GCG/Bioinformatics course at NYU

Stuart M. Brown browns02 at mcrcr.med.nyu.edu
Wed Feb 5 11:12:49 EST 1997

Hello GCG users and administrators in the NY City area.  

I am about to start teaching a course at NYU Medical School 
entitled "Using Computers for Molecular Biology".  

The course will include a basic introduction to the VMS operating 
system (an unplesant necessity for GCG use on our Alpha server), 
extensive coverage of GCG programs from a  biologist's perspecitve 
(both cookbook and some underlying theory), and using the Internet 
for Molecular Biology research.

The course will consist of lectures on Tuesdays 1-2:30 PM at NYU Medical
Center, 550 First Ave, NY, NY and a practical session in a computer
classroom following the lecture. 

I am making an open invitation to academic scientists interested in
Bioinformatics and to GCG system administrators to attend any/all of the
lectures.  I am also making my lecture notes available on the Web: 


(please send comments and critiques of these notes to
browns02 at mcrcr.med.nyu.edu)

Practical exercises can be made available to those who are interested 
by personal arrangement (I don't have it set up as an auto-tutorial).

I hope to see some of you dropping by.

Course Syllabus:
Feb. 11: Introduction to the course
   € The Biologist in the Age of Information 
   € What is GCG

Feb18: The basics of using the RCR DEC Alpha Server
   € Logging in to the RCR Alpha 
   € VMS and the DCL Command Language

Feb 25: More basics of using the Alpha
   € E-mail, News
   € Editing text files

March 6: Finding Sequences by Name, Accession#, Keyword, or by Association

March 11: Database Searching by Similarity
   € Worldwide databases 
   € BLAST vs. FASTA 

March 20: Sequence Comparison and Multiple Alignment

March 25: Sequence-Function Relationships
   € Sequence Homology and Conserved Regions
   € Pattern recognition software

April 1: Using the Internet for Molecular Biology Research

April 8: Restriction Maps and PCR Primers

April 15: Computer Tools for Sequencing Projects
   € The GCG fragment assembly tools
   € Using the Macintosh programs Sequencher, MacVector, and GeneWorks

April 22: Computing Evolution: Phylogenetic Analysis 
   € From Multiple Alignment to Phylogeny
   € GCG vs. PHYLIP

April 29: The New SeqLab Graphical Interface for GCG

Stuart M. Brown, Molecular Biology Consultant 
NYU-MC Research Computing Resource, Dept. of Cell Biology
550 First Ave, New York, NY 10016
Phone: (212)263-7689  FAX: (212)263-8139

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