- Marandon, Jean-Yves; Pollack, M. M.
- Blackmore, C. Craig.
- Image analysis software for proteomics research, including 2D electrophoresis, DIGE, LC-MS and biomarker screening.
- 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.
- Wells, P. S.
- Delano, Warren L.Molecular structure viewer for representing compounds and macromolecular structures in three dimensions.
- 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.
- 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.
- Haahr, Mads.Offers true random numbers. The randomness comes from atmospheric noise, rather than the pseudo-random number algorithms typically used in computer programs.
- Rankin, J.
- Marshall, J. B.; Ranson, John H. C.; Steinberg, W.
- Linn, 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
- A 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.
- 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.
- Risk Assessment Profile (RAP) of Greenfield et al for venous thromboembolism in adult trauma patientsUsers must sign up for a free account for access to siteGearhart, M. M.; Greenfield, L. J.
- Landefeld, C. S.
- Romhilt, D. W.
- Kornelisse, René F.; Marandon, Jean-Yves.
- Goodman, Sasha.Search engine specializing in finding information about the R statistical analysis language.
- Duck 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.
- A scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
- 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)
- Provides 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.
- 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.
- Sequencher 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.
- Mobile Application Soc Teach Fam Med, iPhone download pageMobile Application Soc Teach Fam Med, Android download page
- A leading significance analysis tool for microarray gene expression measurements.
- "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.
- 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)
- Collects 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.
- Departments 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.
- TMAD 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
- Calculates 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.
- 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.
- Integrated collections of programs for identifying novel cis-regulatory elements from groups of upstream sequences.
- 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 .
- Thompson, Andy.Calculator determines if patients are eligible for inclusion in a systemic sclerosis (SSc) study.
- [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.
- Main repository of genomic data from Tetrahymena thermophila.
- TIMI Risk score for STEMI -- TIMI Risk score for UA/NSTEMI.
- A 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.
- Describing eukaryotic cis-acting egulatory DNA elements and their trans-acting factors, ranging from yeast to Homo sapiens. Position-specific matrices are also provided.
- Butte, Atul J.
- 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.
- Herrle, Scott.
- 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.
- Vector NTI is a high-powered yet reasonably easy to use tool for creating cloning vectors.
- Pon, Steven.
- Suite of programs and databases for comparative analysis of large genomic sequences, including for comparative genomics.
- 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.
- 3D 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.
- Waterlow 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.
- Algorithm for aligning a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
- The principal database for the C. elegans model organism. It stores genetic, genomic and phenotypic data for all strains of C. elegans.
- Gilbert, 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.
- Software 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.
- Citation management tool; can manage citations to books, chapters, images, podcasts, videos. Supports export formats such as EndNote and BibTex.
- Carroll, B. J.; Zung, W. W.
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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.