harper@csc.fi (11/05/90)
The Centre for Scientific Computing in Helsinki Finland, will be holding
a course on the GCG paqckage from 21-23rd November 1990. The course is free
to people in Scandinavia, who are attending university, and for people who
attend universities in the EMBO member countries. The main lecturer will
be Dr. Reinhard Doelz from the Biozentrum at the University of Basel,
Switzerland.
Listed below is an outline of the course. Interested people who would
like to attend should notify HARPER@CSC.FI or BJORKLUND@CSC.FI as soon
as possible.
********************* PROGRAMME ***************************
Wednesday 21st November 1990
10:00 -11:00 Introduction. Biosci and EMBL software server
Hardware and software used in Molecular Biology.
Scope and limitations of PCs (IBM+MAC),
Workstations, (Sun, Iris)
Mainframes. (Vax, Unix)
11:00 -11:15 Coffee
11:15 -12:15 VAX Usage
Access (how to log in)
Simple commands:
Viewing, copying, printing, deleting files.
The VAX editor. (EVE, EDT)
Electronic Mail.
12:15 -13:15 Lunch break
13:15 -14:30 Programs available: GCG, PEARSON, NBRF.
Databases available: EMBL, MIPSX, NBRF.
Special databases.
14:30 -14:45 Coffee
14:45 -17:00 Sequences I.
Sequence formats. Sequence format conversion.
The EMBL fileserver. NETSERV@EMBL
How to submit a sequence to the database.
Sequence editing.
Sequence Manipulation, Translation,
Manual Alignment.
18:00 Social get-together at TLP.
Informal meeting with other Finnish molecular
biologists.
Sauna + refreshments.
Thursday 22nd November 1990
9:00 -10:30 DNA Analysis.
Reading frames,
Statistics,
Restriction maps.
10:30 -10:45 Coffee
10:45 -12:15 Protein Analysis.
Secondary structure prediction.
12:15 -13:15 Lunch break
13:15 -14:30 Output of results.
Text output of sequences.
Graphics output of GCG graphics.
The GCG program FIGURE
14:30 -14:45 Coffee
14:45 -16:45 Sequence comparison I.
Comparison Matrices
Dotplots.
Alignment path Matrices
16:45 -17:15 Question time
(Ask help with a particular problem)
Friday 23rd November 1990
9:00 - 10:30 Sequence comparison II.
Fitting two sequences.
10:30 -10:45 Coffee
10:45 -12:15 Database Searches I.
Algorithm used for fast searches for identity
Algorithm used for searches for homology
FASTEMBL
FAMAIL
12:15 -13:15 Lunch break
13:15 -14:30 Database Searches II.
Digesting the output
Problems and strategies for searching sequences.
14:30 -14:45 Coffee
14:45 -16:45 Database Searches III.
Own databases.
Searching with profiles.
Validation of results.
Significance considerations.
16:45 -17:15 Question time
(Ask help with a particular problem)
Exercise: Cookbook preparation.
The user gets a if-then-else scheme which can
be worked through on the screen starting from
entering the sequence, doing dna analysis,
translation to protein, protein secondary
structure prediction, database searches, etc.
RGDS -=ROB=-