bionet.software.staden FAQ

Tim Littlejohn tim at megasun.BCH.UMontreal.CA
Wed Jun 21 17:14:42 EST 1995


bionet.software.staden Frequently Asked Questions (FAQ)
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               (last revised - 21-JUN-95)


Preface.  The Explanation Of The "FAQ"

A FAQ is a way to explain the topic of discussion (bionet.software.staden)
and help avoid repetitive posts about a specific sub-topic.  Before you post
a question about the Staden package, you should read this document to see
if your question has already been answered. 

If you have corrections, additions, suggestions, or comments, send them
to Tim Littlejohn at tim at bch.umontreal.ca 


 
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                             Table Of Contents
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1. What is the charter of this newsgroup?
2. Where can I find archives of previous postings to this newsgroup?
   (including the FAQ)
3. bionet.software.staden access.  How do I:
   a) subscribe to bionet.software.staden
   b) cancel my subscription to bionet.software.staden
   c) get help on the newsgroup
   d) post messages to the group
   e) reply to messages on the group
4. What is the Staden package?
5. Where do I get the Staden package from?
6. What tape formats are available?
7. Is it available by anonymous ftp?
8. What computer platforms does it run on?
9. How should I report problems I see with the package?
10. I'm running out of disk space. What can I do to make more room?
11. How do I contact the developers?
12. Where Can I find other information about the Staden package?
13. Credits

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            bionet.software.staden : Frequently Asked Questions
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             This Edition Overrides All Previous Editions 
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1. What is the charter of this newsgroup?

The newsgroup serves as a communication forum for users of the Staden
Package for molecular sequence analysis.  The package covers most sequence
analysis applications including DNA assembly, DNA analysis, protein sequence
analysis, sequence comparisons, library handling and searching. The assembly
program can handle input from ABI 373A, LI-COR, Pharmacia A.L.F. and Amersham
International BaseScanner instruments, plus digitizers. The package runs on
a large number of hardware/operating system platforms and is available for
a nominal fee.
 
The newsgroup has the following specific objectives:
                            
   1.  to serve as a communication medium for announcing modifications
       to the package;  

   2.  to be a "self help" group, where users with problems can gain from
       the experience of the rest of the user-community (and thereby reduce
       the pressures of the developers to provide support).  The newsgroup will
       provide a forum for answers to frequently asked questions concerning the
       package;

   3.  to exchange ideas and practical advice about getting the most from all
       components of the package, from sequence assembly through to analysis;

   4.  to promote the continued growth and enhancement of the package.

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2. Where can I find archives of previous postings to this newsgroup?

Previous postings can be found at the following URLs:

     gopher://megasun.bch.umontreal.ca:70/11/CMB/Staden
     gopher://gopher.bio.net:70/11/STADEN

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3. bionet.software.staden access. How do I:

========================================================
   a) subscribe to bionet.software.staden

Subscribing
-----------

IF YOU USE USENET NEWS: you need do nothing other than participate in
bionet.software.staden when it appears in your newsreader.  Depending
upon your news software, this may entail you having to answer a prompt
indicating that you want to subscribe.  You might also try the command
"g bionet.software.staden" in rn-like newsreaders.

IF YOU ARE LOCATED IN EUROPE, AFRICA, OR CENTRAL ASIA: please send the
word

help

in the body of your message to MXT at dl.ac.uk to retrieve general server
usage instructions.  To subscribe to the STADEN list, first
be sure that you are sending mail from the address at which you wish
to receive news postings, and then send
the command

SUB bionet-news.bionet.software.staden

to MXT at dl.ac.uk.  This message will be automatically read by the
computer and your e-mail address will be extracted from the mail
header and added to the list.


IF YOU ARE LOCATED IN THE AMERICAS OR THE PACIFIC RIM: log in to the
computer account in which you would like to receive mail (not an
account that you use infrequently) and send a mail message to the
Internet address

biosci-server at net.bio.net

Leave the Subject: line of the message blank and enter the following
line into the body of the mail message:

subscribe staden


This message will be automatically read by our computer and your
e-mail address will be extracted from the mail header and added to the
list.


========================================================
   b) cancel my subscription to bionet.software.staden

Canceling your subscription:
----------------------------

IF YOU ARE LOCATED IN EUROPE, AFRICA, OR CENTRAL ASIA: first be sure
that you are sending mail from the address at which you signed up to
receive news postings, and then send the command (in the body of your
mail message)

UNSUB bionet-news.bionet.software.staden

to MXT at dl.ac.uk.  This message will be automatically read by the
computer and your e-mail address will be extracted from the mail
header and removed from the list.

IF YOU ARE LOCATED IN THE AMERICAS OR THE PACIFIC RIM: send a message
to biosci-server at net.bio.net exactly as described above for
subscribing except include the text

unsubscribe staden

in the body of the message.  Please be sure to send the message from
the account whose address matches the one on the list.  If your
address differs, we will be notified automatically and will remove you
manually from the list if we can determine what was your old address.
Please contact biosci-help at net.bio.net if you have problems.


========================================================
   c) get help on the newsgroup

IF YOU HAVE A PROBLEM:
----------------------

Please send a message to one of the following addresses depending upon
your location

Address                              Location
-------                              --------
biosci at daresbury.ac.uk               Europe, Africa, and Central Asia
biosci-help at net.bio.net              Americas and the Pacific Rim

and someone on the staff will help you.  PLEASE DO NOT send mail to
our personal e-mail addresses as this will delay a response to your
request for help.


========================================================
   d) post messages to the group


How to post a message to the group:
-----------------------------------

If you use news, simply post a message into bionet.software.staden.
Be sure to set your "distribution" to world or else the message might
not leave your site!!

To post by e-mail, mail your message to one of the following addresses
depending upon your location:

Posting Address                      Location
---------------                      --------
staden at daresbury.ac.uk               Europe, Africa, and Central Asia
staden at net.bio.net                   Americas and the Pacific Rim

and your message will be distributed automatically to everyone on the
list and the USENET newsgroup.  There is no editorial intervention.

PLEASE DO NOT SEND SUBSCRIPTION REQUESTS TO THE POSTING ADDRESSES as
you will bother everyone on the newsgroup!!!

========================================================
   e) reply to messages on the group

How to reply to a message on the group:
---------------------------------------

If you are using a newsreader, simply use the reply or follow-up
command on your newsreader (these vary from program to program) to
send either private or public replies.

If you are using e-mail, replies to messages that you receive will
*NOT* be automatically returned to the group.  This is the standard
for Internet mailing lists as opposed to BITNET LISTSERVs which often
send all replies back to everyone.  You must be certain that your
reply contains either of the two newsgroup posting addresses above in
your message header if you want to share it with everyone on the
group.  Otherwise in most cases your reply may go back to only the
original poster of the message to which you are replying.

ALWAYS be certain that you examine the address on your messages before
you send them!!!  Once a message is sent there is no way to cancel it
or bring it back!!!  Some non-Internet compliant mail systems may
attempt to send replies to our error-trapping address called
BIOSCI-REQUEST.  If yours does this, please be sure to readdress your
message to staden at net.bio.net or staden at daresbury.ac.uk if you want
to send it to the newsgroup.

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4. What is the Staden package?

The Staden Package is a software package to perform most aspects of
sequence analysis. Including DNA assembly; DNA analysis; protein sequence
analysis; sequence comparisons; library handling and searching.

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5. Where do I get the Staden package from?
 
Further information can be obtained by sending an email message to:
 
            staden-package at mrc-lmb.cam.ac.uk
 
To order the package, send you name and address together with a request for
licence agreement forms to:
 
        Rodger Staden,
        MRC Laboratory of Molecular Biology,
        Hills Road,
        Cambridge,
        CB2 2QH,
        United Kingdom.

Payment (which for non-profit organisations is simply a small handling charge)
is made by sending a cheque to the MRC or by direct deposit to the following
account:

Bank of England
Threadneedlest St
London
England
A/C No 24070009 Code 10 0000

If you do this, send an email confirming the deposit to:

Mrs. Mona Pembrey
Administration
MRC Centre

E-mail mgp at mrc-lmb.cam.ac.uk

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6. What tape formats are available?

QIC-150 and Exabyte (2.5Gb)

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7. Is it available by anonymous ftp?

No.

The developers say:
"No, but we do sometimes make bug fixes available by anonymous ftp. For
serious bugs we will typically announce the presence of new binaries available
(by ftp) on this newsgroup. Fortunately this doesn't happen often."

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8. What computer platforms does it run on?

The binaries available are compiled under the following system and OS
combinations.

Sun SPARC (SunOS 4.1) eg SPARCstation IPX
Sun SPARC10 (solaris 2.4) eg SPARCstation 10/30
DEC MIPS (Ultrix 4.2A) eg DECSTATION 5000/240
DEC ALPHA (OSF/1 V3.0) eg DEC 3000/500
SGI R4000 (IRIX 4.0.5F) eg Indigo R4000
Alliant fx2800 (Concentrix 2800 2.2.00)

The binaries for a particular OS/machine are likely to work for other releases
of the same OS. However, some specifics though should be noted:

SunOS 4.1.x is the same as Solaris 1.x
SunOS 5.x is the same as Solaris 2.x
Irix 5.x is binary compatible with Irix 4.x (but maybe not vice versa)

When reading details from the licence agreement forms we assume "SunOS" refers
to SunOS 4 and "Solaris" refers to Solaris 2, unless detailed otherwise.

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9. How should I report problems I see with the package?

Send a message to:

	staden-package at mrc-lmb.cam.ac.uk

Stating:

   1) Where did the problem occur?

   2) Is the problem reproducable? If so what inputs were used? Is there
      any test data available for us to use in debugging?

   3) Was a core file produced? If so what do the following produce:
          echo where | dbx `which xgap` core
          echo where | gdb `which xgap` core

      Obviously the above are for an example of a crash with xgap. I list both
      dbx and gdb as one or the other may not be available.

      For many core files will not be produced when a segmentation fault or bus
      error occurs. To enable core files try "unlimit core" (csh and tcsh users)
      or "ulimit -c unlimited" (bash and maybe sh).

   4) Which version of the software do you have?
   
   5) Which machine architecture are you running under and which operating
      system are you using? (Eg a Sparcstation running SunOS 4.1.3)


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10. I'm running out of disk space. What can I do to make more room?

One trick is the "strip" the binary files.  This can be done by using
the strip commant under unix.  This will save you around 25 Meg of disk
space under the SunOS distribution, for example.

NOTE: "stripping" binaries removes their debugging information.  If you
strip your files, you will not be able to perform a full debugging report
for the Staden developers.

The procedure for stripping binaries is as follows:

cd $STADENROOT
(cd bin; strip *)
(cd seqlibs-bin; strip *)
(cd squirrel/bin; strip *)

If you're still running short of disk space then maybe certain areas of the
package could be removed. The developers advise against this generally and
feel that obtaining more disk space is preferable. If you're removing files
from the disk please make sure you have a good copy of everything on tape.
Tapes don't last for ever and this naturally applies to the original tape
sent to you.

Large file collections that maybe considered 'unnecessary' (this obviously
depends on your desired uses for the package) are:

testpackage		13 Meg; Serves as an example (especially with gap) of
				how to use the programs, but is not required
				by any programs.

tables/prosite		10 Meg; The prosite library.

src			 8 Meg; The source code. Nothing in this directory
				is required for simply running the programs.

doc/manual.*		 6 Meg; A PostScript and RTF form of the manual. A
				very useful item, but not needed if you've
				already printed it or if you use the version
				on the Macintosh disk.

bin/???				Many of the binaries are large. The total
				size of the bin directories is typically around
				about 50 megs (77 for DEC Alpha systems). We
				advise against removing binaries though. Many
				programs are used in scripts (eg pregap) so it
				is not immediately obvious which are required.

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11. How do I contact the developers?

For problems/bug reports:

            staden-package at mrc-lmb.cam.ac.uk

For feature changes/additions:

            staden-package-wishlist at mrc-lmb.cam.ac.uk

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12. Where Can I find other information about the Staden package?

Further information about the package can be obtained from the following
URLs:

     gopher://megasun.bch.umontreal.ca:70/11/CMB/Staden

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13. Credits

This FAQ was written by Tim Littlejohn (tim at bch.umontreal.ca). Contributions
kindly made by James Bonfield (jkb at mrc-lmb.cam.ac.uk).

-- 
==============================================================================
Tim Littlejohn

E-mail:     tim at bch.umontreal.ca  

Snail Mail: Departement de biochimie        Phone: (514) 343-6111, x5149
            Universite de Montreal          Fax:   (514) 343-2210 
            C.P. 6128, Centre-ville
            Montreal (Quebec), H3C 3J7
            CANADA
==============================================================================



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