version 23- (Windows)Redwood Room Version 23- (Windows)Stone Room Version 23- (Windows)M051 Version 23- (Windows & Macintosh)Student Computing Version 23- (Windows & Macintosh)
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GoPubMed Database
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Gorlin formula for valve area STAT!Ref
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GPCRDB : DatabaseGPCRDB stores curated sequences, mutation and ligand binding data for G-coupled protein receptors (GPCRs).
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GraphPad StatMate Analytical Tool (Product Information)StatMate is an expensive, easy to use tool for estimating the statistical power of an experiment necessary to detect various hypothetical differences.
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GREAT Analytical ToolA tool for analyzing the functional significance of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Incorporates both proximal and distal binding sites. Incorporates annotations from 20 ontologies.
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GT database DatabaseGTDB and its associated Glycosylation Pathways pages provide a graphical interface for navigating the universe of enzymes involved in glycosylation.
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Health hotlines Mobile Application, iPhone/iPod touch/iPadFulltext (1988) Google BooksFulltext (1992) Google BooksFulltext (1995) Google BooksFulltext (1998) Google Books
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Henderson-Hasselbach equation STAT!Ref
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Hepatitis C virus database (HCV db) DatabaseCentralized repository and clearinghouse of data and tools pertaining to all aspects of the hepatitis C virus: viral subtypes, genomes, sequence alignment tools, ortholog comparisons.
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HGNC Search DatabaseDatabase created by the HGNC under the auspices of HUGO charged with giving unique and meaningful names to every human gene.
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HiMAP, human interactome map Database
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HomoloGene NLM
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Homologous vertebrate genes database DatabaseIdentifies homologous genes in vertebrate using an automated procedure. .
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HOVERGEN DatabaseIdentifies homologous genes in vertebrate using an automated procedure. .
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HPtaa database DatabaseDatabase of computationally predicted potential tumor associated antigenes based upon expression data from multiple sources.
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This site contains the reference sequence for the human and C. elegans genomes.
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Human protein reference database Database
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Hypernatremia treatment algorithm Calculator
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Hyponatremia & hypernatremia Calculator
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Hyponatremia treatment algorithm Calculator
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IARC TP53 mutation database DatabaseCompilation of all TP53 gene mutations identified in human cancers and cell lines that have been reported in the peer-reviewed literature since 1989, including somatic and germline mutations.
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Ideal body weight STAT!Ref
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Ideal body weight percentage STAT!Ref
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iHOP : DatabaseiHOP uses a combination of natural language parsing and gene identifiers to navigate the biomedical literature, thus providing a rapid overview of gene properties.
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Image J Analytical ToolA free multi-platform scientific image analysis and processing program written in Java.
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ImMunoGeneTics (IMGT) Database
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Inches to centimeters conversion calculator Calculator
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Influenza sequence database Database
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Ingenuity pathways analysis Analytical Tool, SUNet ID login and registration requiredIngenuity pathways analysis, IPA, provides information on gene expression and protein-protein interactions within the context of metabolic or signaling pathways.
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InsightII CMGM Unix Software, SUNet ID login and CMGM/PMGM computer account are required to download the softwareSophisticated molecular modeling environment with a powerful graphical interface to algorithms for molecular dynamics, homology modeling, de novo design, and electrostatics. Relevant to protein modelers, computational chemists, and structural biologists.
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Inspiratory capacity STAT!Ref
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InStat Stanf Univ, SUNet ID login and CMGM/PMGM computer account are required to download the softwareA statistical analysis program that is both simple and decently powerful.
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Interactive growth charts Calculator
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Interferon stimulated gene database DatabaseDatabase of genes that are stimulated by interferon, arranged according to gene function or disease association categories.
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InterPro DatabaseA database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
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InterProScan Analytical ToolQuerying tool for searching the InterPro database of protein domains and motifs.
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Focus is on undertaking design and implementation of computational and information systems for life scientists and healthcare providers. Case studies illustrate what design factors lead to success or failure in building systems in complex biomedical environments.
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Introduction to R Video, SUNet ID login requiredR is a computer language and environment for statistical computing and graphics. It is widely used in biostatistics, including microarray and proteomics data analysis.
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IV infusion rate Calculator
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Java Product DescriptionDuck Room Version 7, Update 9 (Windows)Redwood Room Version 7, Update 9 (Windows)Stone Room Version 7, Update 9 (Windows)Student Computing Version 7, Updated 9 (Windows & Macintosh)M051 Version 7, Updated 9 (Windows & Macintosh)
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Java developer's guide to Eclipse Lane Catalog record
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JMP statistical discovery software Product DescriptionDuck Room, Duck-PC1,2,3,5,6,7,8,10, only. Version 9 (Windows)Redwood Room, Redwood-PC2,3,4,5,6,7,8,9, only. Version 9 (Windows)M051 (only on certain computers) Version 9 (Windows & Macintosh)
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Journler. <Current version> 2006-, Macintosh OS onlyJournler is a software-based notebook information manager usable as an electronic laboratory notebook, among other applications. Macintosh only.
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Kawasaki disease diagnostic criteria STAT!Ref
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KChannelDB : Database
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Kinemage Analytical ToolKinemages are ""kinetic protein images"" that accompany many of the articles published in Protein Science. Kinemages are generated by the program MAGE from PDB files that have been processed using the program PREKIN.
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Database of experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligand binding or reaction events described in the literature.
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Kodak Molecular Imaging Software Analytical Tool, SUNet ID login and CMGM/PMGM computer account are required to download the softwareGeneral purpose image analysis software for gels and Southern/Northern/Western blots.
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Kt/V Dialysis dose Barth formula STAT!Ref
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Kt/V Dialysis dose Basile formula STAT!Ref
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Kt/V Dialysis dose Daugirdas formula STAT!Ref
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Kt/V Dialysis dose Jindal formula STAT!Ref
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Kt/V Dialysis dose Kerr formula STAT!Ref
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Kt/V Dialysis dose Keshaviah formula STAT!Ref
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Kt/V Dialysis dose Lowrie formula STAT!Ref
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The KEGG database is designed to facilitate understanding of higher-order protein and cellular functions (e.g., metabolic networks) using genomic and molecular information.
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LabVelocity LabVelocity
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LAGAN Alignment toolkit website Analytical Tool
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LDL cholesterol goal calculator Calculator
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Lexi-CALC online Calculator
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Likelihood ratio MultiCalc STAT!Ref
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LOCATE DatabaseA curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence set.
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LOCK 2 Analytical Tool
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Low density lipoprotein STAT!Ref
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Lung injury score Calculator, Use Internet Explorer only
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Lung volume Multicalc STAT!Ref
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M.I. prediction decision TreeCalc STAT!Ref
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Mainz emergency evaluation score (MEES) Calculator, Use Internet Explorer only
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Malaria parasite metabolic pathways DatabaseA compilation of Plasmodium metabolic pathway maps culled from general biochemistry sites.
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Mangled extremity severity score Calculator
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MatchMiner DatabaseA tool for determining what are the properties associated with an identifier used in genome or transcriptome studies, such as a Gene ID, UniGene cluster or IMAGE clone ID.
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Math calculator STAT!Ref
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MatInspector Web version, Login required
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MATLAB Bioinformatics toolbox. <current version> Product InformationProvides access to genomic and proteomic data formats, analysis techniques, and specialized visualizations for genomic and proteomic sequence and microarray analysis
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MATLAB Statistics toolbox. <current version> Product InformationIncludes functions and interactive tools for analyzing historical data, modeling data, simulating systems, developing statistical algorithms, and learning and teaching statistics.
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MATLAB. Version 2011b. Product DescriptionDuck Room Version R2011b (Windows)Redwood Room Version R2011b (Windows)Stone Room Version R2011b (Windows)Student Computing Version R2011b (Windows & Macintosh)M051 Version R2011b (Windows & Macintosh)
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MDCalc Database
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MDscan Analytical ToolIdentifies protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.
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Mean corpuscular hemoglobin STAT!Ref
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Mean corpuscular volume STAT!Ref
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Medical calculator (iPhone and iPod) Mobile Application, iPhone/iPod touch
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MedMath Palm
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Melanoma risk assessment tool CalculatorThe Melanoma Risk Assessment Tool is an interactive Web-based system designed by scientists at the National Cancer Institute (NCI), the University of Pennsylvania, and the University of California, San Francisco, to estimate a person's absolute risk of developing invasive melanoma.
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MEME Analytical Tool
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Metamorph Analytical Tool, SUNet ID login and CMGM/PMGM computer account are required to download the softwareGeneral purpose image analysis of microscopy images
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MeV Analytical ToolMicroarray data analysis tool for integrated analysis using clustering, visualization, classification, statistical analysis and biological theme discovery.
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Micromedex Drug Information Mobile Application, iPhone/iPod touch/iPadThe app contains the Micromedex DRUGPoints information, the Summary Drug Information, as it is called in Micromedex 1.0. It is completely loaded on the device. Over 1,400 drug monographs on FDA-approved drugs are accessible by generic drug name (includes selected combination products), trade name and therapeutic class.Also includes: black box warnings, adult dosage, pediatric dosage, dose adjustments, indications (differentiated as “FDA labeled” and “non-FDA labeled”), administration, monitoring, how supplied, contraindications, precautions, adverse effects (separated into “common” and “serious”), drug interactions, pregnancy category, breast feeding, mechanism of action, pharmacokinetics, and toxicology.
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Micromedex Drug Interactions Mobile Application, iPhone/iPod touch/iPad"With Drug Interactions, clinicians can check a patient entire medication list simultaneously for potentially harmful interactions and view severity ratings that range from contraindicated to minor. This app provides insight into: Why the drugs in question interact, how the results of those interactions will present in the patient, recommendations for monitoring patient outcomes"--Website.
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Microsoft Access Product DescriptionDuck Room Version 2007 (Windows)Redwood Room Version 2007 (Windows)Stone Room Version 2007 (Windows)Student Computing Version 2007 (Windows & Macintosh)M051 Version 2007 (Windows & Macintosh)
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Microsoft Excel Product DescriptionDuck Room Version 2007 (Windows)Redwood Room Version 2007 (Windows)Stone Room Version 2007 (Windows)Student Computing Version 2007 (Windows & Macintosh)M051 Version 2007 (Windows & Macintosh)
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Microsoft Internet Explorer Product DescriptionDuck Room Version 9- (Windows)Redwood Room Version 9- (Windows)Stone Room Version 9- (Windows)Student Computing Version 9- (Windows & Macintosh)Public Kiosks Version 9- (Windows & Macintosh)M051 Version 9- (Windows & Macintosh)
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Microsoft PowerPoint Product DescriptionDuck Room Version 2007 (Windows)Redwood Room Version 2007 (Windows)Stone Room Version 2007 (Windows)Student Computing Version 2007 (Windows & Macintosh)M051 Version 2007 (Windows & Macintosh)
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Microsoft Word Product DescriptionDuck Room Version 2007 (Windows)Redwood Room Version 2007 (Windows)Stone Room Version 2007 (Windows)Student Computing Version 2007 (Windows & Macintosh)M051 Version 2007 (Windows & Macintosh)
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miRBase sequences DatabaseRepository of miRNA sequences and annotations
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miRNAMap DatabaseAn integrated database that stores known miRNA genes, putative miRNA genes, known miRNA targets and putative miRNA targets.
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MMDB DatabaseMMDB is NCBI's database of biomolecular structures, integrated within Entrez.
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Mozilla Firefox Product DescriptionDuck Room Version 16.0.2- (Windows)Redwood Room Version 16.0.2- (Windows)Stone Room Version 16.0.2- (Windows)Student Computing Version 16.0.2- (Windows & Macintosh)M051 Version 16.0.2- (Windows & Macintosh)
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MPromDb DatabaseDatabase of gene promoters combined with experimentally supported annotation of transcription start sites (TSS), cis-regulatory elements, CpG islands and ChIP-chip experimental for mouse, rat and human. Results are provided using intuitive visualizations.
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Multiple Em for Motif Elicitation (MEME) Analytical Tool
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Multiple myeloma diagnostic criteria STAT!Ref
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MutDB DatabaseMutDB is a gene-centric integration of human variation data with protein structural information and other functionally relevant information, if available.
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Myocardial infarction probability (Goldman) Calculator
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NAR Database collection Database List
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Narcotic equivalence converter Calculator
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Narcotic medication dose conversion STAT!Ref
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National brain databank Database, Login requiredPublicly accessible data repository that provides neuroscience investigators with secure access to cohort collections such as the McLean 66. The databank collects and disseminates gene xpression data from microarray experiments on brain tissue samples, along with diagnostic results from postmortem studies of neurological and psychiatric disorders.
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NCBI Database directory Analytical Tool
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NCBI field guide Video (pt. 1)MP4 podcast of NCBI Field Guide Workshop held at Mission Bay May 3rd and 4th 2007.
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NCBI Gene NCBIIntegrates information from LocusLink and from genes annotated on Reference Sequences from completely sequenced genomes.
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NCBI Genome Database
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NCBI Probe Database
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NCBI Site map Analytical Tool
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NCBI structure DatabaseMMDB is NCBI's database of biomolecular structures, integrated within Entrez.
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NCI Terminology browser Database
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Negative predictive value of a test STAT!Ref
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NIH Image MacintoshPublic domain scientific image processing and analysis program for the Macintosh. It can acquire, display, edit, enhance, analyze and animate images.
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NIH Stroke scale Calculator
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Normal range for body weight STAT!Ref
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NucleaRDB : DatabaseNucleaRDB stores curated sequences, mutation and ligand binding data for nuclear receptors.
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Nutricalc, [infant] nutrition calculator Calculator
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NVivo Product DescriptionRedwood Room (PC-8, only) Version 9.2 (Windows)
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Odds from probability STAT!Ref
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Odds ratio and relative risk STAT!Ref
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Oligo Analytical Tool, CMGM/PMGM registration requiredThe Oligo program is likely the best tool for creating oligonucleotides ("oligos"), i.e., determining the sequence of oligos so that they can be synthesized and used in e.g., polymerase chain reaction (PCR).
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Oncomine research edition DatabaseA repository of transcriptome profiles used for data-mining and visualization for biomarker and therapeutic target discovery and evaluation.
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Online Mendelian inheritance in man DatabaseA catalog of essays reviewing human genetic traits that follow classical Mendelian inheritance patterns. Whenever available information permits, each entry consists of six parts: (1) a preferred designation, and frequently used synonyms, (2) a brief description of the phenotype(s), (3) the nature of the basic defect, (4) a résumé of pertinent genetic information including mapping and molecular genetic details, (5) an exhaustive list and description of known allelic variants, and (6) key references. An attempt has been made to select references that are up to date and/or particularly useful discussions of the genetics involved. The catalog provides a bibliographic guide. OMIM is a full text database searchable by the IRX (tm) software developed by the National Library of Medicine. Access to the database is provided as a service to biomedical professionals by the Johns Hopkins University School of Medicine under the sponsorship of the National Institutes of Health and the Department of Energy.A database that features catalogs of autosomal dominant, autosomal recessive, x-linked, y-linked, and mitochondrial phenotypes. Includes information on human genes and genetic disorders.
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Open REGulatory ANNOtation database (ORegAnno) Database, Login requiredThe ORegAnno database stores curated data derived from scientific literature for known gene regulatory elements.
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Opioid medication dose conversions STAT!Ref
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Oracle SQL developer WebsiteFree, Multi-platform (Win/Mac/UNIX/Linux) graphical tool for database development, supported by Oracle Corp. Suitable for Oracle, Sybase, MySQL and many other relational database managers.
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ORegAnno Database, Login requiredThe ORegAnno database stores curated data derived from scientific literature for known gene regulatory elements.
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Osmolality Estimator (serum) STAT!Ref
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Osmolar clearance STAT!Ref
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Oswestry low back pain disability questionnaire Calculator, Use Internet Explorer only
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Ottawa ankle rules Calculator
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Ottawa knee rules Calculator
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Oxygenation index Calculator
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Oxygenation index (OI) STAT!Ref
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Paediatric coma scale (Simpson & Reilly) Calculator
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Pajek WebsiteNetwork analysis software, suitable for studying networks composed of widely different components: people, molecules, etc.
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Pancreatitis prognosis criteria STAT!Ref
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PantherDB Database
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Papers, your personal library of science 2006-, Macintosh OS onlyPapers is personal literature manager that enables you to search, download, archive, and organize all your articles, including PDFs, within a single application. Macintosh only.
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Partek Genomics suite Analytical Tool, SUNet ID login and CMGM/PMGM computer account are required for web usage of this software"Comprehensive suite of statistics and interactive data visualization designed to reliably extract biological signals from noisy data; can be applied to a variety of genomic data sets, such as gene expression data, exon data, copy number data, mapping data, tiling data, and SNP data. "
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Pathway builder Analytical ToolA quick and easy tool for drawing signal transduction pathways. Contains pre-made pathway templates and illustration items, as well as all pathway items such as membranes, protein/receptor shapes, organelles, etc. have been pre-made.
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PathwayStudio Analytical Tool, Login requiredAnalysis software intended to facilitate the interpretation of experimental results in the context of pathways, gene regulation networks and protein interaction maps.
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PDB DatabasePDB is the primary repository of biomolecular structures. It is cross-referenced with many of the major public Life Sciences databases (e.g., OMIM, GO, and several others).
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Peak expiratory flow calculator Calculator
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Peak expiratory flow prediction STAT!Ref
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Pediatric dosing calculator Calculator
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Pediatric fluids and electrolyte therapy Calculator
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Pediatric trauma score Calculator, Use Internet Explorer only
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Penetrating abdominal trauma index Calculator, Use Internet Explorer only
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Perl Analytical Tool
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PharmGKB Stanf UnivLogin Stanf UnivPharmGKB is an integrated resource about how variation in human genes leads to variation in our response to drugs.
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PhenomicDB DatabasePhenomicDB merges public genotype/phenotype data from a wide range of model-organisms and Homo sapiens. It is unique in enabling ontological querying, i.e., querying using conceptsrather than key words. Stated another way, PhenomcDB is an integrated meta search-engine for phenotypes.
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Phrap Download softwareA Linux/UNIX program for assembling shotgun DNA sequence data.
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Phred Download softwarePhred is Linux/UNIX software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.
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Phylogenetic analysis Video
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PhysioNet WebsiteAn on-line forum for dissemination and exchange of recorded biomedical signals and open-source software for analyzing them, by providing facilities for cooperative analysis of data and evaluation of proposed new algorithms.
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PICU PalmA calculator for pediatric ICU. It calculates defibrillation, vasoactive infusions, reanimation and intubation drugs by simply entering the weight of the patient.
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PIM (Pediatric Index of Mortality) Calculator
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Pittsburgh knee rule Calculator
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PlasmoDB Database, Login requiredProvides genomic and proteomic data for different species of the parasitic eukaryote Plasmodium, as well as its own analytical functions.
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Pneumonia severity index calculator Web versionDownload PDA version PalmDownload PDA version Pocket PC
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Pneumothorax degree of collapse STAT!Ref
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Pocket Pearls Palm
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PolyPhred Download softwareA Linux/UNIX program that compares fluorescence-based sequences across traces obtained from e.g. different individuals to identify heterozygous sites for single nucleotide substitutions.
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Positive predictive value of a test STAT!Ref
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Predicting strep pharyngitis Calculator
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PredictProtein server Analytical Tool
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Pregnancy calculator Calculator
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PrionDB : Database
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PRISM (Pediatric Risk of Mortality) score Calculator
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Probability from odds STAT!Ref
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Probability of acute bacterial sinusitis Calculator
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Probability of pulmonary embolism Calculator
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Progenesis Analytical Tool, SUNet ID login and CMGM/PMGM computer account are required to download the softwareImage analysis software for proteomics research, including 2D electrophoresis, DIGE, LC-MS and biomarker screening.
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ProPhylER DatabaseProPhylER is a tool that quantifies evolutionary constraints to annotate functionally or structurally important regions of proteins. It can be used to predict the impact of coding polymorphisms.
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Prostatism symptom score STAT!Ref
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Protein bound calcium STAT!Ref
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Protein data bank DatabasePDB is the primary repository of biomolecular structures. It is cross-referenced with many of the major public Life Sciences databases (e.g., OMIM, GO, and several others).
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PRoteomics IDEntifications database DatabaseThe PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data. It has been developed to provide the proteomics community with a public repository for protein and peptide identifications together with the evidence supporting these identifications.
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PubGene DatabaseDatabase that provides gene-to-term or gene-to-compound associations.
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Pubmed (PubSearch) Mobile Application, iPhone/iPod touch/iPadPubSearch is a search tool for scientists, medical professionals and students to access the millions of research papers indexed in PubMed. Combines a simple user interface with fast access to the PubMed database.
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PubMed for handhelds Mobile WebsiteStandard PubMed version provides mobile access to the PubMed database to do PICO searches, search Medline/PubMed, read journal abstracts, read fulltext of subscribed materials, and search case reports for disease associations.Pubmed Mobile Beta interface optimized for Mobile devices introduced March 2011.
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PubMed Mobile Mobile WebsiteProvides a simplified mobile friendly Web interface to access PubMed. PubMed Mobile includes the same basic search functionality and content as Standard PubMed.
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PubSearch Mobile Application, iPhone/iPod touch/iPadPubSearch is a search tool for scientists, medical professionals and students to access the millions of research papers indexed in PubMed. Combines a simple user interface with fast access to the PubMed database.
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Pulmonary embolism Wells score STAT!Ref
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Pulmonary vascular resistance STAT!Ref
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PyMol Analytical ToolMolecular structure viewer for representing compounds and macromolecular structures in three dimensions.
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QT interval correction (EKG) STAT!Ref
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QuickTime player Product DescriptionDuck Room Version 7 (Windows)Redwood Room Version 7 (Windows)Stone Room Version 7 (Windows)M051 Version 7 (Windows & Macintosh)Student Computing Version 7 (Windows & Macintosh)
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QUOSA software demo Video
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R commander (Rcmdr) Analytical Tool (Product Description)"Basic-statistics graphical user interface (GUI) for R, a free interactive programming language and environment"--Website.
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R for Windows Product DescriptionDuck Room Version 2.15 (Windows)Redwood Room Version 2.15 (Windows)For statistical computing.
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Mobile Application iPhone/iPod touch/iPadProvides medical information that can be used quickly and efficiently to orient and guide health care providers without formal expertise in radiation safety or radiation medicine during a mass casualty radiation event. Critical information on the Web site is also downloadable for use when Internet connectivity may not be available.
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Random.org Trinity Coll (Ireland)This site is a web interface to the true random numbers.
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Rankin Scale for stroke disability Calculator, Use Internet Explorer only
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Ranson's Prognostic factors in acute pancreatitis Calculator, Use Internet Explorer only
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Rapid disability rating scale Calculator, Use Internet Explorer only
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RapidMiner DatabaseRapidMiner Community Edition is a powerful yet reasonably easy to use, Java-based data mining and visualization environment. It is suitable for the analysis of data derived from biological data types.
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Rash diagnosis algorithm Calculator
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RasMol Analytical Tool
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Rat genome database DatabaseRGD is the principal genome database for the rat model organism. It stores genetic and genomic data for all strains of the genus Rattus.
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Reactome Video
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RefWorks : ProQuest, Users must registerA Web-based bibliographic management tool, used to create personal databases of bibliographic citations by importing the citations from text files or online databases. Citations may be automatically formatted for bibliography and footnotes and may be searched within the personal database.
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Renal failure index STAT!Ref
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Provides visualization and analysis capabilities for proteomics data deposited by NIAID's Biodefense Proteomics Resource Center Research Centers (PRCs) for organisms such as Bacillus anthracis, Brucella abortus, Cryptosporidium parvum, Francisella tularensis, Monkeypox, SARS-CoV, Salmonella typhimurium, Toxoplasma gondii, Vaccinia, Vibrio cholerae and Yersinia pestis.
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Reticulocyte production index STAT!Ref
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Reynolds Risk score Calculator
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Risk Assessment Profile (RAP) of Greenfield et al for venous thromboembolism in adult trauma patients Calculator, Use Internet Explorer only
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Risk score for anticoagulant-related major bleeding in hospitalized patients Calculator, Use Internet Explorer only
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Rseek DatabaseSearch engine specializing in finding information about the R statistical analysis language.
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RTPrimerDB DatabaseRTPrimerDB stores validated primers for real-time PCR and associated probe sequences.
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Saccharomyces genome database Stanf UnivA scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
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SAS Product DescriptionDuck Room, Duck-PC1,5,7,8,10 Version 9.3 (Windows)Redwood Room, Redwood-PC2,3,4,5,6,7,8,9, Version 9.3 (Windows)M051-Lounge-win7-pc1 Version 9.3 (Windows & Macintosh)
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SAS Enterprise Guide Product DescriptionDuck Room, Duck-PC1,5,7,8,10 Version 4.3 (Windows)Redwood Room, Redwood-PC2,3,4,5,6,7,8,9 Version 4.3 (Windows)M051 (only on certain computers) Version 4.3 (Windows & Macintosh)
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SciFinder Web version Research Tool, Users must registerProvides access to several Chemical Abstracts Service databases.
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Aims to provide a detailed and comprehensive description of the relationships of known protein structures. It provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
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Scopus alerts (lite) Mobile Application, iPhone/iPod touch/iPad'Lite' version of Scopus Alerts for existing subscribers. Use the Scopus Alerts mobile app to find articles, create alerts, make notes, and share links instantly.
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Screening for adolescent substance abuse using the CRAFFT questionnaire Calculator, Use Internet Explorer only
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Scriptome Analytical ToolScriptome is a set of tools that filter, format, and merge data in tabular or common biological formats. Use single tools to take a quick look at data, or string tools together in a protocol to explore the data more deeply. The Scriptome was designed especially for non-programmers or beginning programmers, although more experienced programmers may find the site useful as a data manipulation "cookbook". The tools can be used without understanding them. Alternatively, you might find that reading and playing with small, working code examples - and using them on your own data - is a good way to learn Perl.
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Sensitivity of a test STAT!Ref
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Septris Video Game, Runs best on iPad/iPhone or Android. On desktop, requires Google Chrome, Apple Safari, or Firefox. Internet Explorer is not supported.Septris is an online game, "This activity provides a practical approach to early sepsis identification and application of evidence-based management (best practice) and Stanford's Sepsis Guidelines. Interactive case scenarios will be used to put these principles into practice"--Website.
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Sequencher Analytical Tool, SUNet ID login and CMGM/PMGM computer account are required to download the softwareSequencher program is one of the best tools for assembling fragmentary DNA sequences to form longer, continuous sequences, as well as other DNA sequence-related tasks.
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Serum osmolality Calculator
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SI unit conversions. Drugs STAT!Ref
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SI unit conversions. Hematology STAT!Ref
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SigmaPlot Product Description
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Significance Analysis of Microarrays (SAM). Version 3.X. Analytical Tool, Registration requiredA leading significance analysis tool for microarray gene expression measurements.
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Sodium correction in hyperglycemia STAT!Ref
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Sodium deficit in hyponatremia STAT!Ref
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Sophos Antivirus Product DescriptionDuck Room Version 10.0.9 (Windows)Redwood Room Version 10.0.9 (Windows)Stone Room Version 10.0.9 (Windows)M051 Version 10.0.9 (Windows & Macintosh)Student Computing Version 10.0.9 (Windows & Macintosh)
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SOURCE Stanf Univ SOMCollects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports.Provides a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. It is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches.
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Spotfire DecisionSite client Analytical ToolA visualization tool with a easy user interface and data connectivity.
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SPSS Product DescriptionDuck Room Version 20 (Windows)Redwood Room Version 20 (Windows)Stone Room Version 20 (Windows)Student Computing Version 20 (Windows & Macintosh)M051 Version 20 (Windows & Macintosh)Program that allows the user to do statistical analysis.
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Stage III pressure ulcer TreeCalc STAT!Ref
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Stage IV pressure ulcer TreeCalc STAT!Ref
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Stanford Desktop Tool (SDT) Product DescriptionDuck Room Version 3.1.4 (Windows)Redwood Room Version 3.1.4 (Windows)Stone Room Version 3.1.4 (Windows)M051 Version 3.1.4 (Windows & Macintosh)Student Computing Version 3.1.4 (Windows & Macintosh)
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Stanford Microarray Database (SMD) Stanf UnivSMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization. Data is released to the public at the researcher's discretion or upon publication.
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Stanford Tissue microarray database Stanf UnivTMAD is database of raw and processed data from tissue microarray experiments. It can be searched for stained tissue images using markers, disorders and other controlled terms. TMAD also provides methods for data retrieval, grouping of data, analysis and visualization as well as export to standard formats.
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Stats calculator (University of Toronto) Web versionCalculates the Sensitivity, Specificity, PPV, NPV, LR+, and LR-, Relative Risk (RR), Absolute Relative Risk (ARR), Number Needed to Treat (NNT), Odds Ratio (OR), Relative Risk Reduction (RRR).
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StepMiner Analytical ToolTemporal microarray gene expression analysis software.
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Steroid equivalence converter Calculator
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Stool osmolal gap STAT!Ref
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Strep pharyngitis probability score Calculator
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STRING stores known and predicted protein-protein interactions where the interactions are either direct (physical) or indirect (functional) associations.
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structureViz Analytical ToolUCSF structureViz is a Cytoscape plugin that links the visualization of biological networks (and biological relationships expressed as networks) provided by Cytoscape with the visualization and analysis of macromolecular structures and sequences provided by UCSF Chimera.
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Integrated collections of programs for identifying novel cis-regulatory elements from groups of upstream sequences.
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Survey sample size STAT!Ref
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Swami Analytical ToolA free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics, conceptually based on the Biology Workbench.
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SymAtlas DatabaseA repository of microarray gene expression measurements maintained by the Genomics Institute of the Novartis Research Foundation . The atlas is aimed at profiling gene expression in a large number of tissues from Mus musculus and Homo sapiens .
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Symyx ELN Analytical Tool (Product Information)Electronic laboratory notebook suitable for biological and chemical research. Windows only.
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SYSTAT Product DescriptionStudent Computing Version 12 (Windows & Macintosh)M051 Version 12 (Windows & Macintosh)Duck Room Version 12 (Windows)Redwood Room Version 12 (Windows)Stone Room Version 12 (Windows)Program that allows the user to calculate statistics, generate data reports and produce graphics.
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Systemic vascular resistance STAT!Ref
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Telemakus Analytical ToolAn information management and knowledge discovery tool for scientific information that searches both within and across documents to facilitate research.
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TELis DatabaseProvides databases and tools for identifying transcription factors and their cognate DNA motif that are over-represented in a gene expression dataset.
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Ten year CVD risk calculator CalculatorThis risk assessment tool uses information from the Framingham Heart Study to predict a person's chance of having a heart attack in the next 10 years. This tool is designed for adults aged 20 and older who do not have heart disease or diabetes. The calculation is based on age, gender, total and HDL cholesterol, smoker status, systolic blood pressure, and whether current medications are involved.
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Tetrahymena genome database (TGD) Stanf UnivMain repository of genomic data from Tetrahymena thermophila.
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ThreeD Domains NCBI
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TIMI risk score Calculator (for STEMI)TIMI Risk score for STEMI -- TIMI Risk score for UA/NSTEMI.
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Total body water/urea volume of distribution Calculator
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Total lung capacity STAT!Ref
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TranscriptDetector Analytical Tool, Login requiredA tool for finding probes measuring significantly expressed loci in a genomic tiling microarray experiment.
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Database of promoter elements focused on integrating cis- and trans- regulatory elements in mammals. Compilation is created by extracting known promoters from Genbank, EPD and DBTSS, and predicting additional promoters using FirstEF combined with mRNA/EST information and cross-species comparisons.
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TRANSFAC Professional versionDescribing eukaryotic cis-acting egulatory DNA elements and their trans-acting factors, ranging from yeast to Homo sapiens. Position-specific matrices are also provided.
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Transferrin saturation STAT!Ref
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Trauma score for survival probability Calculator
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Tree families database DatabaseDatabase of phylogenetic trees of animal genes and their orthologs.
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UBC Bayesian calculator Calculator
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UCLA Pain assessment tools Calculator
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UCLA-DOE Fold server Analytical ToolImplements algorithms designed to identify the structural fold of a protein using its primary structure as input.
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UMLS semantic network Database
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UniProt Database (unitprot.org)Database EMBL-EBIUniversal Protein Resource ("UniProt") is the largest provider of data on the proteome of organisms. The data are based on submissions to the DNA sequence databases, as well as varying levels of curation. It is the good way to quickly assess a vast set of protein properties, particularly for species that are not model organisms.
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This site contains the reference sequence for the human and C. elegans genomes.
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UNOS MELD score in liver disease STAT!Ref
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Unstable angina risk stratification STAT!Ref
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Vancomycin & aminoglycoside pharmacokinetics Calculator
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VBASE DatabaseA database of manually curated human immunoglobulin variable (V) sequences derived from the literature.
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VBASE2 DatabaseA database of germ-line immunoglobulin variable (V) sequences automatically extracted from Ensembl's mouse and Homo sapiens genomic databases.
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Vector NTI suite Analytical Tool, SUNet ID login and CMGM/PMGM computer account are required to download the softwareVector NTI is a high-powered yet reasonably easy to use tool for creating cloning vectors.
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Ventilation index [calculator] Calculator
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Very low density lipoprotein (VLDL) STAT!Ref
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VISTA Analytical ToolSuite of programs and databases for comparative analysis of large genomic sequences, including for comparative genomics.
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Vital capacity STAT!Ref
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Volocity Analytical Tool, SUNet ID login and CMGM/PMGM computer account are required to download the software3D imaging and reconstruction image analysis software for Life Science research; provides suite of tools for 3D image acquisition, volume visualization, restoration, publication, and object measurement, tracking and charting; Mac and Windows OS.
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Volume of distribution of urea STAT!Ref
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Warfarin dosing TreeCalc STAT!Ref
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Water deficit in hypernatremia STAT!Ref
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WebFEATURE DatabaseStructural analysis tool for scanning structures for functional sites in both proteins and nucleic acids.
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Weights & measures Calculator
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WHAT IF SoftwareVersatile biomolecular modeling package for working with proteins and the molecules in their environment such as water, ligands and nucleic acids.
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Winter's Formula for expected PCO2 STAT!Ref
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Wise2 Analytical ToolAlgorithm for aligning a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
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Mobile Application iPhone/iPod touch/iPad
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WormBase DatabaseThe principal database for the C. elegans model organism. It stores genetic, genomic and phenotypic data for all strains of C. elegans.
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Yep Product Description, Mac onlySoftware program for organizing PDF documents. Also helps you find all the pdfs on your computer: Can search, add tags, rename, move, and delete within the application.
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YMF Analytical ToolA popular DNA motif finder applicable to finding candidates for regulatory factor binding sites by searching for statistically overrepresented motifs. It enumerates all motifs in the search space and is guaranteed to produce those motifs with greatest z-scores
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ZFIN is the zebrafish model organism database, providing genomic, genetic and phenotypic data for the zebrafish Danio rerio.
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Zotero Analytical Tool, This is an add-on to Firefox that requires 2.0 and aboveCitation management tool; can manage citations to books, chapters, images, podcasts, videos. Supports export formats such as EndNote and BibTex.
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Zung self-rating depression scale Calculator, Use Internet Explorer only
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