+----------------------------------------------------------------------+
| Schweizerische Kommission fuer Molekularbiologie S K M B |
| |
| Organized with the help of the Swiss National Science Foundation |
| |
| Computer Concepts for the Sequence Analysis of Macromolecules |
| |
| Organizer: Reinhard Doelz Location: Biozentrum Basel |
| Date: April 6-9, 1992 Audience: Molecular Biologists |
| Fee: None Language: English |
| |
| The course is primarily targeted at swiss scientists . The course |
| requires an elementary knowledge of computers and will be most |
| useful to those with access to a Digital VAX or a UNIX workstation |
| running molecular biology programs.The GCG program package is used |
| to demo the daily sequence analysis work.Attendants will optimally |
| profit if they have also access to SWITCHlan,or any other kind of |
| access to international networks. The program is attached below. |
+---------------------------------+------------------------------------+
Dr. Reinhard Doelz | EAN doelz at urz.unibas.ch
Biocomputing | DECNET 48130::doelz
Biozentrum der Universitaet | X25 psi%46211142::embnet
Klingelbergstrasse 70 | FAX x41 61 267 20 78
CH 4056 Basel | TEL x41 61 267 22 47
+---------------------------------+------------------------------------+
Preliminary program schedule, SKMB course, Basel
Day 1 9:30 Registration, coffee, welcome
10:00 The User Environment:
How do Biologists access computers
- their hardware
- their access to computing centers
- the account application at the center
- the documentation and support
11:30 The Options:
What services can biologists use on computers
- electronic mail
- bulletin board systems
- file transfer capabilities
- software packages
12:30 Lunch (to be obtained individually)
14:00 The Use of The General Options:
How biologists benefit from being on the network
- contacts to individuals (mail, X.500)
- contacts to the community (BIOSCI, NEWS)
- access to databases (WAIS, FTP)
- individual services (MAIL search servers)
- automatic services (EMBnet data transfer)
15:30 Coffee
16:00 The Use of The 'Biological' Options:
How biologists do biological research on computers
- software available at the computing center
- software available on local systems
- interoperability of software
- DNA databases
- protein databases
- supplementary databases
17:15 Break
17:30 Evening Session For Interested People
Biological Resource Access:
How international networking works
Day 2
9:00 The Basics:
Learning to master the computer
- how to log in
- what is a directory, a file, a device
- moving, deletion, copies of files
- printing files and displaying graphics
- how to log out
- what to do in case of PANIC
10:00 Coffee
10:30 Stepping Forward:
Learning how to modify data in the computer
- the 'editor'
- simple typing and editing
- cutting and pasting
- file transfer to the local computer
11:30 Lunch (to be obtained individually)
13:00 Starting Molecular Biology:
Getting the computer to know your sequence
- the sequence editor
- modifying sequences
- genetic constructs
14:15 Break
14:30 First Analysis:
Composition and Patterns
- Counting symbols
- plotting composition statistics
- Searching a Reading Frame
15:30 Coffee
16:00 Looking at Related Sequences:
The Sequence Comparison methods
- comparison matrices
- simple dotplots
- global alignment
- local alignment
17:15 Break
17:30 Evening Session For Interested People
Mathematics in Sequence Comparison:
Alignment Path Matrices
Day 3:
9:00 Asking for More:
Searching a sequence in the database
- searching for identity
- searching for homology
- searching in the twilight zone
10:00 Coffee
10:30 Asking for Even More:
Searching other information
- Accession numbers
- Authors
- Patterns
- Motifs
11:30 Lunch (to be obtained individually)
13:00 Using the Tools of Molecular Biology:
Enzyme restriction maps
- restriction maps: overview
- restriction maps: letter-by-letter
- sorted restriction maps and digestions
- plasmidmaps
14:15 Break
14:30 Working on Proteins:
Secondary Structure Prediction and other protein tools
- Translation and Backtranslation
- Chou & Fasman , Robson & Garnier predictions
- Protein enzyme digestions
15:30 Coffee
16:00 Working on Sequence Alignments:
Automatic procedures and their evaluation
- automatic alignment
- multisequence editor
- plotting similarities
- creating a profile
17:15 Break
17:30 Evening Session For Interested People
Computer methods in Sequence Comparison:
How sequence searching works
Day 4:
9:00 Doing it All:
Evaluation of a protein family
- searching a profile in the database
- looking for homologies to known structures
- molecular modelling
10:00 Coffee
10:30 So What?
Evaluation of Significance
- statistic methods
- justification by experience
- optimizing the question to be asked
11:30 Lunch (to be obtained individually)
13:00 The Beginning Is Easy:
20 cookbook command procedures to survive
1) log in
2) define environment (software, graphics)
3) enter DNA sequence of interest
4) look for a reading frame
5) translate the sequence to a protein
6) do a database search with the protein
7) compare top hit with search sequence
8) display comparison
9) make a restriction map of DNA sequence
10) create a fragment of DNA
11) search this fragment against the database
12) compare top hit with search fragment
13) align two sequences
14) summarize the results
15) fill out database submission form
16) Mail sequence to the database
17) Read the NEWS in Biology
18) Clean up your disk on the computer
19) Transfer important data to local station
20) log out
15:00 ca. END
************************************************************************
Dr. Reinhard Doelz * EAN doelz at urz.unibas.ch
Biocomputing * DECNET 20579::48130::doelz
Biozentrum der Universitaet * X25 psi%022846211142::embnet
Klingelbergstrasse 70 * FAX x41 61 261- 2078
CH 4056 Basel * TEL x41 61 267- 2076 or 2247
************************************************************************
--
Domain: curtiss at umiacs.umd.edu Phillip Curtiss
UUCP: uunet!mimsy!curtiss UMIACS - Univ. of Maryland
Phone: +1-301-405-6710 College Park, Md 20742
