Two Week Course at ANGIS

reisner at angis.su.oz.au reisner at angis.su.oz.au
Thu Mar 25 18:18:59 EST 1993


			      

      TWO WEEK ANGIS LECTURE & PRACTICAL COURSE, JULY 5-16, 1993

         The Analysis of DNA and Protein Sequence Information
		
       To be given by Prof. Douglas Brutlag, Stanford University
                       and the staff of ANGIS

     Prof. Brutlag has given this course annually over the past three years
at Stanford and for EMBO in Trieste.

     This between semesters course will cover the analysis of DNA and protein
sequence information.  The goals of the course are to evaluate critically the
various methods used to understand genetic information. The strengths and
limitations of published methods will be reviewed and discussed. Novel
algorithms will be proposed. Practical experience applying current methods
will be obtained.  Access to computer and network resources will be provided.

  Some of the topics to be covered include:
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Understanding the Genetic Message

     Introduction to the Internet

     Accessing Molecular Databases

     Searching for Patterns

     Classification of sequences

     Aligning Sequences

     Searching for Similarity

     Rapid Database Search: Speed Versus Sensitivity

     Extracting Patterns by Sequence Alignment

     Deducing Phylogenies

     Coming to a Consensus During Sequencing

     Mapping Genomes

     Representing Protein Structure


    The course is aimed at molecular biologists desiring to understand the
major issues concerning representation and analysis of biological sequence
information. Various existing methods will be critically described and the
strengths and limitations of each will be discussed.  Future directions for
development of new methods will also be discussed.  The course will meet
Monday - Friday over the fortnight.  The lectures will be held from 9:00 AM
to 11:30 AM while the practical classes (1:00-4:00 PM) will include tutorials
and demonstrations of the methods as well as hands on experience in the use
of the ANGIS 2-D menu system and XANGIS (ANGIS implementation of the X Window
System).  There will be practical assignments utilising the tools described.
General knowledge about using computers (copying, editing and deleting files)
and typing skills will be valuable and previous use of ANGIS while not
essential is desirable. Knowledge of programming will not be necessary.

       
          PLACES MUST BE LIMITED TO TWENTY-FOUR. 


              Tentative Schedule
              ~~~~~~~~~~~~~~~~~~
July 5	Understanding the Genetic Message
 	Introduction to the Internet

July 6	Locating Information on the Internet
	Molecular Sequence Databases

July 7	Accessing Molecular Databases
	Symbolic Pattern Matching

July 8	Protein Signatures
	Parametric Representation of Proteins

July 9	Sequence and Structure Profiles
 	Symbolic Alignment of Biological Sequences

July 12	Parametric Alignment of Biological Sequences
	Rapid Sequence Database Search

July 13	Index Based Searches for Sequence Similarity
 	Correlations and Structure

July 14	Parallelized Similarity Searches
 	Multiple Sequence Alignment

July 15	Computer Aided Sequencing Projects
 	Restriction Mapping

July 16	Mapping Entire Genomes
	Rule-Based Prediction of Protein Structure 


    Cost of the course (excluding accommodation and meals) will be $500.

    Accommodation can be reserved at The University of Sydney's International
House for the period July 4 - 16 for those individuals outside Sydney who
desire it.  Currently the charge for serviced rooms is $45 per night, while
unserviced the charge is $27 (linen changed and bed made weekly).  Three
meals a day are provided in either case.

    Individuals interested in applying for a place should send their
applications by post to be received before 15 May 1993 to:

  Alex Reisner
  ANGIS
  c/- Electrical Engineering Building, J03
  The University of Sydney
  N.S.W. 2006

  IN YOUR APPLICATION INDICATE YOUR AFFILIATION, POSITION, WHY YOU WISH TO BE
INCLUDED IN THIS COURSE AND ANY OTHER INFORMATION YOU CONSIDER RELEVANT.

  In the event that the number of individuals interested in attending exceeds
the places available we shall make every attempt to have as wide a
representation of centres and institutions as possible.



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