PREFACE ******* Intended Audience ***************** This BioCompanion (ISBN 3-905434-00-8) is intended to serve as an introduction for the new or casual user of computers in molecular biology. 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 sevaral 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 Metafile" (JAM) . 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. How to Use This Guide ********************* Conventions =========== This Guide uses the convention to have a generic example command printed like this: % logout Whereas specific examples are printed like % ls -lsat The executable commands are printed in special font as well, such as % setplot These commands can be executed directly by typing the corresponding command. HTML Format =========== JAM 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 SURVIVAL.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 SURVIVAL.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 most liked 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 a big file but this will hinder indexing afterwards. In any case, add line numbers at the bottom of the page (JAM 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 JAM 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. Copyright ********* This document is Shareware , copyrighted by BioComputing Basel. 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 using the ftp program using the ftp server bioftp.unibas.ch and the survival subdirectory. For details on use of the anonymous ftp , read the BioCompanion section on ftp , and use anonymous as user name, and your electronic mail address as password. Available versions include o Rich Text Format (RTF) for Word Processors o LaTEX typesetting format o HTML pages [NOTE INSERTED: THE SERVER HAS CEASED TO EXIST.] If you view these pages on the WWW browser system electronically, please understand that frequent use on a routine basis to sites outside of Switzerland is not serving the purpose as JAM allows local configuration and installment 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 centers, etc. If you have access to the international internet as academic site, it is possible to download the document electronically via anonymous ftp from the serevr bioftp.unibas.ch. Available versions include o Rich Text Format (RTF) for Word Processors o LaTEX typesetting format o HTML pages o JAM source code Due to its unique format, the JAM source code will allow smooth and easy adaption to your environment. You can either select to produce a site-neutral or a site-specific version, where the latter implies that you modify the corresponding passages in the .STE JAM files. Site adaption ============= 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-specificically: JAM 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 ------------+---------------+--------------------------------------------- | 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 If you want to use the WWW browser system to provide access to the BioCompanion, please understand that you should not just put a link in your page which points to the Basel version of the BioCompanion. Frequent use on a routine basis to sites outside of Switzerland is not serving the purpose as JAM allows smooth and easy modification. Services are provided to aid you installing the BioCompanion at your site (details from the publisher as noted below). If you use the BioCompanion regularly, or the JAM code in order to print it as document for your site, you are encouraged to send a reasonable support to BioComputing Basel (details are available from the publisher as noted below - $300 is the price which will be asked for). Printed version =============== We have a printed version available for you which can be purchased: BioCompanion R. Doelz Biocomputing Essentials series ISBN 3-905 434-00-8 Verlag Dr. Ing. U. Doelz Hebelstrasse 82 4056 Basel Switzerland FAX +41 61 263 0642 [NOTE ADDED: THE CURRENT BIOCOMPANION IS AVAILABLE FROM THE SAME ORGANIZATION. NEW ADDRESS IS AVAILABLE FROM WWW.DOELZ.COM] The price covers handling, printing costs and surface mail. o Switzerland: SFr. 40 o EU member states: ECU 40 o International: $60 If you prefer, you might also get the JAM application and the JAM source code for personal use. The publisher will assist you in preparing own versions for your site, please inquire for details. Conditions of use ================== 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 above. If you want to suggest changes and additions, you are most welcome to add your own STE files, or modify the JAM 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 **************** BioComputing Basel is supported by Basel University and grants from the Schweizerische Nationalfonds and the Bundesamt fuer Bildung und Wissenschaften. We appreciate the effort of the publisher to assist in editorial work and the printing process. JAM produced file: PREFACE1.HTML as [next page] , or [overview] , or [table of contents]