[an error occurred while processing this directive]
[an error occurred while processing this directive]
catalog button
[an error occurred while processing this directive]
navigation

[an error occurred while processing this directive]

ask a librarian button

Field Guide to GenBank and NCBI Molecular Biology Resources
October 12-13, 2006

 

 

Registration:

The course is free but REGISTRATION IS REQUIRED!

Workshop sessions are optional.  Lecture attendance is a mandatory prerequisite for any workshop session.

ATTENTION: The course is limited to members of the Notre Dame community due to budget constraints.

Course Field Guide registration
  (BIOS 60531
   CHEM 50531
    etc.)

Instructors:  Peter Cooper and Eric Sayers

 

For More Information:

Field Guide lecture What's New lecture Course Field Guide
     Prerequistie: None
     Prerequisite: Field Guide lecture Install Cn3D on laptop
Bring laptop & ethernet cable
     
Field Guide workshop What's New workshop  
     Prerequistie: Field Guide lecture      Prerequistie: What's New lecture  


 

Intended Audience for the Field Guide lecture:

The course is designed for principal investigators, postdoctoral fellows, graduate and advanced undergraduate students and others who work with biological sequence data. Both experienced and novice users of NCBI's tools and resources will benefit.


 Field Guide Course Description:

The National Center for Biotechnology Information (NCBI) presents A Field Guide to GenBank and NCBI Molecular Biology Resources, a lecture and hands-on computer workshop on GenBank and related databases covering effective use of the Entrez databases and search service, the BLAST similarity search engine, genome data and related resources.

Now featuring the NCBI assembly and annotation of human, mouse and rat genomes, the updated map viewer genome displays, the new genome-specific BLAST pages, the new NCBI curated conserved domains, and Cn3D 4.1.

The course has two parts: a 3-hour morning lecture followed by optional 2-hour instructor led computer workshops in the afternoon. Additional workshops are available on the following day. Due to the limited number of workstations, multiple workshops will be offered on two dates in order to accommodate as many people as possible. The same content is covered in each workshop.


Topics:

  • GenBank Database: description and scope
  • The NCBI Derivative Databases: RefSeqs
  • Database Searching using Entrez
    • Neighboring and Links
    • Entrez searching
  • The NCBI Structures Database
    • The Molecular Modeling Database (MMDB)
    • Structural Alignments
    • Viewing Structures and Structural Alignments with Cn3D
  • Similarity Searching using NCBI BLAST
    • Local Alignment Statistics
    • Scoring Systems
    • Using BLAST 2.2.8 web services
    • PSI-BLAST
    • RPS-BLAST (CDD Search)
    • Specialized BLAST pages
  • Genomic Resources at NCBI
    • Complete Microbial Genomes in Entrez
    • Higher Genome Resources
      • RefSeq and Genes
      • UniGene
      • Variation Data (SNPs)
      • The Human, Mouse and Rat genomes
      • The Map Viewer
      • Other Genomes
    Lecture-Field Guide:
    Place: McKenna Hall Auditorium
    Date:  Thursday, October 12, 2006
    Size:   200 participants
    Time:  0830 - 1130

    Field Guide Workshops:
    Place:  to be determined
    Date:   Friday, October 13, 2006
    Size:    23 participants in each session
    Times: 0800 - 1000 Session 1
               1030 - 1230 Session 2
               1400 - 1600 Session 3


     
    Intended Audience for the What's New lecture:
    The course is designed for anyone who attended the January 2005 Field Guide lecture.

    What's New Course Description:
    The "what's new" lecture may include a brief introduction to new and other databases not covered int he Field Guide (Probe, GenSat, PubChem) plus information about changes to the sequence databases and BLAST services, new genomes, new displays.

    Instructors:  Peter Cooper and Eric Sayers

    Lecture-What's New:

    Place: McKenna Hall Auditorium
    Date:  Thursday, October 12, 2006
    Size:   200 participants
    Time:  1300 - 1430

    What's New Workshop:

    Place:  to be determined
    Date:   Thursday, October 12, 2006
    Size:    23 participants in each session
    Times: 1500 - 1700 Session 1

    Intended Audience for the Course Field Guide:

    The course is designed for graduate and advanced undergraduate students who need to learn how to find published biological sequence data.  The lecture and hands-on workshop will be combined into one three-hour session.

    Anyone attending this class must bring an Ethernet cable and a laptop to the session with Cn3D version 4.1 preinstalled on the laptop.  To download the software go to
    http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml


    Course Field Guide:
    Place: 101 Jordan
    Date:  Thursday, October 12, 2006
    Size:   200 participants
    Time:  1900 - 2200

    Computer Software:
    * Cn3D structure viewer (http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml)
    * Browser recommendations:
             PC   Netscape, Firefox, Internet Explorer
             Mac Firefox

    Computer Hardware:
    * Laptop
    * Ethernet cable
           
     
    [an error occurred while processing this directive]