Section 1-3: Copyright

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

If you have access to the public Internet, you are allowed to view the electronic document for private use free of charge.

If you view these pages on the WWW browser frequently, please understand that frequent use by many sites 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 - refer to the information from the publisher for details.

Floppy disk versions (DOS 1.44M) are available from the publisher on request. Supported formats include LATEX, HTML and RTF versions.

Access is provided for local installation on the shareware basis as mentioned; you are requested to register as institutional user. 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 by sites outside of Switzerland is not serving the purpose as the JAMF program 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 JAMF code in order to print it as document for your site, you are encouraged to send a reasonable support to the publisher (details are available from the publisher as noted below; $ 300 is the price which will be asked for a site permission using JAMF files).

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 not overwhelming. 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       
  
           Cagliostrostr. 18
  
           4125 Riehen 
  
           Switzerland                     
  
           FAX +41 61 6419012
  

If you prefer, you might also get the JAMF application and the JAMF source code for personal use. The publisher will assist you in preparing own versions for your site, please inquire for details. Electronic versions are available as well on floppy disks.

Printed Version, Conditions of Use

You may not print the BioCompanion, entirely or in part, for commercial purposes. You may not 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. Please refer to the publisher address above for details if you want to submit material.