Determining your location... | View access restrictions

About Access Restrictions to Electronic Resources

Access and use of electronic resources made available by the Becker Medical Library are governed by license agreements between the School of Medicine and publishers or third parties. Several of the electronic resources carry some restriction on their use. Access may be restricted by user location, number of concurrent users, and/or password.

In short, most people experience access limitations based on the network to which their computer is connected. Below is a quick breakdown of what can be accessed from various networks.

BJH (Limited to) SLCH (Limited to) Proxy (Remote Access) WUSM Off Campus
AccessMedicine
STAT!Ref
UpToDate Online
AccessMedicine
American Academy of Pediatrics Journals
Applied Clinical Informatics
MDConsult
Red Book Online
ScienceDirect
STAT!Ref
UpToDate Online
Unrestricted Access to All Becker Resources Unrestricted Access to All Becker Resources No Access without Proxy

NCBI Discovery Workshop - October 2012

Washington University School of Medicine participated as a remote site for the National Center for Biotechnology Information (NCBI) Discovery Workshop held at the University of Michigan in October 2012. The workshop focused on a variety of NCBI resources and consisted of the four sessions listed below.

  1. Sequences, Genomes and Maps
     
  2. Proteins, Domains and Structures
     
  3. NCBI BLAST Services
     
  4. Human Variation and Disease Genes

Session descriptions are provided below along with the video recordings (kindly provided by the University of Michigan’s Taubman Health Sciences Library) and associated slides and handouts.

Sequences, Genomes and Maps

This workshop presents the NCBI integrated biomolecular databases that comprise the Entrez system and shows how to effectively use the Entrez system to find and download data of interest. The workshop focuses on scope and content of the sequence databases and uses these as exemplar Entrez molecular databases. After describing the types and sources of molecular sequence data emphasizing the importance of derivative data such as NCBI Reference Sequences (RefSeqs) and sequence-related Entrez information hubs such as Taxonomy, HomoloGene and Gene; the workshop demonstrates effective use of the Entrez interface including filters, search strategies to collect and download a specific set of records, to narrow the search, and to use the precomputed relationships available in the Entrez system to find related sequences, genomic regions, genomic maps, homologous genes and proteins, pathways and expression information. In addition to the sequence databases, the workshop shows how to access related information in HomoloGene, UniGene and Gene Expression Omnibus (GEO) and shows how to use precomputed BLAST (Blink) to find homologous proteins and genes and introduces the Graphical Sequence Viewer as a tool for exploring large and complex genomic sequences and their annotations.

Video - part 1

Video - part 2

Slides and handouts

Proteins, Domains and Structures

This workshop emphasizes the resources associated with NCBI’s three-dimensional structure records including the Molecular Modeling Database, Entrez Structure, Vector Alignment Search Tool (VAST) alignments, the Conserved Domains Database and the structure viewer Cn3D. The workshop shows how the Entrez system can be used to navigate across protein and structure data starting with the sequence for the bacterial mutL protein, finding, displaying and manipulating the X-ray crystal structure for the protein in Cn3D. Precomputed structural and protein alignments in Cn3D are used to explore conserved structural and sequence elements in the histidine kinase-like ATPase domain of the proteins. Finally, homology modeling in Cn3D and conserved domain information are used to interpret disease associated variations in the human MLH1 protein product, a human homolog of mutL.

Video

Slides and handouts

NCBI BLAST Services

This workshop highlights new features and demonstrates the practical aspects of using the NCBI BLAST, the most popular sequence similarity service in the world. The workshop demonstrates useful but under-used features of the updated service including direct access from the Entrez sequence databases; the integration and expansion of Align-2-Sequences; organism limits, other filters and re-organized databases on the submission forms; formatting options (CDS, sorting by position, taxonomy reports) and downloading options on results; and TreeView analysis of results. It also shows how the new conserved domain enhanced protein BLAST service (DELTA-BLAST) improves the sensitivity and specificity of protein BLAST and demonstrates two new sequence analysis services that have been added to the BLAST area of the NCBI site: Primer BLAST, an oligonucleotide primer designer and specificity checker, and a multiple protein sequence alignment tool (COBALT). These new aspects of BLAST provide easier access and results that are more comprehensive and easier to interpret and analyze.

Video - part 1

Video - part 2

Slides and handouts

Human Variation and Disease Genes

This workshop focuses on resources associated with human sequence variations and phenotypes. The demonstrations use the mouse fig4 gene homolog and the human APOE gene as examples to navigate across the integrated databases to find phenotypes, literature, sequences (genome, mRNA, and protein), and variations. The workshop shows how to map those variations onto genes, transcripts, proteins, and genomic regions. This workshop will emphasize the importance of the Gene database as the best way to access these data. Examples demonstrate additional tools and viewers associated with Entrez including the Graphical Sequence Viewer, the Map Viewer, the Variation Viewer, Gene View in dbSNP, examine variations across populations using the new 1000 Genomes Browser, and introduce the NCBI’s Genome Workbench as a sequence analysis and annotation platform. The workshop emphasizes the power of the precomputed analyses and links across and within databases to uncover relationships.

Video

Slides and handouts