Software
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- This 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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- An extensive repository of antibodies available for purchase. It provides information and purchase information for antibodies.
- iPhone/iPod touch/iPadMatthew Decaro.Multipurpose medical calculator. Includes functionality to analyze arterial blood gasses and to determine drip rate from desired dosing for an infusion (or vice-versa).
- AbMiner 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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- 2007American College of Medical Genetics ; produced by LogicaCMG."Unraveling the human genome is one of the most important endeavors scientists have ever undertaken. Knowing the structure, functions, and relationships to disease will have a transforming effect on healthcare. This genetics education program will show what genes are and how they relate to disease and the development and use of drugs."--Back of container.
- Student Computing Version XI (Windows); Version X (Macintosh)M051 Version XI (Windows)Duck Room Version XI (Windows)Redwood Room Version XI (Windows)Stone Room Version XI (Windows)
- Student Computing Version 11 (Windows)M051 Version 11 (Windows)Duck Room Version 11 (Windows)Redwood Room Version 11 (Windows)Stone Room Version 11 (Windows)
- Redwood Room, on computers Scan 1 & Scan 2, only. Version CS6 (Windows)
- A database of affinity data for structurally resolved protein-ligand complexes from the Protein Data Bank (PDB).
- Pon, Steven.
- AHRQThe ePSS is an application designed to help primary care clinicians identify clinical preventive services that are appropriate for their patients. Based on the current, evidence-based recommendations of the U.S. Preventive Services Task Force (USPSTF)
- 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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- a project of the Allen Institute for Brain Science.The 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.
- Alvarado, A.
- Pon, Steven.
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- ASAS
- 1977/78-2002/03, <2004/05>Status: Not Checked OutLane Catalog Record
- IBCP
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- "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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- no. 106-, 2003- Acad Search Prem, Full text delayed 12 monthsv. 119-, 2006- WileyAlso available: Print – v. 1-118, 1988-2005.
- [collaboration between the Carnegie Institution of Washington, Department of Plant Biology, and the National Center for Genome Resources].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.
- Version 10.3.1Redwood Room Version 10.3.1Stone Room Version 10.3.1Product description Version 10.3.1ArcGIS is used for creating and using maps; compiling geographic data; analyzing mapped information; sharing and discovering geographic information; using maps and geographic information in a range of applications; and managing geographic information in a database. Contains integrated applications that are intended to be used in order to do comprehensive mapping and geographical analysis. ArcGIS Pro is used for creating and working with spatial data on your desktop. It provides tools to visualize, analyze, compile, and share your data, in both 2D and 3D environments.
- Users must sign up for a free account for access to siteBernard, G. R.; Le Gall, J. R.; Monchi, M.
- EMBL-EBIA public repository for microarray data which aims at storing well annotated data in accordance with MGED recommendations.
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- A 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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- 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.
- Statistical analysis software for analyzing qualitative data, such as focus group discussions, patient interviews and survey results.
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- [developed with the collaboration of guest exhibition curator Marius Kwint and neuroscientist Richard Wingate ; game design by Phil Stuart and Chris Cox from Preloaded]."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"--Wellcome Collection Website.
- Ballard, J. L.
- Benedict, Francis Gano; Harris, J. Arthur; Pon, Steven.
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- Stanford users must download software to view fulltextInteractive digital atlas eHumanBassett, David L.; Brown, W. Paul; Chase, Robert A.; Herbranson, Eric; Mathers, Lawrence H.; Montgomery, Kevin; Vogel, Bruce B.; Whitmore, I.
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- 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.
- Tsai, Jerry.
- Database of experimentally-determined binding affinities of protein-ligand complexes, including small molecule ligands.
- Metasearching sequence motif finding tool that enables easy comparison of outputs from AlignACE, BioProspector, CONSENSUS and MEME for transcription factor binding site prediction.
- (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.
- BioCyc 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
- The 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.
- BioMart 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.
- 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.
- BioPerl is a vast collection of Perl packages for performing typical analytical and management tasks for biological data
- Brutlag, Douglas L.; Liu, Jun S.; Liu, X. S.A powerful tool for identifying DNA and protein motifs.
- 1926- Thomson
- 1926- Thomson
- SUNet ID login requiredBalise, Raymond R.
- A web-accessible annotated database of over 1200 online resources of interest to molecular biologists and neurobiologists.
- BioWarehouse 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.
- NLMNucleotide or protein sequence similarity using the BLAST algorithm. BLAST compares a nucleotide sequence against the GenBank nucleotide sequence database.
- BOV enables users to interactively visualize BLAST high-scoring segment pairs to understand matching patterns between a query and a subject sequence.
- Web versionDownload iPhone App iPhone App
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- Barnas, Gary; Hu, Charles; Kneusel, Ron.
- Barnas, Gary; Hu, Charles; Kneusel, Ron.
- STAT!RefDu Bois, Delafield; Du Bois, Eugene F.
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- A 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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- Univ CologneLogin Univ CologneCologne University BioInformatics Center.BRENDA 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.
- Barnas, Gary; Hu, Charles; Kneusel, Ron.
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- Stanf Univ[developed by] Department of Genetics, School of Medicine, Stanford University.Stores and organizes highly curated data for the yeast Candida albicans.
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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.
- Integrated software environment for pharmacophore modeling and three-dimensional modeling, with applications for rational drug design.
- The 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).
- A 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.
- Package of molecular modeling and simulations programs, with applications in rational drug design and structure-based drug design.
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- Database SciFinder Web, Users must registerRequired Registration Portal SciFinder WebAlso available: Print – v. 1, pt. 1-3 , 1907.
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- An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
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- 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).
- Windows & Macintosh
- 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.
- A 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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- Users must sign up for a free account for access to siteCharlson, M. E.
- Altman, Russ B.; Batzoglou, Serafim; Liu, X. S.; Liu, Yueyi Irene; Wei, Liping.Gibbs sampling search tool biased to search in promoter regions that are conserved across species to identify motifs for transcription factors.
- Institute for Genomic Research.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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- Elber, Ron; Scheraga, Harold Abraham.
- Brutlag, Douglas L.
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- A module of Vector NTI for generating and analyzing biomolecular sequence contigs.
- Ibelgaufts, Horst.
- Database 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.
- Barnas, Gary; Hu, Charles; Kneusel, Ron.Predicts 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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- Bhagwat, Medha.
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2006
Andy Budd ; with Cameron Moll and Simon Collison.Status: Not Checked OutLane Catalog Record- AHADownloadable spreadsheet that "enables health care providers and patients to estimate 10-year and lifetime risks for atherosclerotic cardiovascular disease (ASCVD), defined as coronary death or nonfatal myocardial infarction, or fatal or nonfatal stroke."
- Visualization, modeling and analysis tool for molecular and genetic interaction networks.
- NCBI
- 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.
- Login requiredDatabase of experimentally observed protein-protein interactions
- A data mining and extraction tool for statistical data from US and international government agencies, including US Census and the National Center for Health Statistics.
- 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.
- NLMA database of human genetic variation.
- Windows & MacintoshDiemand, Alexandre; Peitsch, Manuel C.; Schwede, Torsten.Powerful biomolecular structure and analysis program that interacts with SWISS-MODEL.
- Database of commercially available, highly characterized knockout mice.
- Thomson
- Users must register
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- Alguire, P.
- Schwartz, Alan.
- Comprehensive database of natural products organised according to product chemical and physical properties.
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- ACPAlguire, P.; Bartlett, J.
- A 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.
- Compilation of data derived from the literature regarding therapeutic proteins and nucleic acids that are known drug targets.
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- 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).
- A navigation tool for visualizing pre-computed evolutionary relationships in vertebrates and non-vertebrates based on whole-genome primary sequence alignment.
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- AHRQThe ePSS is an application designed to help primary care clinicians identify clinical preventive services that are appropriate for their patients. Based on the current, evidence-based recommendations of the U.S. Preventive Services Task Force (USPSTF)
- EMBOSS is a high-quality package of free, Open Source software for molecular biology. It performs all of the classical molecular biological analytical tasks.
- 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.
- Database Medscape, Free but Users must register and login (existing accounts are valid)"Medscape Reference is the most authoritative and accessible point-of-care medical reference for physicians and health care professionals. All content is available free of charge, both online and via mobile devices. Medscape Reference articles represent the expertise and practical knowledge of top physicians and pharmacists from leading academic medical centers in the US and worldwide. In addition, our rigorous literature survey process allows us to rapidly integrate new practice-changing information into the relevant topics by systematically reviewing the major medical and pharmacy journals, news announcements, and important practice guidelines"--Website.
- A tool allowing local or regional planners to assemble an inventory of critical resources that would be useful in responding to a bioterrorist attack.
- Duck Room Version X7 (Windows)Redwood Room Version X7 (Windows)Stone Room Version X7 (Windows)Student Computing Version X7 (Windows)M051 Version X7 (Windows)
- Thomson Reuters, Users must register from a computer on campus or on the Stanford network, and login
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- NLMIncludes information cited in MEDLINE. GenBank, EMBL, DDBJ, SWISS-PROT, PIR, PDB, PRF, dbEST and U.S. and European patents.
- Release Notes -- Introduction -- Searching a Database -- Uploading UIDs to Entrez -- Downloading Document Summaries -- Downloading Full Records -- Finding Related Data Through Entrez Links -- Getting Database Statistics and Search Fields -- Performing a Global Entrez Search -- Retrieving Spelling Suggestions -- Demonstration Programs -- For More Information.
- Provides access to gene expression and sequences for genes active in mouse and human beta cells.
- iPhone/iPod touch/iPadIncludes drug guide, formulary information and drug interaction checker.
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- creator/project lead, Jeehyung Lee ; principal investigators, Rhiju Das, Adrien Treuille ; developed by Carnegie Mellon University and Stanford University."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.
- Annotated non-redundant collection of data on eukaryotic POL II promoters for which the transcription start site has been determined experimentally.
- Users must sign up for a free account for access to siteNashef, S. A.
- Curated database of commercial monoclonal antibodies.
- [developed by Paul Jones].
- EXPASyExPASy provides integrated access to a variety of databases and analytical tools dedicated to understanding proteins.
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- 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.
- Martz, Eric.A simple tool for macromolecular visualization.
- "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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- Barnas, Gary; Hu, Charles.Determines if renal failure is due to pre-renal, post-renal, or intrinsic renal pathology.
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- Galaxy 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.
- A 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 .
- NCBIA gene expression and hybridization array data repository, as well as a curated, online resource for gene expression data browsing, query and retrieval.
- CSHLChen, Tim; Zhang, Michael.
- The Gene Ontology project provides a set of controlled vocabularies to describe gene and gene product attributes in any organism.
- Orchard, Sandra.
- 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.
- Computational biology tool for determining whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states
2012 Springer Protocols
edited by Jean Peccoud.Part I. Assembly of oligonucleotides in synthons. Building block synthesis using the polymerase chain assembly method / Julie A. Marchand and Jean Peccoud. Oligonucleotide assembly in yeast to produce synthetic DNA fragments / Daniel G. Gibson. Topdown real-time gene synthesis / Mo Chao Huang [and others] De novo DNA synthesis using single-molecule PCR / Tuval Ben Yehezekel, Gregory Linshiz, and Ehud Shapiro -- Part II. Synthon assembly. SLIC : a method for sequence- and ligation-independent cloning / Mamie Z. Li and Stephen J. Elledge. Assembly of standardized DNA parts using bioBrick ends in E. coli / Olivia Ho-Shing [and others] Assembling DNA fragments by USER fusion / Narayana Annaluru [and others] Fusion PCR via novel overlap sequences / Kamonchai Cha-aim [and others] Using recombineering to generate point mutations : the oligonucleotide-based "Hit and Fix" method / Suhwan Chang, Stacey Stauffer, and Shyam K. Sharan. Using recombineering to generate point mutations : galK-based positive-negative selection method / Kajal Biswas, Stacey Stauffer, and Shyam K. Sharan. Assembling large DNA segments in yeast / Héloïse Muller [and others] Recursive construction of perfect DNA molecules and libraries from imperfect oligonucleotides / Gregory Linshiz, Tuval Ben Yehezkel, and Ehud Shapiro. Cloning whole bacterial genomes in yeast / Gwynedd A. Benders. Production of infectious poliovirus from synthetic viral genomes / Jeronimo Cello and Steffen Muller -- Part III. Software for gene synthesis. In silico design of functional DNA constructs / Alan Villalobos, Mark Welch, and Jeremy Minshull. Using DNAworks in designing oligonucleotides for PCR-based gene synthesis / David Hoover. De novo gene synthesis design using TmPrime software / Mo-Huang Li [and others] Design-a-gene with GeneDesign / Sarah M. Richardson [and others] -- Part IV. Education and security. Leading a successful iGEM team / Wayne Materi. The Build-a-Genome course / Eric M. Cooper [and others] DNA synthesis security / Ali Nouri and Christopher F. Chyba.- Weizmann Institute
- Overview SUNet ID login and CMGM/PMGM computer account are required for web usage of this softwareWeb-based gene expression microarray analysis environment.
- 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.
- Help Page Login requiredThe package is a vast collection of high-quality biological analysis tools and databases
- Provides a microarray-based genome-wide gene expression measurements in the HapMap samples.
- MITBurge, Christopher B.
- Padma Sudarshana ... [et. al.].
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- 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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- Users must sign up for a free account for access to siteGrauer, H.
- Barratt, T. Martin; Counahan, R.; Schwartz, G. J.
- Levey, A. S.
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- Rouchka, Eric C.; Thompson, Bill.A powerful, well-documented DNA and protein motif finder program.
- A DNA motif finder that is optimized for the identification of relatively weak motifs.
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- Users must register
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- Tool for biological interpretation of 'omic' data; can process large gene or protein lists.
- Free, simple charting service provided by Google. Suitable for charting simple to moderately complex biomedical data types. Large number of chart types and options.
- Duck Room Version 29- (Windows)Redwood Room Version 29- (Windows)Stone Room Version 29- (Windows)M051 Version 29- (Windows)Student Computing Version 29- (Windows); Version 26- (Macintosh)
- Andreas Doms and Michael Schroeder.
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- GPCRDB stores curated sequences, mutation and ligand binding data for G-coupled protein receptors (GPCRs).
- Duck Room, duck-win7-pc9 and duck-win7-pc10 Version 6 (Windows)
- StatMate is an expensive, easy to use tool for estimating the statistical power of an experiment necessary to detect various hypothetical differences.
- Bejerano, Gill.A 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.
- GTDB and its associated Glycosylation Pathways pages provide a graphical interface for navigating the universe of enzymes involved in glycosylation.
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- iPhone/iPod touch/iPadOnline database NLM"Health Hotlines is a compilation of organizations with toll-free telephone numbers. It is derived from DIRLINE, the National Library of Medicine's Directory of Information Resources Online. This database contains descriptions of over 14,000 biomedical information resources, including organizations, databases, research resources, etc."--WebsiteAlso available: Print – 1988-89, 1992, 1995, 1998.
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- Centralized 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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- Database created by the HGNC under the auspices of HUGO charged with giving unique and meaningful names to every human gene.
- NLM
- Identifies homologous genes in vertebrate using an automated procedure. .
- Identifies homologous genes in vertebrate using an automated procedure. .
- Database of computationally predicted potential tumor associated antigenes based upon expression data from multiple sources.
- This site contains the reference sequence for the human and C. elegans genomes.
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- Compilation 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.
- Allows users to convert ICD-9 to ICD-10 codes. ICD-9 is being expanded from 17,000 to 141,000 ICD-10 codes. This tool only converts ICD-10-CM codes, not ICD-10-PCS. Clinical Modification ICD-10-CM is used for diagnosis coding. The effective implementation date for ICD-10-CM (and ICD-10-PCS) is October 1, 2014.
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- Bhagwat, Medha.
- Hoffmann, Robert.iHOP uses a combination of natural language parsing and gene identifiers to navigate the biomedical literature, thus providing a rapid overview of gene properties.
- A free multi-platform scientific image analysis and processing program written in Java.
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- 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.
- 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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- 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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- A database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
- Querying tool for searching the InterPro database of protein domains and motifs.
- Xu, Rong.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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- Duck 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)
- Duck Room, Duck-PC1,2,3,4,5 only. Version 11 (Windows)Redwood Room, Redwood-PC1,2,3,4,5 only. Version 11 (Windows)JMP Pro statistical analysis software from SAS provides the capabilities for interactive data visualization, exploration, analysis and communication of JMP. In addition, JMP Pro offers a multitude of sophisticated techniques including predictive modeling with cross-validation using a number of different methods, modern modeling techniques, model comparison and averaging features.Also available: Print – 2016
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- Kinemages 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.
- 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.
- 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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- Bioinformatics Center, Institute for Chemical Research, Kyoto University.The KEGG database is designed to facilitate understanding of higher-order protein and cellular functions (e.g., metabolic networks) using genomic and molecular information.
- LabVelocity
- Barnas, Gary.
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- Users must download the app, obtain a product code and register per instructions on website.Includes these databases in Lexi-Comp's complete Clinical Reference Library: -- - Lexi-Drugs Online -- - Pediatric Lexi-Drugs Online -- - AHFS Essentials (Adult and Pediatric) -- - AHFS DI (Adult and Pediatric) -- - Geriatric Lexi-Drugs Online -- - Natural Products Database. Includes these local databases: -- - Lucile Packard Children's Hospital Housestaff Manual (Formulary) -- - Stanford Hospital & Clinics Formulary.
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- A 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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- Users must sign up for a free account for access to siteMaskara, S.; Murray, J. F.
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- Users must sign up for a free account for access to siteKirkpatrick, J. R.
- A compilation of Plasmodium metabolic pathway maps culled from general biochemistry sites.
- [Daniel G. Brown and Todd J. Vision].
- A 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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- Web version, Login required
- Provides access to genomic and proteomic data formats, analysis techniques, and specialized visualizations for genomic and proteomic sequence and microarray analysis
- Includes functions and interactive tools for analyzing historical data, modeling data, simulating systems, developing statistical algorithms, and learning and teaching statistics.
- Duck Room Version R2014b (Windows)Redwood Room Version R2014b (Windows)M051 Version R2014b (Windows)
- [developed by Graham Walker].Website consisting of a collection of medical equation calculators.
- Brutlag, Douglas L.; Liu, Jun S.; Liu, X. S.Identifies 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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- iPhone/iPod touch/iPadMedical calculator ... designed for rapid calculation of common medical formulas and scores used in anesthesiology, pediatrics, emergency, intensive care and internal medicine.
- iPhone/iPod touch
- "This is a complete and self-contained course in modern medical terminology. It is suitable for all students of the health occupations who will have a need to communicate with physicians, dentists, and other medical professionals. Little prior knowledge of anatomy, physiology, and pharmacology is required."
- Database Medscape, Free but Users must register and login (existing accounts are valid)"Medscape Reference is the most authoritative and accessible point-of-care medical reference for physicians and health care professionals. All content is available free of charge, both online and via mobile devices. Medscape Reference articles represent the expertise and practical knowledge of top physicians and pharmacists from leading academic medical centers in the US and worldwide. In addition, our rigorous literature survey process allows us to rapidly integrate new practice-changing information into the relevant topics by systematically reviewing the major medical and pharmacy journals, news announcements, and important practice guidelines"--Website.
- Database Medscape, Free but Users must register and login (existing accounts are valid)"Medscape Reference is the most authoritative and accessible point-of-care medical reference for physicians and health care professionals. All content is available free of charge, both online and via mobile devices. Medscape Reference articles represent the expertise and practical knowledge of top physicians and pharmacists from leading academic medical centers in the US and worldwide. In addition, our rigorous literature survey process allows us to rapidly integrate new practice-changing information into the relevant topics by systematically reviewing the major medical and pharmacy journals, news announcements, and important practice guidelines"--Website.
- MEGAauthors: Sudhir Kumar, Koichiro Tamura, Ingrid Jakobsen, Masatoshi Nei.
- The 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.
- Bailey, Timothy; Elkan, Charles; Grundy, Bill.
- SUNet ID login and CMGM/PMGM computer account are required to download the softwareGeneral purpose image analysis of microscopy images
- Microarray data analysis tool for integrated analysis using clustering, visualization, classification, statistical analysis and biological theme discovery.
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- 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.
- Duck Room Version 2013 (Windows)Redwood Room Version 2013 (Windows)Stone Room Version 2013 (Windows)Student Computing Version 2013 (Windows); Version 2008 (Macintosh)M051 Version 2013 (Windows)
- Duck Room Version 2013 (Windows)Redwood Room Version 2013 (Windows)Stone Room Version 2013 (Windows)Student Computing Version 2013 (Windows); Version 2008 (Macintosh)M051 Version 2013 (Windows)
- Duck 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)
- Duck Room Version 2013 (Windows)Redwood Room Version 2013 (Windows)Stone Room Version 2013 (Windows)Student Computing Version 2013 (Windows); Version 2008 (Macintosh)M051 Version 2013 (Windows)
- Student Computing Version 2013 (Windows)M051 Version 2013 (Windows)Duck Room Version 2013 (Windows)Redwood Room Version 2013 (Windows)Stone Room Version 2013 (Windows)
- Duck Room Version 2013 (Windows)Redwood Room Version 2013 (Windows)Stone Room Version 2013 (Windows)Student Computing Version 2013 (Windows); Version 2008 (Macintosh)M051 Version 2013 (Windows)
- 2007Department of Making Pregnancy Safer, World Health Organization.[Vol. 1.] Foundation module : the midwife in the community -- [v. 2.] Managing postpartum haemorrhage -- [v. 3.] Managing prolonged and obstructed labour -- [v. 4.] Managing puerperal sepsis -- [v. 5.] Managing eclampsia -- [v. 6.] Managing incomplete abortion -- [v. 7.] Providing antenatal care.
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- Repository of miRNA sequences and annotations
- An integrated database that stores known miRNA genes, putative miRNA genes, known miRNA targets and putative miRNA targets.
- NCBIMMDB is NCBI's database of biomolecular structures, integrated within Entrez.
- Duck Room Version 19- (Windows)Redwood Room Version 19- (Windows)Stone Room Version 19- (Windows)Student Computing Version 19- (Windows), Version 24- (Macintosh)M051 Version 16.0.2- (Windows)
- Database 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.
- Corpetby Florence Corpet.
- Bailey, Timothy; Elkan, Charles; Grundy, Bill.
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- Mooney, Sean.MutDB is a gene-centric integration of human variation data with protein structural information and other functionally relevant information, if available.
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- 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.
- NCBIIntegrates information from LocusLink and from genes annotated on Reference Sequences from completely sequenced genomes.
- NCBIMMDB is NCBI's database of biomolecular structures, integrated within Entrez.
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- 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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- Gray, J. E.; Marandon, Jean-Yves.
- NucleaRDB stores curated sequences, mutation and ligand binding data for nuclear receptors.
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- Apkon, Michael.
- Redwood Room (PC-8, only) Version 10 (Windows)
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- Database of bioinformatics databases and software tools.
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- 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).
- A repository of transcriptome profiles used for data-mining and visualization for biomarker and therapeutic target discovery and evaluation.
- A 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.
- 1989-
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- Free, 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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- Users must sign up for a free account for access to siteFairbank, J. C.
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- Ortiz, R. M.; Pon, Steven.
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- Marandon, Jean-Yves; Reilly, P. L.; Simpson, D.
- 2014Includes four PDFs of different kinds of pain assessment scales.
- developed by Vladimir Batagelj and Andrej Mrvar ; some procedures were contributed also by Matjaž Zaveršnik.Network analysis software, suitable for studying networks composed of widely different components: people, molecules, etc.
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- 2012- Users must register and login for a short-term trial.
- 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.
- 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. "
- Metadatabase of resources for biological pathway analysis.
- A 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.
- PDB 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).
- Pon, Steven.
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- Users must sign up for a free account for access to site
- UNOS
- Leteurtre, S.; Marandon, Jean-Yves.
- Users must sign up for a free account for access to siteMoore, E. E.
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- Stanf Univ, USERS NEED TO REGISTERLogin Stanf UnivPharmGKB is an integrated resource about how variation in human genes leads to variation in our response to drugs.
- PhenomicDB 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.
- Redwood Room, on computers Scan 1 & Scan 2, only. Version CS6 (Windows)
- A Linux/UNIX program for assembling shotgun DNA sequence data.
- Phred is Linux/UNIX software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.
- Felsenstein, Joe.
- An 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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- 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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- A 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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- Barnas, Gary; Hu, Charles; Kneusel, Ron.
- The 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.
- Whitehead InstituteRozen, Steve; Skaletsky, Helen.
- Duck Room, duck-win7-pc9 and duck-win7-pc10 Version 6 (Windows)
- Marandon, Jean-Yves; Pollack, M. M.
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- Blackmore, C. Craig.
- 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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- PDB 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).
- The 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.
- Database that provides gene-to-term or gene-to-compound associations.
- Provides a simplified mobile friendly Web interface to access PubMed. PubMed Mobile includes the same basic search functionality and content as Standard PubMed.
- STAT!RefWells, P. S.
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- Delano, Warren L.Molecular structure viewer for representing compounds and macromolecular structures in three dimensions.
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- Duck Room Version 7 (Windows)Redwood Room Version 7 (Windows)Stone Room Version 7 (Windows)M051 Version 7 (Windows)Student Computing Version 7 (Windows & Macintosh)
- MacKenzie, Malcolm.
- "Basic-statistics graphical user interface (GUI) for R, a free interactive programming language and environment"--Website.
- 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.
- Trinity Coll (Ireland)Haahr, Mads.Offers true random numbers. The randomness comes from atmospheric noise, rather than the pseudo-random number algorithms typically used in computer programs.
- Users must sign up for a free account for access to siteRankin, J.
- Users must sign up for a free account for access to siteMarshall, J. B.; Ranson, John H. C.; Steinberg, W.
- Users must sign up for a free account for access to siteLinn, M. W.
- RapidMiner 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.
- Lynch, Peter J.
- Sayle, Roger.
- RGD is the principal genome database for the rat model organism. It stores genetic and genomic data for all strains of the genus Rattus.
- Croft, David.
- 2015- Users must register and login
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- 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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- 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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- Users must sign up for a free account for access to siteGearhart, M. M.; Greenfield, L. J.
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- Users must sign up for a free account for access to siteLandefeld, C. S.
- STAT!RefRomhilt, D. W.
- Kornelisse, René F.; Marandon, Jean-Yves.
- Goodman, Sasha.Search engine specializing in finding information about the R statistical analysis language.
- 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 stores validated primers for real-time PCR and associated probe sequences.
- 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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- Duck 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)
- Duck 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)
- Users must registerProvides access to several Chemical Abstracts Service databases.
- Alexey G. Murzin, Bartlett G. Ailey, Steven E. Brenner, ... [et al].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.
- Calculator Users must sign up for a free account for access to siteSherin, K. M.
- Scriptome 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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- Runs best on iPad/iPhone or Android. On desktop, requires Google Chrome, Apple Safari, or Firefox. Internet Explorer is not supported.Stanford University School of Medicine ; course planners and authors, Lisa Shieh, Eileen P. Pummer, William Daines, Paul M. Maggio, Matthew Strehlow, Irina Tokareva ; technical design and development, Brian Tobin, Jamie Tsui, James Laird, Glenn Zephier.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.
- 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.
- Barnas, Gary; Hu, Charles; Kneusel, Ron.Calculates expected serum osmolarity, for comparison to measured osmolarity to detect unmeasured compounds in the serum.
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- Soc Teach Fam MedMobile Application Soc Teach Fam Med, iPhone download pageMobile Application Soc Teach Fam Med, Android download page
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- Registration requiredA leading significance analysis tool for microarray gene expression measurements.
- 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.
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- Duck 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)
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- Princeton UnivCollects 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.
- A visualization tool with a easy user interface and data connectivity.
- Duck Room Version 22 (Windows)Redwood Room Version 22 (Windows)M051 Version 22 (Windows)Program that allows the user to do statistical analysis.
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- Stanf UnivDepartments of Biochemistry and Genetics at the School of Medicine, Stanford University.SMD 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.
- 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.
- Duck Room Version 14 (Windows)Redwood Room Version 14 (Windows)Statistical analysis package that supports all typical biomedical statistical tests, as well as generating graphical displays of results
- 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).
- Debashis Sahoo.Temporal microarray gene expression analysis software.
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- STRING stores known and predicted protein-protein interactions where the interactions are either direct (physical) or indirect (functional) associations.
- Babbitt, Patricia C.; Ferrin, Thomas E.; Huang, Conrad C.; Morris, John H.UCSF 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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- ExPASy
- SUNet ID login and CMGM/PMGM computer account are required to download the software
- A 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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- Thompson, Andy.Calculator determines if patients are eligible for inclusion in a systemic sclerosis (SSc) study.
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- [collaboration between the Carnegie Institution of Washington, Department of Plant Biology, and the National Center for Genome Resources].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.
- Provides databases and tools for identifying transcription factors and their cognate DNA motif that are over-represented in a gene expression dataset.
- This 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.
- Stanf UnivMain repository of genomic data from Tetrahymena thermophila.
- NCBI
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- TIMI Risk score for STEMI -- TIMI Risk score for UA/NSTEMI.
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- 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.
- 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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- Butte, Atul J.
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- Database of phylogenetic trees of animal genes and their orthologs.
- Implements algorithms designed to identify the structural fold of a protein using its primary structure as input.
- 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.
- Orchard, Sandra.
- This site contains the reference sequence for the human and C. elegans genomes.
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- STAT!RefHerrle, Scott.
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- A database of germ-line immunoglobulin variable (V) sequences automatically extracted from Ensembl's mouse and Homo sapiens genomic databases.
- A database of manually curated human immunoglobulin variable (V) sequences derived from the literature.
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- 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.
- Pon, Steven.
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- Suite of programs and databases for comparative analysis of large genomic sequences, including for comparative genomics.
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- Duck Room Version 2.0.1 (Windows)Redwood Room Version 2.0.1 (Windows)Stone Room Version 2.0.1 (Windows)Student Computing Version 2.0.1 (Windows & Macintosh)M051 Version 2.0.1 (Windows)"VLC is a free and open source cross-platform multimedia player and framework, that plays most multimedias files as well as DVD, Audio CD, VCD, and various streaming protocols"--Website.
- 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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- STAT!RefWaterlow J.
- Structural analysis tool for scanning structures for functional sites in both proteins and nucleic acids.
- Gert Vriend.Versatile biomolecular modeling package for working with proteins and the molecules in their environment such as water, ligands and nucleic acids.
- STAT!Ref
- Algorithm for aligning a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
- iPhone/iPod touch/iPad
- The principal database for the C. elegans model organism. It stores genetic, genomic and phenotypic data for all strains of C. elegans.
- GilbertGilbert, Don.
- Created by staff at Cushing/Whitney Medical Library, Yale University, the analyzer simplifies the creation of a MeSH analysis grid by presenting the ways articles are indexed in the MEDLINE database in a tabular format. It retrieves the article metadata and automatically formats the grid.
- 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.
- A 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.
- 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.
- Users must sign up for a free account for access to siteCarroll, B. J.; Zung, W. W.
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Lane RSS feeds (Really Simple Syndication)A medical search engine provides access to 9,000 medical and procedural videos, 1,000 books and over.All online issues of the Journal of the American Medical Association.Nature, the international weekly journal of science.New England Journal of Medicine.Search Ovid databases.A repository of medical knowledge from internal medicine, cardiology, genetics, pharmacy, diagnosis and management, basic sciences, patient care, and more.
Continuously expanding, all databases in the repository contain the latest editions of selected medical titles.
MicroMedex: Premier pharmaceutical information source containing multiple databases and drug reference tools. Of particular value is DRUGDEX Evaluations, one of the most comprehensive drug sources available.DynaMed Plus is a clinical information resource used by physicians to answer clinical questions quickly and easily at the point of care. Topics are updated daily as new evidence becomes available.Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings.A drug information resource containing: American Hospital Formulary System (AHFS), drug formulary for Lucile Packard Children's Hospital (LPCH) and Stanford Hospital & Clinics (SHC), Lexi-Drugs (adverse reactions, dosage and administration, mechanism of action, storage, use, and administration information), Lexi-Calc, Lexi-ID, Lexi-I.V. Compatibility (King Guide), Lexi-Interact, and Lexi-PALS.Cumulative Index to Nursing and Allied Health Literature (CINAHL) contains coverage of nursing and allied health literature.A knowledge database that provides access to topic reviews based on over 6000 clinically relevant articles. The evidence-based content, updated regularly, provides the latest practice guidelines in 59 medical specialtiesProvides critical assessments of systematic reviews compiled from a variety of medical journals.Selects from the biomedical literature original studies and systematic reviews that are immediately clinically relevant and then summarizes these articles in an enhanced abstract with expert commentary.Multidisciplinary coverage of over 10,000 high-impact journals in the sciences, social sciences, and arts and humanities, as well as international proceedings coverage for over 120,000 conferences.
Includes cited reference searching, citation maps, and an analyze tool.
Features systematic reviews that summarize the effects of interventions and makes a determination whether the intervention is efficacious or not.
Cochrane reviews are created through a strict process of compiling and analyzing data from multiple randomized control trials to ensure comprehensiveness and reliability.
Provides systematic coverage of the psychological literature from the 1800s to the present through articles, book chapters and dissertations.BMJ Clinical Evidence. A clinical information tool built around systematic reviews summarizing the current state of knowledge about prevention and treatment of clinical conditions.PIER (Physicians' Information and Education Resource) is a Web-based decision-support tool designed for rapid point-of-care delivery of up-to-date, evidence-based guidance for primary care physicians.Cochrane Central Register of Controlled Trials (CENTRAL) provides access to 300,000 controlled trials that have been identified the Cochrane Collaboration.Provides drug information targeted for patients.A continually updating drug monograph.The National Guideline Clearinghouse (NGC): A comprehensive database of evidence-based clinical practice guidelines and related documents.MedlinePlus: A repository of health information from the National Library of Medicine. Links are from trusted sites. No advertising, no endorsement of commercial companies or productsLPCH CareNotes via MicroMedex: Patient education handouts customized by LPCH clinical staffMicromedex Lab Advisor: Evidence based laboratory test informationA drug database organized by generic name, trade name and drug class.LPCH / Stanford Hospital Formulary.A goldmine of trusted consumer health information from the world's largest medical library.A trusted source of expert advice for and about kids, providing the information necessary to help patients and parents understand their unique needs.Provides patient handouts from the American Academy of Family Physician.Access to the Stanford Health Library for patients.Lane provides access to over 5,000 eBooks many of which provide helpful background material that will prepare you to better tackle primary literature.Largest, broadest eBook package; covers all sciences, as well as technology (including software), medicine, and humanities.
In addition to covering Wiley and Springer, MyiLibrary is also the only provider for Oxford and Cambridge University Press titles. No seat restrictions.
A collection of biomedical books that can be searched directly by concept, and linked to terms in PubMed abstracts.A web-based, decision support system for infectious diseases, epidemiology, microbiology and antimicrobial chemotherapy. The database, updated weekly, currently includes 337 diseases, 224 countries, 1,147 microbial taxa and 306 antibacterial (-fungal, -parasitic, -viral) agents and vaccines.
Over 10,000 notes outline the status of specific infections within each country.