ALLAccess restricted to Stanford unless otherwise noted
- 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.
- Prostatism symptom score STAT!Ref
- Protein bound calcium STAT!Ref
- 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).
- 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.
- PubGene DatabaseDatabase that provides gene-to-term or gene-to-compound associations.
- 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.
- 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.
- 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.
- 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.
- Pulmonary embolism Wells score STAT!Ref
- Pulmonary vascular resistance STAT!Ref
- PyMol Analytical ToolMolecular structure viewer for representing compounds and macromolecular structures in three dimensions.
- QT interval correction (EKG) STAT!Ref
- QuickTime player Product DescriptionDuck Room Version 7 (Windows)Redwood Room Version 7 (Windows)Stone Room Version 7 (Windows)M051 Version 7 (Windows)Student Computing Version 7 (Windows & Macintosh)
- QUOSA software demo Video
- R commander (Rcmdr) Analytical Tool (Product Description)"Basic-statistics graphical user interface (GUI) for R, a free interactive programming language and environment"--Website.
- R for Windows Version 3.1.1 (Windows)Duck Room, Duck-PC1,2,3,4,5,6,7,8,9,10 Version 3.3.1 (Windows)Redwood Room, Redwood-PC1,2,3,4,5,6,7,8 Version 3.3.1 (Windows)M051-PC1,2,3,4 Version 3.3.1 (Windows)For statistical computing.
- 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.
- Random.org Trinity Coll (Ireland)This site is a web interface to the true random numbers.
- Rankin Scale for stroke disability Calculator, Use Internet Explorer only
- Ranson's Prognostic factors in acute pancreatitis Calculator, Use Internet Explorer only
- Rapid disability rating scale Calculator, Use Internet Explorer only
- 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.
- Rash diagnosis algorithm Calculator
- RasMol Analytical Tool
- 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.
- Reactome Video
- 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.
- Renal failure index STAT!Ref
- 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.
- Reticulocyte production index STAT!Ref
- Reynolds Risk score Calculator
- Risk Assessment Profile (RAP) of Greenfield et al for venous thromboembolism in adult trauma patients Calculator, Use Internet Explorer only
- Risk score for anticoagulant-related major bleeding in hospitalized patients Calculator, Use Internet Explorer only
- Rseek SearchEngine/DatabaseSearch engine specializing in finding information about the R statistical analysis language.
- RStudio Open Source EditionDuck Room, Duck-PC1,2,3,4,5,6,7,8,9,10 Open Source EditionRedwood Room, Redwood-PC1,2,3,4,5,6,7,8 Open Source EditionM051-PC1,2,3,4 Open Source Edition"RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management."--Website.
- RTPrimerDB DatabaseRTPrimerDB stores validated primers for real-time PCR and associated probe sequences.
- 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.
- SAS Product DescriptionDuck Room, Duck-PC1,2,3,4,5,6,7,8,9,10 Version 9.4 (Windows)Redwood Room, Redwood-PC1,2,3,4,5,6,7,8 Version 9.4 (Windows)M051-PC1,2,3,4 Version 9.4 (Windows)
- SAS Enterprise Guide Product DescriptionDuck Room, Duck-PC1,2,3,4,5,6,7,8,9,10 Version 4.3 (Windows)Redwood Room, Redwood-PC1,2,3,4,5,6,7,8 Version 4.3 (Windows)M051-PC1,2,3,4 Version 4.3 (Windows)
- SciFinder Web version Research Tool, Users must registerProvides access to several Chemical Abstracts Service databases.
- 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.
- 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.
- Screening for adolescent substance abuse using the CRAFFT questionnaire Calculator, Use Internet Explorer only
- 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.
- Sensitivity of a test STAT!Ref
- 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.
- 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.
- Serum osmolality Calculator
- Shots immunization schedules Soc Teach Fam MedMobile Application iPhone download page Soc Teach Fam MedMobile Application Android download page Soc Teach Fam Med
- SI unit conversions. Drugs STAT!Ref
- SI unit conversions. Hematology STAT!Ref
- SigmaPlot Product Description
- Significance Analysis of Microarrays (SAM). Version 3.X. Analytical Tool, Registration requiredA leading significance analysis tool for microarray gene expression measurements.
- Skyscape clinical calculator Mobile Application, Various Platforms"With formulas from Aa gradient to Z-score conversion and a full range of specialty indexing, Skyscape Clinical Calculator provides a comprehensive free set of basic tools available for mobile devices.
- Sodium correction in hyperglycemia STAT!Ref
- Sodium deficit in hyponatremia STAT!Ref
- 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)Student Computing Version 10.0.9 (Windows & Macintosh)
- 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.
- Spotfire DecisionSite client Analytical ToolA visualization tool with a easy user interface and data connectivity.
- SPSS Product DescriptionDuck Room Version 22 (Windows)Redwood Room Version 22 (Windows)M051 Version 22 (Windows)Program that allows the user to do statistical analysis.
- Stage III pressure ulcer TreeCalc STAT!Ref
- Stage IV pressure ulcer TreeCalc STAT!Ref
- 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)Student Computing Version 3.1.4 (Windows & Macintosh)
- 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.
- 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.
- 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).
- StepMiner Analytical ToolTemporal microarray gene expression analysis software.
- Steroid equivalence converter Calculator
- Stool osmolal gap STAT!Ref
- Strep pharyngitis probability score Calculator
- STRING stores known and predicted protein-protein interactions where the interactions are either direct (physical) or indirect (functional) associations.
- 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.
- Integrated collections of programs for identifying novel cis-regulatory elements from groups of upstream sequences.
- Survey sample size STAT!Ref
- Swami Analytical ToolA free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics, conceptually based on the Biology Workbench.
- 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 .
- Symyx ELN Analytical Tool (Product Information)Electronic laboratory notebook suitable for biological and chemical research. Windows only.
- SYSTAT Product DescriptionM051 Version 12 (Windows)Duck Room Version 12 (Windows)Redwood Room Version 12 (Windows)Program that allows the user to calculate statistics, generate data reports and produce graphics.
- Systemic Sclerosis Calculator CalculatorCalculator determines if patients are eligible for inclusion in a systemic sclerosis (SSc) study.
- Systemic vascular resistance STAT!Ref
- TAIR DatabaseMaintains 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.
- TELis DatabaseProvides databases and tools for identifying transcription factors and their cognate DNA motif that are over-represented in a gene expression dataset.
- 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.
- Tetrahymena genome database (TGD) Stanf UnivMain repository of genomic data from Tetrahymena thermophila.
- ThreeD Domains NCBI
- TIMI risk score Calculator (for STEMI)TIMI Risk score for STEMI -- TIMI Risk score for UA/NSTEMI.
- Total body water/urea volume of distribution Calculator
- Total lung capacity STAT!Ref
- TranscriptDetector Analytical Tool, Login requiredA tool for finding probes measuring significantly expressed loci in a genomic tiling microarray experiment.
- 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.
- 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.
- Transferrin saturation STAT!Ref
- Trauma score for survival probability Calculator
- Tree families database DatabaseDatabase of phylogenetic trees of animal genes and their orthologs.
- UBC Bayesian calculator Calculator
- UCLA Pain assessment tools Calculator
- UCLA-DOE Fold server Analytical ToolImplements algorithms designed to identify the structural fold of a protein using its primary structure as input.
- UMLS semantic network Database
- 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.
- This site contains the reference sequence for the human and C. elegans genomes.
- UNOS MELD score in liver disease STAT!Ref
- Unstable angina risk stratification STAT!Ref
- Vancomycin & aminoglycoside pharmacokinetics Calculator
- VBASE DatabaseA database of manually curated human immunoglobulin variable (V) sequences derived from the literature.
- VBASE2 DatabaseA database of germ-line immunoglobulin variable (V) sequences automatically extracted from Ensembl's mouse and Homo sapiens genomic databases.
- 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.
- Ventilation index [calculator] Calculator
- Very low density lipoprotein (VLDL) STAT!Ref
- VISTA Analytical ToolSuite of programs and databases for comparative analysis of large genomic sequences, including for comparative genomics.
- Vital capacity STAT!Ref
- 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.
- Volume of distribution of urea STAT!Ref
- Warfarin dosing TreeCalc STAT!Ref
- Water deficit in hypernatremia STAT!Ref
- WebFEATURE DatabaseStructural analysis tool for scanning structures for functional sites in both proteins and nucleic acids.
- Weights & measures Calculator
- WHAT IF SoftwareVersatile biomolecular modeling package for working with proteins and the molecules in their environment such as water, ligands and nucleic acids.
- Winter's Formula for expected PCO2 STAT!Ref
- Wise2 Analytical ToolAlgorithm for aligning a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
- Mobile Application iPhone/iPod touch/iPad
- WormBase DatabaseThe principal database for the C. elegans model organism. It stores genetic, genomic and phenotypic data for all strains of C. elegans.
- 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.
- 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
- ZFIN is the zebrafish model organism database, providing genomic, genetic and phenotypic data for the zebrafish Danio rerio.
- 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.
- Zung self-rating depression scale Calculator, Use Internet Explorer only
Shortcut to Licensed Content
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