SKMB 1992 Biocomputing course

[Reinhard Doelz]

+----------------------------------------------------------------------+
|    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   
************************************************************************
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