Tufts Resources

Databases

The following resources require a Tufts username for access:

• Biobase Proteome-the proteomics databases
  The Proteome suite of the six protein databases YPD, Human PSD, WormPD, GPCR-PD, PombePD, and MycopathPD is a comprehensive data collection on proteins, and includes information about proteins in mammals, yeasts, neamotodes, and fungi. The databases feature quality content based on detailed literature-based curation, comprehensive references, disease information, BioKnowledge transfer and integrated resources. Please Note: Creating a username & password is required when using for the first time.
  
  
• BIOSIS Previews (Biological Abstracts)
  Access via ISI Web of Science
  Comprehensive coverage of nearly 5,500 life science journals and 1,500 items from international meetings, review articles, books, and unique additional references from Biological Abstracts and Biological Abstracts/RRM.
  
  
• Chemical Abstracts
  Chemical Abstracts covers the literature of chemistry and chemical engineering including patents.
  
  
• Current Protocols Online
  Laboratory manuals on methods giving step by step procedures. Tufts subscribes to the following sections only: Cell Biology, Human Genetics, Molecular Biology, Nucleic Acid Chemistry, and Protein Science.
  
  
• EcoSal
  Comprehensive archive of the entire corpus of knowledge on the enteric bacterial cell.
  
  
• Journal Citation Reports
  Access via ISI Web of Knowledge
  Ranks journals in various fields by ISI's impact factors.
  
  
• MEDLINE
  International biomedical journal literature includes over 11 million journal citations and abstracts in the fields of medicine, nursing, dentistry, veterinary medicine, healthcare systems, and pre-clinical sciences.
  
  • Access via Ovid
    
  • Access via PubMed (use this link with your Tufts username for e-journals licensed to the Tufts community)
    
    
• Oncomine
  Compendia Bioscience
  A repository of transcriptome profiles used for data-mining and visualization for biomarker and therapeutic target discovery and evaluation.
  
  
• Science Citation Index
  Access via ISI Web of Science
  Science Citation Index contains bibliographic information gathered from thousands of scholarly journals. Science Citation Index can be searched by: subject, author, journal, author address and/or articles that cite a known author or work.
  
  
• SCOPUS
  An index to the scientific technical and medical literature covering 14,000 scholarly titles including 2,700 titles in Social Science, Psychology, and Economics. Updated daily. Full-text linking is available wherever the technology and the access arrangements permit and continues to expand as such arrangements allow. Integrated web searching and patent searching by Scirus.

E-Journals

E-Books

Collections:

• Springer-Link Biomedical and Medical Textbook Collection
• Knovel Biochemistry, Biology & Biotechnology reference book collection
  Under "Browse" select Biochemistry, Biology & Biotechnology

Key titles:

• C. Elegans II

• The cell : a molecular approach

• Cold Spring Harbor (CHS) Protocols

• Current Protocols in Cell Biology

• Current Protocols in Human Genetics

• Current Protocols in Molecular Biology

• Current Protocols in Nucleic Acid Chemistry

• Current Protocols in Protein Science

• Encyclopedia of Life Sciences

• Genes and Diseases

• Genomes

• Harper's Illustrated Biochemistry

• Methods in Enzymology

• Molecular cell biology

• Oxford Desk Reference - Clinical Genetics

• WormBook (C. elegans)

 

U.S. Government Databases

The following databases were created and/or funded by the U.S. governemnt and are freely available to the public:

• BLAST (Basic Local Alignment Search Tool)
  Finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
• DAVID (Database for Annotation, Visualization and Integrated Discovery)
  DAVID  provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes. For any given gene list, DAVID tools are able to: Identify enriched biological themes (particularly GO terms); Discover enriched functional-related gene groups; Visualize genes on BioCarta & KEGG pathway maps; Search for other functionally related genes not in the list; List interacting proteins; Explore gene names in batch; Link gene-disease associations;Highlight protein functional domains and motifs;
  Redirect to related literatures
  
• Entrez Gene
  NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that have an active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is updated as new information becomes available.
  
• Entrez SNP
  Single Nucleotide Polymorphism (SNP) database is a public-domain archive for a broad collection of simple genetic polymorphisms.
  
• Human Protein Reference Database
  A centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data.
• OMIM - Online Mendelian Inheritance in Man
  Catalog of human genes and genetic disorders;contains textual information and references.
• PharmGKB
  PharmGKB is a publicly available Internet research tool developed by Stanford University with funding from the National Institutes of Health (NIH) and is part of the NIH Pharmacogenetics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs.
• RefSeq
  The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms.
• U.S. Patent and Trademark Office Patent Databases: Full-Text and Images
  Searchable database of patent grants and applications registered with the U.S. Patent and Trademark Office.

Research Centers & Institutes

• Broad Institute of MIT and Harvard
  A collaboration between Harvard and the Massachusetts Institute of Technology, the Eli & Edythe L. Broad Institute focuses on tools for genomic medicine and making them available to the scientific community.
  
• European Molecular Biology Laboratory (EMBL) / European Bioinformatics Institute (EBI)
  EBL is a non-profit organisation and a basic research institute funded by public research monies from 19 member states. Research at EMBL is conducted by approximately 80 independent groups covering the spectrum of molecular biology. EBI is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.
• International Nucleotide Sequence Database Collaboration (INSDC)
  Collaboration between NCBI, EBI/EMBL, and DDBJ (DNA Data Bank of Japan) in gathering and publishing nucleotide sequence and annotation. Provides links to the three partners' data submission and retreival tools.
• National Center for Biotechnology Information (NCBI)
  Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.
• Wellcome Trust Sanger Institute
  Provides access to BLAST servers, software, news, and career opportunities.
• Whitehead Institute for Biomedical Research
  A non-profit, independent research and educational institution with pioneering programs in stem cells, cancer research, immunology, neurological disorders, developmental biology, genetics and genomics.
  

Resources Guides & Web Tools

• Biological and Chemical Data Resources
  From the Broad Institute, a research collaboration between MIT, Harvard and it's affiliated hospitals, and the Whitehead Institute.
• BioNetbook
  Searchable directory of web resources; from the Pasteur Institute.
• BioResearcher Toolkit
  A collection of links to a molecular biology resources including: genomics, bioinformatics, protein and Nucleic Acid Analysis; from the University of Washington Health Sciences Libraries.
• Broad Institute Software Tools
  Software tools for the analysis of large genome-related datasets. These tools openly available to the scientific community.
• Cell and Molecular Biology Online
  A general resource for online information on cell and molecular biology.
• GeneCards: human genes, proteins and diseases
  GeneCards is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others;from the Weizmann Institute.
• GeneTests
  A publicly funded medical genetics information resource developed for physicians, other healthcare providers, and researchers. Provides GeneReviews, an expert-authored, peer-reviewed, current disease descriptions that apply genetic testing to the diagnosis, management, and genetic counseling of patients and families with specific inherited conditions. Also features an international directory of genetic testing laboratories and prenatal diagnosis clinics
• IUPAC Nomenclature Home Page
  Contains recommendations on organic and biochemical nomenclature,symbols and terminology from the International Union of Pure and Applied Chemistry (IUPAC). Also contains the full text of IUPAC recommendations and bibliographic information.
• Molecular Biology & Genetics
  Created by the Health Sciences Library System of University of Pittsburgh, this guide provides extensive listings of resources grouped into the following categories: Genome Analysis, Laboratory Work, Literature Retrieval, Nucleic Acid Analysis, and Protein Analysis.
• Molecular Biology Techniques
  A portal for molecular biology which contains immunology methods and protocols, bioinformatics, and news categorized by DNA, RNA, protein, and proteomics. Also discuss and ask questions about molecular research techniques in the forum.
• Molecular Biology Toolkit
  A Java-based protein visualization and analysis toolkit. The toolkit provides classes for efficiently loading, managing and manipulating protein structure and sequence data. The MBT also provides a rich set of graphical 3D and 2D visualization components which can be easily "plugged together" to produce applications having sophisticated graphical user interfaces.
  
• National Center for Biotechnology Information (NCBI)
  Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.
• National Institutes of Health -- Grants and Funding Opportunities
• Protocol Online
  Database of research protocols in a variety of life science fields. It contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites.
• PubCrawler
  A free "alerting" service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases; from the Department of Genetics at Trinity College Dublin.
• TB (Tuberculosis) Database
  Contains TB-related gene expression and genome sequences. TB Database is a multi-institutional collaboration makes available the tools and resources available at the Stanford Microarray Database and the Broad Institute.
• University of Waterloo Bioinformatics Group Software Tools
  Contains a variety of software tools including tools for protein folding and sequencing, homology searching, gene finding, and phylogenetic analysis.
• WormBook (C. elegans)
  A comprehensive, open-access collection of original, peer-reviewed chapters covering topics related to the biology of Caenorhabditis elegans (C. elegans). WormBook also includes WormMethods, an up-to-date collection of methods and protocols for C. elegans researchers.

Tutorials

• Bioinformatics
  Created by the European Bioinformatics Institute (EBI). Provides short and concise introductions to basic concepts in molecular and cell biology and bioinformatics.
• BLAST (Basic Local Alignment Search Tool)
  Designed to help the first time BLAST user. This tutorial will teach you to input a sequence into the Basic BLAST web page, choose a program and database, and examine the results; from NCBI.
• Coffee Break
  A collection of short reports on recent biological discoveries prepared by NCBI.
• Introduction to Molecular Biology Information Resources
  Overview of flagship search systems and databases available at the NCBI. Emphasizes how one's current search skills apply to molecular biology databases. A tour of advanced Entrez search features illustrates techniques for effective and efficient retrieval of molecular data. Also introduces more technical search systems, including BLAST, Map Viewer, and the Cn3D viewer for three-dimensional protein structures.
• Just the Facts: a Basic Introduction to the Science Underlying NCBI Resources
• NCBI Mini-Courses
  These online mini-courses are either problem based, such as "Identification of Disease Genes" or NCBI resource based such as "BLAST Quick Start". The courses are 2.5 hours in length with first hour and half devoted to an overview that is followed by a one hour hands-on session. The courses are free.
  
• PubMed
  Interactive tutorial highlighting the features and services of PubMed, including MEDLINE. Requires Macromedia FlashÈ player version 4.0 and higher. Created by the National Library of Medicine.
• Web of Science
  Overview of the features and use of ISI Web of Science; from ISI.
• What is Bioinformatics?
  A brief overview of the field of bioinformatics prepared by the National Center for Biotechnology Information (NCBI). Includes links to NCBI tutorials, a glossary of fequently used terms, and a bibliography of useful print resources.