JAMF Archive BioCompanion as published in 1995 THIS IS THE REFERENCE CODE AS PUBLISHED. Doelz, R. Optimal production of biological documentation: the JAM format. Comput. Applic. Biosci. 11, 224-226 (1995). The version you are currently viewing is the one printed and distributed via the Internet from the server of BioComputing Basel. Version 3.1 of the BioCompanion was published with version 2 of the JAMF software. The server that was indicated in the documentation has ceased to exist. Version 3.2 of the BioCompanion was not publicly available for free but was shareware that was distributed with GCG's software release 9. For the purpose of enhanced editing, JAMF was partially rewritten and the proprietary version 3.x of JAMF was used from 1996 onwards. The Biocompanion is available in a current version from the publisher . It has significantly changed both in software and content.
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Preface

[This document is called Version 3.1, November 1995]

Intended Audience

The "BioCompanion" , is intended to serve as an introduction for the new or casual user of computers in molecular biology. ISBN numbers are assigned to the Basel-specific version for VMS systems (ISBN 3-905434-00-8) and the site-neutral version for UNIX systems (ISBN 3-905434-02-4).

The "BioComputing Tutorial" (Doelz, R. 1990) included similar background information, and a worked-out cookbook was available as "Survival Guide" (Doelz, R. 1993). A tutorial-like book, covering several packages, was also available from bookstores as "Computer Analysis of Sequence Data", A.Griffin, H.Griffin (ed)., Humana Press, ISBN 0-89603-246-9 (pt.1), ISBN 0-89603-276-0 (pt.2).

The BioCompanion focuses mostly on the GCG software (Genetics Computer Group, (1991), Program Manual for the GCG Package, Version 8, September 1994, 575 Science Drive, Madison, Wisconsin, USA 53711. Quotation of manual passages with permission.), but also includes examples from the ATLAS software from PIR International, the MPsrch software from IntelliGenetics, Inc. and the SRS software from T.Etzold, EMBL.

Note on the Type of this Document

The BioCompanion is a configurable document, which is achieved by the format Just Another Metaformat (JAMF). This means that, depending on your environment, you will read this text as a printed booklet, in a brochure, or as on-line document on the screen. The contents of this text is configurable as well.

Site-specific files are for the Biozentrum Basel. Specifically configured for this version were VMS , ATLAS , DECNET , EGCG , ENTREZ , PEARSON , RCP , READSEQ , SRS .

How to Use this Guide

This guide uses the convention to have a generic example command printed like:

$ logout

Whereas specific examples are printed like:

 
  
$ dir/date  
  

The JAMF code produces a set of HTML files which are indexed and listed accordingly. The JAMINX.HTML file is the startup page.

LATEX Format

The auxiliary file BIOCOMPANION.TEX (part of the distribution) has to be used in the LATEX processor (adopt margins if you do not use European DIN A4 format). Before rerunning LATEX the second time you need to run the 'makeindex' program which should generate the file BIOCOMPANION.IND. This file is not part of the original distribution, thus, possibly generates an error message in the first run.

RTF Format

Load the RTF file in your preferred word processor. (Be sure that this one can digest over 100 pages, and be prepared to wait.) You might consider producing several small files instead of one big file, but this will hinder indexing afterwards. In any case, add line numbers at the bottom of the page (JAMF RTF files have the header with the chapter name in it). Next, jump to the end of the file and add the Chapter Index. You might need to select an 'options' box in order to accommodate the 'Table Entry Fields' as the JAMF program does not produce 'Header Styles' (i.e., it uses .c. paragraphing). Last, generate a keyword index with the index creation tool. Save the file as Word Processor file and print this file only after reopening it.

Exercises

This document does provide XX exercises which shall help the reader to validate the understanding of the read explanations. The last two are 'advanced' exercises. In order to practice, the reader must have access to a system which runs a licensed GCG installation .

 
Exercise               Topic   
  
  1     WPI exercise: Run a 'fasta' search           
  2     Editor exercise: Type in a DNA sequence          
  3     Editor exercise: Create a DNA sequence fragment          
  4     Hunting exercise: Find the DNA alphabet in the documentation          
  5     DNA composition: Determine the G/C content of a DNA sequence           
  6     DNA reading frame analysis: Prediction of an ORF           
  7     Summary of single-sequence protein analysis tools          
  8     Schematic pairwise DNA analysis: Compare two sequences           
  9     Internal repeat analysis: Analyse a single sequence           
 10     Pairwise sequence analysis: Comparison matrices  
 11     Patterns: Use of the motif searching program  
 12     Sequence searching: Use of the 'blast' and 'fasta' searching programs            
 13     Understand the benefit, scope and limitations of a rigorous searching method.    

Copyright

This document is shareware, copyrighted by Reinhard Doelz. The electronic access to the document for personal use is free of charge. You can obtain this document electronically or in printed fashion.

Electronic Access: Private Use

If you have access to the international Internet, you are allowed to download the document electronically. Use the program 'ftp' to access the ftp server bioftp.unibas.ch and go to the subdirectory survival. For details on 'anonymous ftp' read the corresponding section on 'ftp' . Use anonymous as user name, and your electronic mail address as password. Available versions include

• Rich Text Format (RTF) for word processors

• LATEX typesetting format

• HTML pages

If you view these pages on the WWW browser system electronically, please understand that frequent use by sites outside of Switzerland is not serving the purpose as JAMF allows local configuration and installation at your site. We would like to negotiate with you how to install the BioCompanion at your site.

Electronic Access: Institutional Use

Service Providers, Software Consultants, Computing Centres, etc.

If you have access to the international Internet as an academic site, it is possible to download the document electronically via 'anonymous ftp' from the ftp server bioftp.unibas.ch. Available versions include:

• Rich Text Format (RTF) for word processors

To produce a site-specific version of the BioCompanion, the main files (*.JAM) need not be changed. The effort to modify the .STE files is less than half an hour. Assistance may be provided if you desire to use this feature. Please inquire for details. Briefly, the following data are configurable site-specifically:

 
  
JAMF defines| STE files     |  Purpose  
------------+---------------+---------------------------------------------  
biological issues   
------------+---------------+---------------------------------------------  
ATLAS       |  ATLAS.STE    | Use of the ATLAS system from PIR International  
EGCG        |  none         | various; explains additional programs (Rice et al.)  
ENTREZ      |  ENTREZ.STE   | Use of the ENTREZ browser from NCBI  
PEARSON     |  none         | various;  explains additional programs (W.Pearson)  
READSEQ     |  none         | Use of the 'readseq' program (W.Gilbert)  
SRS         |  SRS.STE      | various;  explains SRS programs (Etzold and others)  
            |  BLAST.STE    | How BLAST is run at this site   
            |  BLOCKS.STE   | Access to non-GCG motif databases   
            |  DATABASE.STE | Which databases are available at this site  
            |  GCG.STE      | GCG setup at this site   
            |  GENEPRED.STE | Access or availability of genome analysis  
            |  LOOKSTR.STE  | Preference/description of 'lookup' and 'stringsearch'  
            |  PROFILES.STE | How are profile methods run locally   
            |  SWSEARCH.STE | How are Smith and Waterman searches run locally  
------------+---------------+---------------------------------------------  
technical issues  
------------+---------------+---------------------------------------------  
            |  CONFIG.STE   | Label file to name your site   
            |  ACCESS.STE   | Methods of access (TCP/IP, LAT, etc.)  
            |  ACCOUNT.STE  | Where to obtain accounts  
            |  LOCAL.STE    | (human) Local help  description  
            |  PRINT.STE    | How to print locally   
RCP         |  COPY_UNIX.STE| 'rcp' copy command in UNIX  
DECNET      |  COPY_DEC.STE | Decnet Phase IV copy command   
            |  EDIT_XXX.STE | XXX = UNX or VMS, editor description   
            |  MAIL_XXX.STE | XXX = UNX or VMS, mail description   
VMS         |  everywhere   | to produce the VMS flavour of command syntax  
------------+---------------+---------------------------------------------  
techniques used to access BioComputing installations   
------------+---------------+---------------------------------------------  
                BROAD.TEC   - Broadband  
                DECNET.TEC  - DECNet (Phase IV)  
                LAT.TEC     - Local Area Transport (DEC)  
                TCP.TEC     - TCP/IP Terminal server  
                TELNET.TEC  - 'telnet' and direct TCP/IP  
  

We have a printed version available for you which can be purchased:

 
  
           BioCompanion   
           R. Doelz  
           BioComputing Essentials series   
           VMS, Basel: ISBN 3-905 434-00-8  
           UNIX, International: ISBN 3-905 434-02-4  
  
           Verlag Dr. Ing. U. Doelz         *NEW ADDRESS* Feb 1, 1996:  
           Hebelstrasse 82                                Cagliostrostr. 18  
           4056 Basel                                     4125 Riehen   
           Switzerland                                    Switzerland  
           FAX +41 61 263 0642                            FAX +41 61 XXX XXX  
  

You may not print the BioCompanion, entirely or in part, for commercial purposes, nor reprint and distribute it at your own expense other than adhering to the shareware status as described above. If you want to suggest changes and additions, you are most welcome to add your own STE files, or modify the JAMF files, and send these via electronic mail to BioComputing Basel if you want them included in future versions. We would like to encourage further packages and programs to be included, and certainly appreciate additions in theoretical or technical matters as well.

Acknowledgements

The author has prepared this document during nights and weekends while working at BioComputing Basel, which is supported by Basel University and grants from the Schweizerische Nationalfonds and the Bundesamt fuer Bildung und Wissenschaften. The effort of the publisher to assist in editorial work and the printing process is appreciated. Dr. Nicole Redaschi, working at BioComputing Basel, is acknowledged additionally for careful reading of the manuskript and helpful suggestions.