This UNIX version is called 3.2.7, created in November, 1996. GCG9 features are active. Seqlab is emphasized.
This BioCompanion copy is the GCG CD copyrighted version .
The "BioCompanion" is intended to serve as an introduction for the new or casual user of computers in molecular biology who needs to apply sequence analysis programs. ISBN numbers are assigned initially to the 3.1 versions of Basel-specific version for VMS systems (ISBN 3-905434-00-8) and the site-neutral (international) version for UNIX systems (ISBN 3-905434-02-4). The version used to prepare this document is based on the initial 3.1 version but has been significantly enhanced to include the version 9 of the GCG package, as well as other software components. The document version which you are currently viewing has been defined to include this information. A major addition to the 3.2 version of the BioComputing concerns the EGCG package, which is now fully integrated into the methods description.
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 source focuses mostly on the GCG software (Genetics Computer Group, (1991), Program Manual for the GCG Package, Version 9, December 1996, 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 NCBI in Washington, R.Staden's package, W.Pearson's FASTA package, the MPsrch software from IntelliGenetics, Inc. and the SRS software from T.Etzold, EMBL.
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. The
version you are currently viewing is a UNIX-specific version. VMS documentation can be accomplished
easily with a single switch on the JAMF processing.
This BioCompanion copy is the GCG CD copyrighted version
.
Specifically configured for this version was the operating system dependency of no VMS . Technical
issues in this configuration were no PCIPONLY (techniques only for PC in standard IP environment),
LAN (Appendix section on the LAN technology), no DECNET , no RCP (remote copy in UNIX trusted
environments) and no EMAIL (explicit explanations of electronic Mail tools).
Biological packages included features of no ATLAS , no EGCG , no ENTREZ , no ENTREZC (client)
, no ENTREZWWW (WWW) , no PEARSON , no READSEQ , no SRS , no SRSCURS (SRS via curses) , no SRSWWW
(SRS via WWW) , no STADEN , no BIRNEY (WiseTools), GCG9 (GCG version 9 features) and no NOWPI
(emphasis on command line mode). The annotation of sequences described only for Seqed from GCG
(no SEQUIN). Sequin (PC/Mac based tool) is not explicitly mentioned. The management of plasmids
is described only for tools from GCG (no CLONE4). The detection of primers is described only
for tools from GCG (no PRIMED). No FastAlert or similar tool is explained. (no FASTALERT).
The version you are currently viewing has been configured to work with the GCG package as provided
on the CD-ROM distribution of GCG in the 'unsupported' section. No specific documentation of
the JAMF production system has been included into this document. The BioCompanion has been described
in the literature to be produced with the JAMF system. The JAMF software is no longer available
in source code on public file servers since version 3.2 of the software.
Reference:
Doelz, R. Optimal production of biological documentation: the JAM format. Comput-Appl-Biosci(1995)
11, 224-226.
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