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Bioinformatics Outreach

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Bioinformatics Outreach

The Bioinformatics Outreach Project of the Vermont Genetics Network is made possible through a grant to the VGN funded by NIH / NIGMS. The bioinformatics outreach tutorial was developed in the spring and summer of 2006 in association with Dr. William Barnes on sabbatical from Clarion University of Pennsylvania. The beta test of the module was run at the University of Vermont in the fall of 2007. The first outreach delivery was at Green Mountain College in the fall of 2007 and was subsequently delivered at Norwich University in the spring of 2008. To date the module has been taught thirteen times at five different Vermont colleges (Saint Michael's College, Lyndon State College, Castleton University, Green Mountain College and Norwich University).

GOAL:

The goal of VGN Bioinformatics Outreach is to expose undergraduates in the state of Vermont to online databases and data mining techniques. We strive to increase the computational biology skills of undergraduate science students within the state and hope that these additional skills help them in their future career development.

OVERVIEW:

The ability to manipulate organisms genetically has been revolutionized in the last ten years. Biological information produced by this revolution is represented in many forms: sequence data, structural data, and functional data. These data can often be accessed and interpreted only with the help of computers. Data Mining is now an established tool for predicting structure and understanding function in genomics and proteomics. It is becoming impossible for molecular biologists and biochemists to do research without the aid of computer based tools. The advent of computational biology also offers new opportunities for those in chemistry, physics, mathematics, and computer science.

This module is an introduction to the concepts, and the principal data bases of bioinformatics and structural biology/chemistry. This course enables students to access and analyze sequence and structure data, create and edit images of molecules, and present results in several formats.

 
MATERIALS:

The bioinformatics outreach module consists of an online tutorial and an independent research project. Click HERE to view the tutorial outlined below and access other information.

Session One

  • -Introduction to Bioinformatics and Databases
  • -Introduction to the NCBI Databases and ENTREZ
  • -Literature Search Tools
    •      Online Mendelian Inheritance in Man
    •      Introduction to PubMed

Session Two

  • -Introduction to the Sequence Databases and Formats
  •      ENTREZ Gene
  •      The RefSeq Database
  •      Other NCBI Databases
  • -GenBank
    •      The GenBank Flat File Format
    •      Dissection of a Flat File

Session Three

  • -Introduction to Sequence Similarity Searches and BLAST
    •      Blast Queries
    •      Understanding Conserved Domains
    •      Understanding the Blast hit list
  • -Multiple Alignment and Phylogenetic Analysis
    •      Biology Workbench at SDSU
    •      BLASTP
    •      CLUSTALW
    •      BOXSHADE
    •      Phylogenetic Trees (DRAWTREE
    •           and DRAWGRAM)

Session Four

  • -Protein Structure and Databases and 3D Viewers
    •      Jmol DNA Tutorial
    •      Jmol Hemoglobin Tutorial
    •      RCSB PDB and NCBI MMDB
    •     PyMOL

Questions about the module? E-mail Tabitha.Finch@uvm.edu

Contact Information:

Vermont Genetics Network
University of Vermont
120A Marsh Life Science Building
Burlington, VT 05405-0086
(802) 656-9119
(802) 656-2914 - FAX
vgn@uvm.edu

Contact the Webmaster:
vgnwebstaff@list.uvm.edu

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