A Bioinformatics Workshop at Boston University

Zhiping Weng zhiping at bu.edu
Thu Jul 24 20:04:29 EST 1997


 
                          BIOINFORMATICS WORKSHOP
               http://engpub6.bu.edu:7105/bioinfo/workshop.html

                             Boston University
                     Biomedical Engineering Department
                        September 7, 8, 9, 10, 1997

    Sponsered by Biomedical Engineering Department , Boston University in
  conjunction with the Center for Computational Science , Boston University
          and with partial support from the Department of Energy.

============================================================================

Making the Most Sense of a New DNA/Protein Sequence

Our team of researchers will present:

   * Major tools for sequence comparison, structure and function
     identification;
   * State of the art methodologies for extracting maximum information from
     sequence and function databases;
   * Application of cuting edge computing and communications technologies in
     3-D structure visualization.

Workshop participants will gain hands on experience with practical problem
solving in our High Performance Computing Laboratory.

===========================================================================

Organizers Professor Temple Smith
           Professor Charles Cantor
           Professor Charles DeLisi
           Professor Sandor Vajda
           Dr. Zhiping Weng

 Topics    1. For query sequences with significant homology to sequences in a
           known protein family, you will learn how to:

           * identify the protein family;
           * search sequence databases for all the homologous sequences in
             this protein family;
           * search structure databases for all the 3-D protein structures
             in this protein family;
           * search databases for the functional motif/pattern;
           * identify the receptor (or ligand) of the query sequence;
           * construct a phylogenetic tree for this protein family by
             multiple sequence alignment;
           * carry out multiple structure alignment and construct a 3-D
             structure model for the query sequence;
           * visualize the 3-D protein structures;
           * analyze the 3-D protein structures.

           2. For query sequences with NO significant homology to sequences in
           a known protein family, you will learn how to:

           * interpret the (BLAST/FASTA) search results at the twilight
             zone;
           * carry out multidomain alignment;
           * construct position-dependent profiles and use them to search
             databases.

     Where Department of Biomedical Engineering, Boston University
  Deadline Aug 18, 1997.
           Enrollment is limited to 18 participants; please respond ASAP.
     Cost  Includes opening reception, continental breakfast, coffee break
           $1,000 for commercial employees
           $500 academic employees
           Travel and accommodation are the responsibility of the individual.
           We will aid in any necessary room and board arrangements.
    How to Prepare a short description of your background and experience
    apply  with bioinformatics and how this workshop will benefit you. Send
           this along with your name, address, affiliation, and phone
           number to zhiping at bu.edu by email, or to Dr. Zhiping Weng,
           Department of Biomedical Engineering, 44 Cummington Street,
           Boston University Boston, MA 02215 by mail. Call 617-353-2800
           with any questions.

           Qualified applicants will be notified promptly.
           Additional details will be mailed with your notification of
           acceptance.

========================================================================
                       Bioinformatics Workshop Agenda

At each afternoon of the four day workshop there will be two hands on
practical computer exercises sessions, held in the High Performance
Computing Labarotory using Silicon Graphic workstations. During each
session, a set of practical problems will be given based on the presented
material. Each participant will be expected to choose among the available
tools and/or databases to tackle the presented tasks. In between the two
sessions there will be detailed discussions of the obtained results and an
opportunity to investigate additional alternatives.

Sunday, September 7

 9:00-9:30   Overview of Bioinformatics
 9:30-10:30  Pairwise Alignment and Database Search algorithms
             (BLAST/FASTA);
             conserved patterns and motifs (consensus, regular expression,
             weight matrix expressions, PROSITE pattern)
 10:30-11:00 Introduction to the wealth of currently available databases
             and associated on-line resources (GenBank, Genpep, PDB, BLOCK,
             PROSITE)
 11:00-11:30 Coffee break
 11:30-12:30 Computer demonstrations of database searching
 12:30-1:30  Lunch
 1:30-2:00   Prediction of the coding region of a nucleic acid sequence
             (GRAIL)
 2:00-3:30   Practical computer exercises
 3:30-4:00   Summary of database search results
 4:00-5:00   Practical computer exercises

Monday, September 8

 9:00-10:00  Algorithms for multiple sequence alignment (PILEUP, PIMA,
             BLOCK) and constructing philogenetics trees (PAUP)
 10:00-11:00 Algorithms for structure alignment
 11:00-11:30 Coffee break
 11:30-12:30 Computer demonstrations of multiple sequence alignment
 12:30-1:30  Lunch
 1:30-2:15   Display of multi-alignment results (MASE with protein
             secondary structure shown)
 1:30-3:30   Practical computer exercises
 3:30-4:00   Summary of multiple sequence alignment and structure alignment
             results
 4:00-5:00   Practical computer exercises

Tuesday, September 9

 9:00-10:00  The problems of the biological/statistical significance of
             sequence/profile matches
 10:00-11:00 Constructing profiles from multiple sequence alignment
             results; search databases using profiles
 11:00-11:30 Coffee break
 11:30-12:30 Computer demonstrations of profile construction and search
 12:30-1:30  Lunch
 1:30-2:00   Multidomain alignment
 2:00-3:30   Practical computer exercises
 3:30-4:00   Summary of profile construction and search
 4:00-5:00   Practical computer exercises

Wednesday, September 10

 9:00-10:00  Display protein 3-D structures (RASMOL, MOLSCRIPT, SCULPT)
 10:00-11:00 Construction of a 3-D model by homologous extension (CONGEN),
             analysis of structural features (Secondary structures,
             hydrophobics)
 11:00-11:30 Coffee break
 11:30-12:30 Computer demonstrations of structure modeling
 12:30-1:30  Lunch
 1:30-2:00   Identify the binding site residues
 2:00-3:30   Practical computer exercises
 3:30-4:00   Summary of structure modeling
 4:00-5:00   ImmersaDesk (Virtual Reality Station) for protein 3-D
             structure Display






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