From owner-acedb@hgmp.mrc.ac.uk  Sat Jan  1 15:39:51 2000
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From: qsaklasyclwyktqx@hotbot.com
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Subject: Extra $5000 - $10,000/Month Forever                                                   ijdww
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MELISSA

---


From owner-acedb@hgmp.mrc.ac.uk  Mon Jan  3 21:10:41 2000
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To be removed from future mailings:
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(or copy and paste in your browser:  http://63.87.81.221/mtg_lead.html?716  ).
Go to the bottom of the page. Enter ALL addresses you wish removed and send.
Thank You!
		


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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

<html>
<head>
<title>Ad Mtg Blues</title>
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<tr>
<td width=3D"500" align=3D"left" bgcolor=3D"#000064">
<font size=3D"+1" color=3D"#EAF0F4" face=3D"Arial">
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its after the holidays do you feel <font color=3D"Blue">blue</font>?</font>
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<tr>
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<font size=3D"+1" color=3D"#EAF0F4" face=3D"Arial">
If you own a Home, we can help take the blues away. 
Do you want to consolidate all those holiday bills, do some remodeling or 
take a much needed winter vacation?
</font>
<br><br>
<font size=3D"+2"><b><font color=3D"#FFFF80"><A HREF=3D"http://63.87.81.
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</td>
</tr>
<tr>
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<font size=3D"1" color=3D"#EAF0F4" face=3D"Arial">To be removed from future 
mailings <A HREF=3D"http://63.87.81.221/mtg_lead.html?716">click here.</A><br>
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Thank You!</font>
</td>
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</table>
</body>
</html>

------=_NextPart_53661060315303425265422205633--

---


From owner-acedb@hgmp.mrc.ac.uk  Tue Jan  4 08:17:05 2000
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From owner-acedb@hgmp.mrc.ac.uk  Tue Jan  4 09:32:30 2000
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From owner-acedb@hgmp.mrc.ac.uk  Fri Jan  7 10:57:30 2000
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From: puze91@cs.uwindsor.ca (jmnsie)
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Subject: -Tons of books : Free-
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THOUSANDS OF FREE BOOKS TO DOWNLOAD.

OUT OF THE THOUSANDS OF FREE BOOKS ON THE WEB THERE
IS NOT ONE THAT WILL HOLD YOUR ATTENTION LIKE THIS ONE!

THE IMMORTAL   By   J. J. Dewey

For this and links to thousands of other free books do not hit return
but send reply to: junny45@bigfoot.com  type   IMMORTAL  in the
subject area.

The Immortal is the story of an average truth seeker who stumbles
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The first question addressed in Book I is WHO OR WHAT AM I?  The
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http://www.am
---


From owner-acedb@hgmp.mrc.ac.uk  Fri Jan  7 13:11:18 2000
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From: "Tim Corp." <station@nursat.kz>
X-Newsgroups: bionet.software.acedb
Subject: Pro AVP anti-virus packet for Win95/98/NT
Date: Fri, 7 Jan 2000 18:41:40 +0600
Organization: Tim Corp.
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E-mail: station@nursat.kz




From owner-acedb@hgmp.mrc.ac.uk  Sat Jan  8 05:00:22 2000
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From: schwartz@uclink4.berkeley.edu
X-Newsgroups: bionet.software.acedb
Subject: Solaris 7 window manager bug
Date: Sat, 08 Jan 2000 04:53:27 GMT
Organization: Deja.com - Before you buy.
Lines: 16
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Hi All,

Thanks to everyone that helped me.  I had an awful bug running ACeDB
4.7el&m with the latest release of Solaris 7(November).  ACeDB froze and
commandeered the screen almost immediately.  It had worked with the
older releases of Solaris 7.

I just tried the newest 4.8 Solaris binary I retrieved from Sanger and
it works fine.

Jody



Sent via Deja.com http://www.deja.com/
Before you buy.


From owner-acedb@hgmp.mrc.ac.uk  Sun Jan  9 19:33:38 2000
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From: gnhotels16@flashmail.com ("MS SUNITA MATHUR")
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Subject: ENJOY YOUR STAY IN DELHI & SHIMLA
Date: 9 Jan 2000 19:33:34 -0000
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---


From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 10 17:50:58 2000
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From owner-acedb@hgmp.mrc.ac.uk  Tue Jan 11 10:04:44 2000
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Hi all,

I am trying to set up AceDB, through webace, for people in my lab.

I am experiencing problems setting up the aceserver through inetd. Hope
someone can help me!

Things that work:
Acedb (4_7I) is running OK locally
Following the help file "running the aceserver", I've made a link to
aceserver (rpc.acedb), 
edited /etc/rpc (added a line "acedb     20000114  "), 
as well as /etc/services (added a line "acedb    20000114/tcp") 
and /etc/inetd.conf ("acedb/1 stream rpc/tcp wait user.group
/usr/local/bin/ rpc.acedbd /home/Database/acedb/ 20000114 1200:1200:0") 

I have restarted inetd (kill -HUP PID# ; I also tried a complete reboot)

I can start aceserver by issuing the command: "aceserver
/home/Database/acedb 20000114", and then the aceclient by typing
"aceclient ip_address -port 20000114 -time_out 60"

Things that don't work:
I cannot start the aceserver by starting the aceclient (without starting
the acesever manualyy).
I get the message:
//! cannot establish connection
//! usage: aceclient host [-port number] [-time_out secs] [-access_info]
[-ace_out] [-ace_in] [-f reportfile parameters]  

I'd appreciate clues on how to resolve these problems. I should add that
I am not used to UNIX (I have been running my Linux box for a few months
only), so the solution might be trivial for a UNIX expert; however,
reading inetd man pages did not help me much.

Sincerely,

François

--
**********************************************************
François Coulier,
"Laboratoire d'Oncologie Moléculaire" et "Atelier de 
Bioinformatique et d'Imagerie",
INSERM Unité 119, 27 bd Leï Roure, 13009 Marseille, France 
Tel: 33 (0) 4 91 75 84 11       Fax: 33 (0) 4 91 26 03 64
mél: coulier@marseille.inserm.fr
Site ouaibe: http://olan.marseille.inserm.fr/
**********************************************************


From owner-acedb@hgmp.mrc.ac.uk  Tue Jan 11 12:19:21 2000
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From: edgrif@sanger.ac.uk (Ed Griffiths)
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Francois,

your entries for /etc/rpc and /etc/services look OK, your entry for
/etc/inetd.conf if not OK.....the underlined bits are wrong...


"acedb/1 stream rpc/tcp wait user.group
                             ----------
/usr/local/bin/ rpc.acedbd /home/Database/acedb/ 20000114 1200:1200:0"
---------------         


user.group  This should be the name of the userid used to start the server,
----------  e.g. if you wanted the server started with your permissions then
            you should put your userid here instead of user.group


/usr/local/bin/  This should be the _fullpath_ to the server executable, so if
---------------  you have put rpc.acedbd in /usr/local/bin, then this field
                 should be /usr/local/bin/rpc.acedbd. Otherwise inetd will not
                 find the executable.

Try making these changes, if that still doesn't work then let me know.

cheers Ed

 ------------------------------------------------------------------------------
| Ed Griffiths, Informatics Group,                                             |
|               The Sanger Centre, Wellcome Trust Genome Campus,               |
|               Hinxton, Cambridge CB10 1SA, UK                                |
|                                                                              |
| email: edgrif@sanger.ac.uk      URL: http://www.sanger.ac.uk/Users/edgrif    |
|   Tel: +44-1223-494780 (switch  +44 1223 834244) Fax: +44 1223 494919        |
 ------------------------------------------------------------------------------

---


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From: adraorg5@thekeyboard.com ("DR. BAZLIEL")
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---


From owner-acedb@hgmp.mrc.ac.uk  Wed Jan 12 19:02:26 2000
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---


From owner-acedb@hgmp.mrc.ac.uk  Thu Jan 13 12:20:52 2000
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From: zgudmunt@my-deja.com
X-Newsgroups: bionet.software.acedb
Subject: AcePerl coding
Date: Thu, 13 Jan 2000 12:07:06 GMT
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   To AcePerlers (L. Stein?): I have been trying to set up some
webinterfaces to an Aceserver. It's really a basic data update homepage.
I've managed to step through the process from a perl script, but I am
having trouble handling write blocks. Is there any way for me to
establish a lock on a dbase-object, or at least find out beforehand if
somebody has a lock on? That way I can decide if the update should take
place immediately, or be put in temporary files in an update directory.


                         Gudmundur


Sent via Deja.com http://www.deja.com/
Before you buy.


From owner-acedb@hgmp.mrc.ac.uk  Thu Jan 13 23:00:03 2000
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From: mieg@ncbi.nlm.nih.gov (Jean Thierry-Mieg)
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Subject: Re: AcePerl coding
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nthere is no object locking in the system
but you just update automaytically just the fields yoe
edit

whereas the other client may edit other fields at the same time


---


From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 17 11:36:36 2000
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From: cepoi8@webdev.it (sam)
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Subject: Private Offshore Club pays you by the Minute!.
Date: 17 Jan 2000 11:36:28 -0000
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Hi, 

I just want you to take a quick look at this TRULY
PHENOMENAL one-of-a-kind, PRIVATE OFFSHORE Wealth 
Building Program. 

It's a PRIVATE By-Invitation-Only OFFSHORE CLUB, 
where many of us are earning $500 to $3,500 per DAY! 

We get paid BY-THE-MINUTE directly into our Private 
Offshore Bank Accounts - 24 hrs a day, 7 days a week 
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money here. You'll want to further investigate this 
opportunity. 

People are JOINING US FAST and you earn $500 EACH. 
And that's just from ONE Income Stream - there are 
3 MORE! Many are making $80,000 to $100,000 in just 
10 to 12 weeks. Yes - it is REALLY TRUE! 

Some people are already making 5 figures PER WEEK 
from ONE of the other Income Streams that requires
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program works for everyone. Sales ability is not 
required. 


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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 

SEND an email to  catcg39@eastmail.com

And write "PRIVATE OFFSHORE INFO" in the Subject. 

Please DO NOT just HIT the REPLY button to this email.
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

-------------------------------------------------------
If you DON'T want to receive any email we will honor
that. Send an email to  rem90_1999@yahoo.com
-------------------------------------------------------


28612629537542861817
2'
---


From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 17 15:56:15 2000
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From: Mark Wilkinson <markw@cheerful.com>
X-Newsgroups: bionet.software.acedb
Subject: Going from EMBL annotations to ACE - sequence objects...
Date: Mon, 17 Jan 2000 16:20:22 +0100
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Dear Ace'ers,

My 'community' is in the habit of submitting to EMBL just the genomic
sequence of a given gene, nicely annotated with introns and exons and
such.... but not always submitting the corresponding cDNA sequence.

had presumed that you would be able to simply tell ACE which parts of
the genomic sequence object corresponded to exons and which corresponded
to introns (in much the same way as it is able to assign other EMBL
features to regions) but this doesn't appear to be the case.

I want to generate these "pretty pictures" where the exon/intron
structure is overlayed on the sequence, but it appears that this can
only be done when the db contains both the genomic *and* the cDNA
sequence objects, and strangely this information is contained in the
cDNA sequence object rather than the genomic sequence object!  This
seems counter-intuitive to me... intron/exon information is in genomic
DNA not in cDNA!!

Can someone explain the logic to me? and isn't it a bit redundant to
have both sequence objects when a genomic with annotations does the same
thing?

Cheers all!
Mark




From owner-acedb@hgmp.mrc.ac.uk  Tue Jan 18 21:12:09 2000
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From: jfousry784549@abak.com
X-Newsgroups: bionet.software.acedb
Subject: Offshore Wealth!
Date: 18 Jan 2000 21:12:04 -0000
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  Hi, 

· I just want you to take a quick look at this PHENOMENAL, One of 
a kind, 100% legal - PRIVATE OFFSHORE Wealth Building Program. 
· It's a PRIVATE BY-INVITATION-ONLY CLUB, where many of us 
are easily earning $500 to $3,500 per DAY! 

· We get paid BY-THE-MINUTE direct to our own Private Offshore 
Class A Bank Accounts, 24 hours a day - 7 Days a week AS PEOPLE 
JOIN! We are talking about some serious money here. You will want 
to further investigate this opportunity. 

· They're JOINING US FAST and you earn $500 EACH... that's just 
from ONE Income Stream... and there are 3 MORE! Many are making 
$80,000 to $100,000 in just 10 to 12 weeks. Yes - it is REALLY TRUE! 

· Some people are already making 5 figures PER WEEK from just ONE 
of the other INCOME STREAMS which requires NO SPONSORING! 
That's right, this program works for everyone.....

Sales ability is not required. 
ARE YOU INTERESTED IN LEARNING MORE ...... 
· If you like what you have seen so far, and want to learn about real 
people who are making more money than they have ever made before.

I'll send instructions to my site with 2 amazing Real Audio messages! 
· You can listen for free over your computer, it will blow you away. 
· This program works better and faster than any I've been in and it's 
working for those who have been unsuccessful at other programs. 
You join just once, but the cash keeps rolling in! 

I love this program :-) 

GOOD NEWS FOR INTERNATIONAL INVESTORS .... 
This amazing OFFSHORE private wealth building program works for 
people living in EVERY country in the WORLD .... 
USA, Australia, Canada, Japan, Mexico, South America, England, 
Norway, Italy, Germany, France, and more.... 
(Exponential growth - 78 countries in 14 weeks) 

THIS IS A PRIVATE BY-INVITATION-ONLY CLUB .... 
· As a member of this exclusive Private Offshore Investment Club, 
you receive your own legal Private Offshore Class A Bank Account.
PLUS daily direct deposits in US dollars into your Private offshore 
bank account. 

· You'll also receive your own Private International Debit Card that 
you can use to withdraw your cash from bank machines all around 
the world... with no daily limit. 

· Plus, your own Private Encrypted Banking Software Program to 
manage your Private Offshore Bank Account from anywhere in the 
world and your own ........

Secure Private Encrypted Email Account, all from your PC. 

· Access to the MEMBERS ONLY "on-line" listings of the latest 
amazingly profitable, carefully guarded international investment 
opportunities. (13 Cream of the Crop High Yield) 

· Members can also avail themselves to a number of International 
Services at special prices reserved for members only - i.e. Offshore
Trusts, (IBC's) International Business Companies, Offshore 
Corporations and many other financial vehicles, at steep discounts. 

· All international service providers have been screened for track
records and investigated by this PRIVATE CLUB for the protection 
of it's members. 
With the advent of the Internet - Offshore Banking, Offshore Trusts 
and International wealth building opportunities have now become 
accessible and affordable for just about anyone in the world today. 

· Offshore banking and Offshore Trusts were once reserved only for
the super rich and large corporations to protect their assets. But now 
the playing field has been leveled, and those same financial tools
are now available to the rest of us thanks to the Internet. You can
now control your financial destiny and assets with absolute privacy. 

· This is a 100% legitimate and legal business opportunity and it will
make you more money than you've ever made in your life. Just as it 
has for us - and many other happy and successful Club Members. 
Some ambitious Members of this Private Club have retired in just 
120 days. 

· No kidding - this is for real. Don't you ever wonder how the rich 
became rich and stayed rich? Wouldn't you like to discover how to
do the same for yourself? You are about to find out.

TO LEARN HOW YOU CAN BECOME A MEMBER ....
AND DISCOVER HOW YOU CAN ALSO RECEIVE ....
ALL OF THESE FINANCIAL BENEFITS NOW....
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
For My Website With Audio
Just send an email to:
sales2000@telekbird.com.cn?subject=SendCLUBinfo 

or for AOL <a href="mailto:sales2000@telekbird.com.cn?subject=sendClubinfo">
Click Here!</a> 

============================================================ 

NOTE: You have received this email because you have either
sent us your offer or requested information from us in the
past thereby adding yourself on our in-house mailing list.
We do not sell our list to anyone.
__________________________________________________ 
Simple Removal instructions:
To be removed from our in-house list simply click here...
mailto:results2000@telekbird.com.cn?subject=remove or
send blank email to results2000@telekbird.com.cn with 
" Remove " in the *SUBJECT* field... 
Or hit reply with "REMOVE" in the *SUBJECT* field.
___________________________________________ 



---


From owner-acedb@hgmp.mrc.ac.uk  Tue Jan 18 22:55:40 2000
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From: "ariel catane" <ariel2@multiqtl.com>
X-Newsgroups: bionet.software.acedb
Subject: MultiQTL - The best genetic QTL mapping software - FREE
Date: Wed, 19 Jan 2000 00:38:58 +0200
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MultiQTL - The best QTL mapping software!


Dear Colleague,

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From owner-acedb@hgmp.mrc.ac.uk  Wed Jan 19 11:03:36 2000
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From: dsmith@ucsd.edu (Doug Smith)
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Subject: Subclass problem
Date: 19 Jan 2000 11:03:30 -0000
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I am having a bizarre problem with Subclasses.

First:
I have 2 subclasses of class ?Sequence:  Dicty_cDB_Seq and Other_Sequence
These are declared in subclasses.wrm as follows:

Class Dicty_cDB_Seq
Visible
Is_a_subclass_of Sequence
Filter Dicty_cDB

Class Other_Sequence
Visible
Is_a_subclass_of Sequence
Filter "NOT Dicty_cDB"

Sequences either have tag Dicty_cDB or not


Second:
I have 3 subclasses of class ?Clone:  YAC_Clone, Dicty_cDB_Clone, Other_Clone
These are declared in subclasses.wrm as follows:

Class YAC_Clone
Visible
Is_a_subclass_of Clone
Filter YAC

Class Dicty_cDB_Clone
Visible
Is_a_subclass_of Clone
Filter Dicty_cDB

Class Other_Clone
Visible
Is_a_subclass_of Clone
Filter "NOT Dicty_cDB, NOT YAC"

Clone items have either tag YAC or tag Dicty_cDB or neither tag


THE PROBLEM:
Initializing a database indexes the Sequence subclasses properly BUT DOES NOT
appear to index the Clone subclasses  !?!

So for Class: Dicty_cDB_Seq , the tags are as follows:

Belongs_to_class   41
Is_a_subclass_of   Sequence
Visibility  Visible
Mask  2
Filter  Dicty_cDB
Index  -----> 24  (these 24 jibe with the ?Sequence class)


BUT FOR Class Dicty_cDB_Clone, the ONLY tags are as follows:

Is_a_subclass_of  Clone
Visibility  Visible
Filter  Dicty_cDB


The effect is that the Clone Subclass objects are not listed in the Main
Keyset
when selected from the Main Window ... they are listed only when Class Clone is
selected ...

The frustrating thing is that I can see no difference between what I am doing
with the Sequence subclasses and the Clone subclasses ...

Thanks very much for any suggestions ...
  -Doug


PS  What I have works fine with MacAce but not with xace ...




---


From owner-acedb@hgmp.mrc.ac.uk  Wed Jan 19 16:20:46 2000
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From: crepinau@sb-roscoff.fr (crepinau)
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    Hello ACEDB users.

It seems everybody is going on the net :-)

And as usual, I am a bit confused. In a message dated from 15 jul 1999,
D and J Thierry-Mieg stated that :
"
AcePerl is a great success and the webace code of Bigwood et al,
(thanks Doug for this excellent work that we did use for deveral
years), has now been superseeded on several sites, including
www.sanger, by aceperl, although, and this is very confusing, aceperl
was renamed webace on the sanger site.

Webace is the code of 95 by Bigwood et al,
Aceperl is the code of 98 by Stein et al,
"

so apparently aceperl (from L Stein) is the same as webace from the
Sanger.

However from the Stein web pages I got this image :

ACEDB ::::> AcePerl ::::> AceBrowser

and Acebrowser is intended to supplement the full-featured WebAce system
that is maintained on the Sanger Centre.

And from the webace page at Sanger I got this image :

ACEDB ::::> gifaceserver ::::> aceclient ::::> webace

Finally from the sanger center homepage I got this :


               Acedb databases can be accessed via the Web, using the
Webace interface, which serves a
               number of human databases, or the AceBrowser system,
which serves a local installation of the
               C. elegans Genome Database .

So which one is which? Are they equivalent? Is one dependent on the
other?

Thank you in advance.

By the way, while browsing I found this How To page :

http://stein.cshl.org/AcePerl/docs/ACE_SERVER_TRAPS.HOWTO.html

Has anybody ever written a real trouble shouting guide to ACEDB ?

Sincerely your's

Florent

---


From owner-acedb@hgmp.mrc.ac.uk  Wed Jan 19 16:49:00 2000
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From: rd@sanger.ac.uk (Richard Durbin)
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Webace and AceBrowser are not the same.

AceBrowser is the more modern system, it is being actively maintained
and developed, and the official position of the acedb developers is
that you should use it.  AceBrowser comes from Lincoln Stein, and is
built on AcePerl also from Lincoln.

The Webace at the Sanger Centre was the work of Tim Hubbard, building
very heavily on the earlier webace work of Doug Bigwood and colleagues
at NAL, who in turn built on work of Guy Decoux.

Both AceBrowser/AcePerl and Webace use the gifaceserver and aceclient
code from the core acedb package.

The reason that the webace pages continue to exist at the Sanger
Centre, and that we still have servers running from it, is that webace
has features not present in AceBrowser that particular people are not
prepared to give up.

I apologise about not making this clear on the acedb home page here.
I have changed the text to now read:

> Acedb databases can be accessed via the Web, using the AceBrowser
> system, which serves a local installation of the C. elegans Genome
> Database . There is also an older web implementation, Webace, which is
> now deprecated, but continues to serve a number of human databases.

Richard
---


From owner-acedb@hgmp.mrc.ac.uk  Thu Jan 20 08:44:11 2000
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From: sey36@spoe.at (sandra)
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Subject: Private Offshore Club Pays You by the Minute
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q
---


From owner-acedb@hgmp.mrc.ac.uk  Thu Jan 20 12:56:35 2000
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From: alltherightstuff@crescotek.com
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From owner-acedb@hgmp.mrc.ac.uk  Fri Jan 21 12:50:29 2000
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From: zgudmunt@my-deja.com
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   You say that there is no locking in the system...does that apply to
the process when AcePerl uses its own internal code to communicate with
a server? I am using a local server -> AcePerl uses tace to talk to the
dbase. Is the locking mechanism (the lock file) active then?
  My situation is the following: I have a few data upload homepages on
an intranet which are working fine throug AcePerl and local dbase
connection. But my concern is when someone is using Xace to browse and
perhaps update the data -> AcePerl is locked out. Can I go around this
problem by making AcePerl contacting the server -> no locking? Won't
that slow the procedure way down?

  How about disabling the locking system altogether? Is it possible to
rely on the OS (Linux 6 in my case) as to not allowing file corruption?
My users are more or less only modifying their own stuff, so folks
changing things at the same time should be very unlikely.


                      Mummi



In article <200001132259.RAA13569@ncbi.nlm.nih.gov>,
  mieg@ncbi.nlm.nih.gov (Jean Thierry-Mieg) wrote:
> nthere is no object locking in the system
> but you just update automaytically just the fields yoe
> edit
>
> whereas the other client may edit other fields at the same time
>
> ---
>


Sent via Deja.com http://www.deja.com/
Before you buy.


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if you disabled acedb locking (global) you are garanteed
to get complete database corruption evry soon

if you want to update via aceperl and look graphically via 
xace, just arrange unix authorisation so that only aceperl is allowed to write

if you want to update via aceperl and graphically use a graphc client
 xaceclient

---


From owner-acedb@hgmp.mrc.ac.uk  Fri Jan 21 23:38:23 2000
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---


From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 24 03:44:20 2000
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From: newyou22@conexiong.com.mx
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Subject: Just released...the "updated" Seven Steps to the "New" You program
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---


From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 24 06:01:58 2000
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From: dsmith@ucsd.edu (Doug Smith)
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Subject: Text in Graphics Sequence display - 2
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Hi all,

I am still having troubles with Text display in the Sequence Graphics display.

Hamis McWilliam suggested I do the following:

>I found the following worked for me (thanks to R. Durbin for this one).
>
>Update ?Method in models.wrm:
>
>?Method Remark ?Text
>        Display Colour  #Colour
>                Frame_sensitive
>                Strand_sensitive  Show_up_strand  #Colour
>                Score   Score_by_offset
>                        Score_by_width
>                        Score_bounds  UNIQUE  Float  UNIQUE  Float
>                        Percent
>                Overlap_mode UNIQUE     Overlap
>                                        Bumpable
>                                        Cluster
>                Width  UNIQUE  Float
>                Symbol  UNIQUE  Text
>                Right_priority  UNIQUE  Float
>                Max_mag UNIQUE Float
>                Min_mag UNIQUE Float
>                Show_text
>        Blastn
>
>Show_text is the important bit here (see ACEDB 4.7 models.wrm).
>
>Also add the following to ?Sequence
>
>          Method UNIQUE ?Method
>
>Now define a Method object which makes the Visible stuff display, e.g.
>
>Method : Default_Sequence
>Remark "A default display method for sequences."
>Display Show_Text
>
>Now add this method to all your sequences object that you want to have
>text annotation.
>
>I hope this helps. Hamish.
>


I did this ... and it works ... but, for me, only in part, to wit:

1. only the Visible information from the *.cds Subsequence objects is
displayed !?!
2. Visible information from other Subsequence objects and from the Sequence
object
   itself is not displayed.

Second, this displayed text information appears to be of a 'Text Features' type
... that is, it is removed from the Seq Graphics display when one toggles the
'Text Features' in 'Columns'

Perhaps the additional text information should be displayed in the column
called 'Brief Identifications' ??
I have not been able to get this column to display anything ...
If this is what I should be using, how does one use it?
Does it involve an additional Method to the 'Show_Text' method above?
If so, what is the Method?

I appreciate any comments here ...
Thanks
  -Doug






---


From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 24 11:27:09 2000
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From: j.mcinerney@nhm.ac.uk (James McInerney)
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Dear all,

Firstly, apologies for cross-posting.

Secondly, This is an announcement and call for applications for the
second Annual NUIM International Bioinformatics Summer School. 
Following on from the success of last years school, we are pleased to
announce a week-long intensive course.

More information and an application form can be found at:

http://www.may.ie/academic/biology/jmbioinformatics.shtml

and follow the link to "Summer School 2000"

If you want additional information you can email:

mailto:james.o.mcinerney@may.ie?subject=Summer School 2000

or

mailto:bioinformatics@ireland.com


Kindest regards,


James


-- 
             Dr. James O. McInerney,
Dept. Biology,                       Dept. Zoology,
Natl. Univ. Ireland,                 The Natural History Museum,
Maynooth,                  and       Cromwell road,
Co. Kildare, Ireland                 London SW7 5BD, UK.
Phone +353 1 708 3860                +44 171 938 9163
Fax   +353 1 708 3845                +44 171 938 9158
email james.o.mcinerney@may.ie       j.mcinerney@nhm.ac.uk
http://www.may.ie/academic/biology/jmbioinformatics.shtml
---


From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 24 12:00:28 2000
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   Thanks alot, Jean-T. I´ll try the xaceclient. Does the xaceclient
work in the same way as the AcePerl, only aquiring the lock when it
really is writing?
   The problem may actually be solved in the way you propose, by
forbidding xace-editing for most users. I will have a backup for my
WWW-update CGI-scripts so that if a write lock is encountered (should be
rare) the data is written to acefile and updated via tace-cronjob update
script.

            Has anybody tried a setup similar to the one I have been
describing?


                           Mummi


In article <200001211705.MAA17557@aires.nlm.nih.gov>,
  mieg@aires.nlm.nih.gov (Jean Thierre-Mieg) wrote:
> if you disabled acedb locking (global) you are garanteed
> to get complete database corruption evry soon
>
> if you want to update via aceperl and look graphically via
> xace, just arrange unix authorisation so that only aceperl is allowed
to write
>
> if you want to update via aceperl and graphically use a graphc client
>  xaceclient
>
> ---
>


Sent via Deja.com http://www.deja.com/
Before you buy.


From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 24 14:03:11 2000
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From: dsmith@ucsd.edu (Doug Smith)
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Subject: Text in Graphics Sequence display - 3
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RE my following email from yesterday,
I am having troubles getting the 'Sequences and ends' column in the Sequence
Graphics display to work for composite sequences, in either xace-4.7, in
WebAce,
or in AceBrowser.

This is in addition to troubles getting the 'Brief Identifications' to work.

If someone could let me know what tags control these displays, or what methods
are appropriate, and what modifications I need to make in *.wrm files, or
whatever, I would be most appreciative.

Thanks
  -Doug



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>From: dsmith@ucsd.edu (Doug Smith)
>X-Newsgroups: bionet.software.acedb
>Subject: Text in Graphics Sequence display - 2
>Date: 24 Jan 2000 06:01:52 -0000
>Organization: MRC Human Genome Mapping Project Resource Centre
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>	by biomail.ucsd.edu (8.9.3/8.9.3-IH) with ESMTP id WAA13911
>	for <acedb@net.bio.net>; Sun, 23 Jan 2000 22:01:48 -0800 (PST)
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>Precedence: bulk
>
>Hi all,
>
>I am still having troubles with Text display in the Sequence Graphics display.
>
>Hamis McWilliam suggested I do the following:
>
>>I found the following worked for me (thanks to R. Durbin for this one).
>>
>>Update ?Method in models.wrm:
>>
>>?Method Remark ?Text
>>        Display Colour  #Colour
>>                Frame_sensitive
>>                Strand_sensitive  Show_up_strand  #Colour
>>                Score   Score_by_offset
>>                        Score_by_width
>>                        Score_bounds  UNIQUE  Float  UNIQUE  Float
>>                        Percent
>>                Overlap_mode UNIQUE     Overlap
>>                                        Bumpable
>>                                        Cluster
>>                Width  UNIQUE  Float
>>                Symbol  UNIQUE  Text
>>                Right_priority  UNIQUE  Float
>>                Max_mag UNIQUE Float
>>                Min_mag UNIQUE Float
>>                Show_text
>>        Blastn
>>
>>Show_text is the important bit here (see ACEDB 4.7 models.wrm).
>>
>>Also add the following to ?Sequence
>>
>>          Method UNIQUE ?Method
>>
>>Now define a Method object which makes the Visible stuff display, e.g.
>>
>>Method : Default_Sequence
>>Remark "A default display method for sequences."
>>Display Show_Text
>>
>>Now add this method to all your sequences object that you want to have
>>text annotation.
>>
>>I hope this helps. Hamish.
>>
>
>
>I did this ... and it works ... but, for me, only in part, to wit:
>
>1. only the Visible information from the *.cds Subsequence objects is
>displayed !?!
>2. Visible information from other Subsequence objects and from the Sequence
>object
>   itself is not displayed.
>
>Second, this displayed text information appears to be of a 'Text Features'
>type
>... that is, it is removed from the Seq Graphics display when one toggles the
>'Text Features' in 'Columns'
>
>Perhaps the additional text information should be displayed in the column
>called 'Brief Identifications' ??
>I have not been able to get this column to display anything ...
>If this is what I should be using, how does one use it?
>Does it involve an additional Method to the 'Show_Text' method above?
>If so, what is the Method?
>
>I appreciate any comments here ...
>Thanks
>  -Doug
>
>
>
>
>
>
>---
>


---


From owner-acedb@hgmp.mrc.ac.uk  Mon Jan 24 21:09:20 2000
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From: jfousry745689@deniz.com
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Subject: Offshore Wealth!!!!
Date: 24 Jan 2000 21:09:15 -0000
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---


From owner-acedb@hgmp.mrc.ac.uk  Tue Jan 25 17:45:01 2000
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From: Hamish McWilliam <Hamish.McWilliam@bbsrc.ac.uk>
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Subject: Re: Text in Graphics Sequence display - 2
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Doug Smith wrote:
> 
> Hi all,
> 
> I am still having troubles with Text display in the Sequence Graphics display.
> 
<Stuff snipped>
> 
> I did this ... and it works ... but, for me, only in part, to wit:
> 
> 1. only the Visible information from the *.cds Subsequence objects is
> displayed !?!
> 2. Visible information from other Subsequence objects and from the Sequence
> object
>    itself is not displayed.
> 
> Second, this displayed text information appears to be of a 'Text Features' type
> ... that is, it is removed from the Seq Graphics display when one toggles the
> 'Text Features' in 'Columns'
> 
> Perhaps the additional text information should be displayed in the column
> called 'Brief Identifications' ??
> I have not been able to get this column to display anything ...
> If this is what I should be using, how does one use it?
> Does it involve an additional Method to the 'Show_Text' method above?
> If so, what is the Method?
> 
> I appreciate any comments here ...
> Thanks
>   -Doug

Having just had a little play with the setup I recommended earlier, I
see the same behavior. Although I get the Visible info displayed from
both CDS and mRNA subsequences.

As for Brief 'Identifications' I actually do have this column working
although I cannot say if it works for the sequence it does seem to work
for my subsequences. These are derived from the value of the 
Visible -> Brief_identification tag, and are displayed independently of
the other text features.

While this is probably not of much help, now that I looked at it afresh,
I would still like to be able to get the other Visible data to display.

Any ideas anyone?

Hamish.
-- 
=====================================================================
Hamish McWilliam
Brassica and Oilseeds Research
John Innes Center
Norwich Research Park
Colney Lane
Norwich
NR4 7UH

Tel: +44(0)1603-452571
WWW: http://jiio10.jic.bbsrc.ac.uk/
---------------------------------------------------------------------
God invented Brownian motion to stir his coffee.
=====================================================================


From owner-acedb@hgmp.mrc.ac.uk  Tue Jan 25 21:10:30 2000
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From: vx56yvxc@yahoo.com
X-Newsgroups: bionet.software.acedb
Subject: Accept Credit Cards TODAY!!!
Date: 25 Jan 2000 21:10:24 -0000
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---


From owner-acedb@hgmp.mrc.ac.uk  Wed Jan 26 01:06:42 2000
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From: janety@u.washington.edu (Janet Young)
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Subject: one object, many names
Date: 26 Jan 2000 01:06:34 -0000
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Hi

I am working out how to make a model to best fit my data. I have a set
of clones which I'd like to refer to by several names (i.e. 96 well
location, 384 well location, rearrayed plate location etc) when entering
data of different types (end sequence, PCR results). I have a table of
how these names relate to one another.

I'd like to be able to enter data using any of the different name types
(they have a suffix to distinguish different name types) but for data
from each of the entries to be collected under one object in the
database, rather than be dispersed over several objects of different
name-type which actually refer to the same clone. 

Does anybody have any ideas of how to set up the model to deal with
this, or should I work out a script to convert the names to a 'master'
name before data entry? I have a feeling it should be possible with some
sort of
?Clone General Synonymous_with ?Clone XREF Synonymous_with 
kind of model but then I'll end up with several different objects
representing the same BAC with the data dispersed between them according
to which name I entered the data under.

thanks

Janet

------------------------------------------------------------------- 
                         Dr. Janet Young 
Dept. Molecular Biotechnology 
University of Washington             tel: (206) 685 9254 
Health Sciences Building             fax: (206) 685 7301 
PO BOX 357730                        email: janety@u.washington.edu 
Seattle, WA 98195, USA
---


From owner-acedb@hgmp.mrc.ac.uk  Wed Jan 26 14:53:03 2000
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    Hello ACEDB users.

I am going on the net. Thanks to R. Durbin things are a lot clearer now.
However, I am having a little problem that I could not find the answer
in the previous messages on this list nor in the various readme and
instalation guides.

Acedb is 4.7l
Perl is 5.005_03
CGI.pm is 2.56
AcePerl is 1.57
AceBrowser is 2.10
Apache is something
Netscape is 4.5
Solaris is 7 / sun OS 5.7

Everything is going fine except that I have this message :

jaffar# tail /var/adm/messages
Jan 26 13:45:47 jaffar rpcace[2104]: svc_tli_create: could not do
t_sync: Illegal file descriptor
Jan 26 13:45:47 jaffar rpcace[2104]: cannot create tcp service.
Jan 26 13:45:47 jaffar inetd[181]: /usr/local/bin/rpc.acedb: Hangup
Jan 26 13:45:50 jaffar rpcace[2109]: svc_tli_create: could not do
t_sync: Illegal file descriptor
Jan 26 13:45:50 jaffar rpcace[2109]: cannot create tcp service.
Jan 26 13:45:50 jaffar inetd[181]: /usr/local/bin/rpc.acedb: Hangup
Jan 26 13:45:53 jaffar rpcace[2114]: svc_tli_create: could not do
t_sync: Illegal file descriptor
Jan 26 13:45:53 jaffar rpcace[2114]: cannot create tcp service.
Jan 26 13:45:53 jaffar inetd[181]: /usr/local/bin/rpc.acedb: Hangup

and this message in netscape :

Software Error

Couldn't open database.


The acedb compilation was OK the first time but just in case I
recompilled using rpcace_svc.crick but that did not change anything.
Runing the server in foreground is OK.
Accessing this server is OK.

/etc/rpc :
# 26 janvier 2000
digitata	20000114	rpc.acedb

/etc/services :
# 26 janvier 2000
digitata        20000114/tcp        rpc.acedb

/etc/inetd.conf :
# pour le serveur ACEDB
20000114/1	stream	rpc/tcp	wait	est	/usr/local/bin/rpc.acedb	rpc.acedb
/opt2/digitata 20000114 600:600:0

SiteDefs.pm :
%DATABASES = (
	      'digitata' => {
		  host       => 'jaffar.sb-roscoff.fr',        # database host
		  port       => 20000114,             # database port
		  stylesheet => '/stylesheets/elegans.css',                 #
stylesheet to use
		  searches   => [qw(simple grep search expr_search query blast)], #
search scripts available
		  url_mapper => \&elegans_mapper,               # object class->url
mapping
		  displays   => \%elegans_displays,             # special displays for
certain objects
                  home       => ['C. elegans home' =>
'/elegans/'],        # home sweet home 			    
		  title      => <<END,
<center><span class=banner><cite>L. digitata</cite> EST Database</span>
P


Do you have any idea of what is not going well ?

Thank you very much in advance.

Florent
---


From owner-acedb@hgmp.mrc.ac.uk  Wed Jan 26 15:20:56 2000