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From owner-acedb@hgmp.mrc.ac.uk  Tue Feb  1 09:51:35 2000
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From: Ed Griffiths <edgrif@sanger.ac.uk>
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Dave,

> We're seeing the same /var/adm/messages when we try to run ace4_7m under inetd
> under Solaris 7.  Also one other one:
> 
> Jan 22 16:23:49 gn rpcace[8501]:  rendezvous_request : no suitable transport
> 
> We're not having this problem with Solaris 2.6, just with 7.
> 
> - Dave
> ---

We have no boxes on site that are at 2.7, I will ask systems support to
upgrade at least one box so I can do some testing.

In the mean time it would be good if when people report problems with
particular levels of operating systems they could also post the output
of the
uname command (with the -a option), e.g.

ics-sparc1[edgrif]42: uname -a
SunOS ics-sparc1 5.5 Generic_103093-27 sun4u sparc SUNW,Ultra-1

this just helps to make things clear.

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        |

------------------------------------------------------------------------------


From owner-acedb@hgmp.mrc.ac.uk  Wed Feb  2 05:19:09 2000
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Do you have too many projects and limited time? If high level protein =
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<META content=3D"text/html; charset=3Diso-8859-2" =
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</HEAD>
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<DIV>
<DIV>
<P>Do you have too many projects and limited time? If high level protein =

expression is one of your goals, C&amp;P Biotech is ready to help you =
with=20
sub-cloning and protein purification in E. coli.</P>
<OL>
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insertion=20
    mutation.=20
    <P>PRICE: US$ 600.00 per sample.</P>
    <LI>Protein expression and purification based on GST or =
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<P>Give yourself the chances to concentrate on other important projects =
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<P>C&amp;P Biotech</P>
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<P>Email: <A href=3D"mailto:suehan@sprint.ca"><FONT=20
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<P>Tel: 905 886 1898</P>
<P>Fax: 905 886 1898</P></DIV></DIV></BODY></HTML>

------=_NextPart_000_0069_01BF6D13.9D13F400--

---


From owner-acedb@hgmp.mrc.ac.uk  Wed Feb  2 18:52:43 2000
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From: leahjg@pacbell.net (Leah Jaffe-Greenwood)
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Check out www.DoubleTwist.com, it's a new portal that uses 'automated
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it's all programmed in.  Also, they keep monitoring the databases and
notify you by email if something new related to your sequence is found.

Leah Jaffe-Greenwood, Ph.D.



---


From owner-acedb@hgmp.mrc.ac.uk  Wed Feb  2 23:04:26 2000
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From owner-acedb@hgmp.mrc.ac.uk  Thu Feb  3 09:32:18 2000
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From: cmantsy@yahoo.com ("B.Rajarajeswari")
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Subject: FATAL ERROR
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 Dear sirs,
                       I have downloded and installed the Acedb
software,i have down loded Ricegenes database, which has the  acedb
software as the backbone, while reinitializing the data, it's saying the
following  error.

FATAL ERROR reported by program xace, in file disknew.c, at line 1404:
No DataBase map and no old style DataBase!!

Can i get a remedy for this.

Thanking you.

Rajeswari


---


From owner-acedb@hgmp.mrc.ac.uk  Thu Feb  3 09:36:46 2000
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From: sugantham@yahoo.com (rajarajeswari balasubramanian)
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Dear sirs,
                   I have installed Acedb software,
and downloded Ricegenes from ricegenes home page, but
while reinitializing the data it's saying,

FATAL ERROR reported by program xace in file
disknew.c, at 
line 1404: No Database map and no old style Databse!!

Can get a remedy for this.

Thanking you

Rajeswari
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From owner-acedb@hgmp.mrc.ac.uk  Thu Feb  3 13:05:22 2000
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From: Mark Wilkinson <markw@mpiz-koeln.mpg.de>
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Subject: Administration of GIF images from gifaceserver/AcePerl
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Hi Group!

Quick question - the images generated by Gifaceserver/Aceperl are stored
in a series of folders - do these have to be administered by hand (i.e.
deleted)?  I am a bit confused about the caching of these images in any
case... what happens if the database has been updated and the image is
no longer identical?  Does AcePerl recognie this, or does it still pull
up the cached image?

??

Mark




From owner-acedb@hgmp.mrc.ac.uk  Thu Feb  3 14:10:28 2000
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From: mieg@eta.crbm.cnrs-mop.fr (Danielle et jean Thierry-Mieg)
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yes you should have a chron job to rm these images
and if you donot aceperl reuses the previous image

the image is obtained from gifaceserver, stored there
and the file name is passed to netscape
teh system does not know when netscape will recover it

---


From owner-acedb@hgmp.mrc.ac.uk  Thu Feb  3 15:16:41 2000
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thanks :-)
M


Danielle et jean Thierry-Mieg wrote:

> yes you should have a chron job to rm these images
> and if you donot aceperl reuses the previous image



From owner-acedb@hgmp.mrc.ac.uk  Fri Feb  4 16:06:44 2000
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I have got lots of softwarez (Pro Engineer 2000i, Pro Mechanica 2000i,
Mechanical Desktop 4,Autocad 2000, Unigraphics 16, Solidworks 99 :etc.). If
you are interested in some PC programs, please contact me:
vadri@getmessage.com
cdzcd@postmark.net
ICQ: 51449232








From owner-acedb@hgmp.mrc.ac.uk  Sat Feb  5 00:40:18 2000
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Hi,

Just to back up a touch.  We had a horrible bug with the new version of
the Solaris 7 operating system running acedb_4.7* (it took over the
Xwindows manager).  I got the new executable 4.8, from the Sanger site
and it works just fine.  But it's changed a bit.  We have a sequence as
both a Clone and a Sequence.  Under that there are subsequences, the
genes.  The subsequences require a method to be displayed, but
previously the Sequence did not.  I can not now access the main sequence
from the sequence's display.  It's name is no longer visible on the
Sequence map.  There must be something new that I need to add to my
input.  Does anyone know what that might be?  Do I need to add a method
to display it where it was before, on the yellow side bar, I think?

thanks to everyone.
Jody


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


From owner-acedb@hgmp.mrc.ac.uk  Sat Feb  5 19:11:44 2000
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There is a 'method' that appears upon the query 'find method' for
many of the ACEDB databases present at Cornell called:
  FMAP_Sequences_and_ends

This however is an 'empty object'.

Does anyone know what this is?  if it exists?
Where to find it if it does exist?

It looks like it might be useful in getting the 'Sequences and Ends'
column in the FMAP Sequence Display to display subsequences ...

-Doug


---


From owner-acedb@hgmp.mrc.ac.uk  Mon Feb  7 00:56:39 2000
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From owner-acedb@hgmp.mrc.ac.uk  Mon Feb  7 16:43:29 2000
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Hi,

I am having a problem with trying to add/configure our map displays.  

Our map display currently contains items in the Locus class.  I was led to
believe that you should be able to configure the map displays to
include/display various types of queries.

E.g. I can change the interval_SRK column to contain a relatively simple
query such as 'Find Locus' and that works fine.

However if I try something like:

Find Locus FOLLOW Sequence FOLLOW Allele

then nothing appears in the column, even though I can construct this is as
a query in the query window, and it returns a list of matches.

I've also tried 'Find Locus Sequence FOLLOW Allele' but then I get an
error message box appear which says 'Confusion in condMatch
at: PIPEQUERY: Find Locus Sequence FOLLOW Allele'.  Whenever you
click continue the box reappears and you are forced to kill xace as there
seems to be no other way of exiting.

Any ideas?  We currently use xace version 4.7g on a Solaris platform.

Keith


~  Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR)
~  Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/
~  University Park, University of Nottingham, NG7 2RD, UK
~  Tel: (0115) 951 3091 





From owner-acedb@hgmp.mrc.ac.uk  Mon Feb  7 16:50:43 2000
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Hi everybody!

I have set up Acebrowser on my machine, and it was working fine with
aceserver.

Now, I want graphics! So, I went ahead and tried to set up gifaceserver,
much the same way I did for aceserver (inetd.conf etc..). 

And everything works, but the graphic display...

I get a "Sequence: F55H2.3 Requires IE or Netscape version 4.0 or
higher" message on my browser (I have Netscape 4.7).

If I look at server.log, I have:
New Client 25, 1 active clients
Client     25 (1 active). Query: 
Client     25 (1 active). Query: find Sequence "F55H2.3"
Client     25 (1 active). Query: list -j -b 0 -c 65536
Client     25 (1 active). Query: gif display   Sequence "F55H2.3" ;
gifdump -
Client     25 (1 active). Query: Quit

Closing Client 25, 0 active clients

And if I look in the database directory, I have a -.gif file, which is
what I wanted...
and in /httpd/html/ace_images/elegans/Sequence/ I have a F55H2.3.gif
which contains an error message.

Does anyone could help me, telling me where I am wrong?

Thanks again for your help,

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  Mon Feb  7 17:20:29 2000
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Hi Keith,

Your chain of FOLLOWs has to end at the object that's to be displayed
or highlighted.  In your case maybe:

Find Locus FOLLOW Sequence FOLLOW Allele FOLLOW Sequence FOLLOW Locus


GrainGenes has a working example like this in View "Default", used in Map
Hordeum-NABGMP1-2H for example.

- Dave


> I can change the interval_SRK column to contain a relatively simple
> query such as 'Find Locus' and that works fine.
> 
> However if I try something like:
> 
> Find Locus FOLLOW Sequence FOLLOW Allele
> 
> then nothing appears in the column
---


From owner-acedb@hgmp.mrc.ac.uk  Tue Feb  8 09:59:27 2000
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From: rd@sanger.ac.uk (Richard Durbin)
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Subject: Re:  AceBrowser and gif images
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You did not want a "-.gif" file.  You wanted to dump the gif to stdout
for AceBrowser to pick up.  You are using a version of gifaceserver
that is too old, and does not have the feature that filename "-" dumps
the gif to stdout.

Richard
---


From owner-acedb@hgmp.mrc.ac.uk  Tue Feb  8 10:28:12 2000
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Richard Durbin wrote:
> 
> You did not want a "-.gif" file.  

OK, I should have said "I have a -.gif file, which _contains_ what I
wanted..."

> You wanted to dump the gif to stdout
> for AceBrowser to pick up.  You are using a version of gifaceserver
> that is too old, and does not have the feature that filename "-" dumps
> the gif to stdout.

I am using gifaceserve.LINUX.gz I got from
ftp://ftp.sanger.ac.uk/pub/webace/gifaceserver/

Once gunziped, it is  4555147 bytes; where can I get the latest version?

Thanks for your help,

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 Feb  8 11:19:35 2000
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Hi everybody,

I just started to create a new database with the 4.7 version on solaris.
I have a strange bug which seems to appear randomly, possibly everytime
I use a map display: the mouse right-button menu (the one with "quit,
help, print, preserve ...) becomes completely inactive and I cannot
select items from that menu anymore. I have no idea what causes this
problem. This is specific to acedb, the right button menu on the sun
desktop is working fine.

The only way to restore this function is to exit acedb AND log out /log
in, which of course is really a pain.

Has anybody heard of such a problem? any solution?

Cheers
-- 
Philippe Gautier

MRC Human Genetics Unit
Western General Hospital
Crewe Road
Edinburgh EH4 2XU
United Kingdom

Phone: +44 (0)131 332 2471 
Fax:   +44 (0)131 343 2620


From owner-acedb@hgmp.mrc.ac.uk  Tue Feb  8 12:58:09 2000
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Acedb '2000 is happening!

A meeting for all experienced developers and curators of ACEDB will be
hosted at Simon Fraser University, Burnaby, British Columbia, Canada
from June 12th to 16th, 2000 inclusively.

WWW site for information: http://www.sanger.ac.uk/Info/Events/Acedb2000

Email meeting notification service: send 'subscribe acedb2000' in the body
of an email message to majordomo@sanger.ac.uk

Registration details to be posted this week on the WWW site.

Cheers from Cambridge,
========================================================
Dr. Richard Bruskiewich		<rbsk@sanger.ac.uk>
	WWW: http://www.sanger.ac.uk/Users/rbsk/
Human Analysis/Bioinformatics
The Sanger Centre		Tel:  +44-(0)1223-834244
Wellcome Trust Genome Campus,	Fax:  +44-(0)1223-494919
Hinxton, Cambridge   CB10 1SA
United Kingdom
========================================================

---


From owner-acedb@hgmp.mrc.ac.uk  Tue Feb  8 12:59:15 2000
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From: rd@sanger.ac.uk (Richard Durbin)
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> I am using gifaceserve.LINUX.gz I got from
> ftp://ftp.sanger.ac.uk/pub/webace/gifaceserver/

webace is an old deprecated way of putting acedb onto the web, as
stated on the www.acedb.org home page. 

> Once gunziped, it is  4555147 bytes; where can I get the latest version?

I believe the version in ftp://ftp.sanger.ac.uk/pub/acedb/ace.4_7l/
should work for you, or ask/look at the AceBrowser home pages at
http://stein.cshl.org/AcePerl/AceBrowser/ for Lincoln's direct
recommendations.

Richard
---


From owner-acedb@hgmp.mrc.ac.uk  Tue Feb  8 13:03:41 2000
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I guess the menu becomes inaccessible when the CAPS-LOCK button is
down.  This is an old issue with Suns which does not appear on other
platforms.

Richard

> I just started to create a new database with the 4.7 version on solaris.
> I have a strange bug which seems to appear randomly, possibly everytime
> I use a map display: the mouse right-button menu (the one with "quit,
> help, print, preserve ...) becomes completely inactive and I cannot
> select items from that menu anymore. I have no idea what causes this
> problem. This is specific to acedb, the right button menu on the sun
> desktop is working fine.
> 
> The only way to restore this function is to exit acedb AND log out /log
> in, which of course is really a pain.
> 
> Has anybody heard of such a problem? any solution?
---


From owner-acedb@hgmp.mrc.ac.uk  Tue Feb  8 13:16:44 2000
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Richard Durbin wrote:
> 
> > I am using gifaceserve.LINUX.gz I got from
> > ftp://ftp.sanger.ac.uk/pub/webace/gifaceserver/
> 
> webace is an old deprecated way of putting acedb onto the web, as
> stated on the www.acedb.org home page.
> 
> > Once gunziped, it is  4555147 bytes; where can I get the latest version?
> 
> I believe the version in ftp://ftp.sanger.ac.uk/pub/acedb/ace.4_7l/
> should work for you, or ask/look at the AceBrowser home pages at
> http://stein.cshl.org/AcePerl/AceBrowser/ for Lincoln's direct
> recommendations.
> 
> Richard
> ---

Thank you so much! It was indeed a problem with the version of
gifaceserver. Everything looks OK now.
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 Feb  8 13:53:40 2000
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> I guess the menu becomes inaccessible when the CAPS-LOCK button is
> down.  This is an old issue with Suns which does not appear on other
> platforms.
> 
> Richard

It is most likely that your problem is as Richard says, but you should
note that the CAPS-LOCK problem exists on most systems, not just Suns.
This is
a problem to do with the way we instantiate Athena toolkit pop-up
windows.
We don't intend to fix this because it would be a lot or work on code
that
is being superceded by the 4_8 version of xace that uses the GTK toolkit
(where the problem does not exist) instead of Athena.

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        |

------------------------------------------------------------------------------


From owner-acedb@hgmp.mrc.ac.uk  Tue Feb  8 21:59:53 2000
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Subject: Softwares for good prices
From: ugnyte@takas.lt
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You need wares - no problem :

Newest wares  for good price: 

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... and more others !!! 

Please write to:  saran@prontomail.com ; markstudent@england.com ;  wirgisam-wolf@prontomail.com 

fax: (0870)133-4048
ICQ: 57092777

 




From owner-acedb@hgmp.mrc.ac.uk  Wed Feb  9 02:31:57 2000
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From: ezone2k@softhome.net
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Subject: Receive $20 Cash Immediately for Opening a FREE Checking Account
Date: 9 Feb 2000 02:31:52 -0000
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Hello:

Instead of offering people a free gift for joining their bank,
there is an online bank that pays its customers $20 Cash.

Furthermore. their banking services are simple and easy to use.
And frankly, their full range of financial services are the best I
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and bond funds.

Plus, a whole lot more!

So click on this link right now, and get your $20!

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(if this link is not highlighted, copy & paste it into your web browser)


If there are delays onto their site, it is because of the traffic generated
by the overwhelming success of this program.   Please try again.


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From owner-acedb@hgmp.mrc.ac.uk  Wed Feb  9 11:29:45 2000
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rajarajeswari,

> Dear sirs,
>                    I have installed Acedb software,
> and downloded Ricegenes from ricegenes home page, but
> while reinitializing the data it's saying,
> 
> FATAL ERROR reported by program xace in file
> disknew.c, at
> line 1404: No Database map and no old style Databse!!
> 
> Can get a remedy for this.
> 

The error is saying that xace cannot find the file that describes how
your ricegenes database was laid out on disk. You say that you
reinitialised the
database, what did you actually do ?  I'm wondering if you accidentally
deleted some of the files that acedb needs to reinitialise ?

I would suggest that you get a fresh copy of the Ricegenes database and
check that the database/ sub directory contains the file database.map.
It's because this file is missing that ultimately you are having the
above problem.

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        |

------------------------------------------------------------------------------


From owner-acedb@hgmp.mrc.ac.uk  Wed Feb  9 17:02:14 2000
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Hello:

Instead of offering people a free gift for joining their bank,
there is an online bank that pays its customers $20 Cash.

Furthermore. their banking services are simple and easy to use.
And frankly, their full range of financial services are the best I
have seen anywhere -- FREE high interest checking account (4%),
FREE checks, FREE No minimum bond, mutual and money market funds,
and more.

Just click on the link below, and sign up for an account at X.com.

Also please keep in mind, it takes less than two minutes,
and they will immediately put $20 cash into your account
to get you started.  Give them a try.  You've got nothing to lose.

What do you'll get?

FREE $20 cash deposited immediately
into your new checking account

FREE money transfers (send money
instantly to anyone's email)

No obligation, no minimum balance,
no monthly fees

Super-high interest on any money
in your checking account

FREE starter checks, and a FREE VISA
debit card.

No minimum, no fee mutual, money market,
and bond funds.

Plus, a whole lot more!

So click on this link right now, and get your $20!

https://www.x.com/new_account.asp?Referrer=ezone2k@softhome.net
(if this link is not highlighted, copy & paste it into your web browser)


If there are delays onto their site, it is because of the traffic generated
by the overwhelming success of this program.   Please try again.


________________________________________________
Your were sent this message because your address
is in our subscriber data base.  If you wish to
be removed please reply with the subject "Remove"
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From owner-acedb@hgmp.mrc.ac.uk  Thu Feb 10 03:51:13 2000
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Subject: Re: Extra $5000 - $10,000/Month Forever                                                   ijdww
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send me more info on this money maker


* Sent from RemarQ http://www.remarq.com The Internet's Discussion Network *
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From owner-acedb@hgmp.mrc.ac.uk  Thu Feb 10 07:49:38 2000
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From: dsmith@ucsd.edu (Doug Smith)
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Subject: Subsequences and ends ... and BLASTN
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As some of you may have noticed, I have recently had troubles displaying
Subsequences in the Sequence FMAP Graphic display.

I found one solution to this problem:

simply include the tag:

Genomic_canonical

in the Sequence objects, both Source and Subsequence objects.

This tag comes up under 'Properties'.  Declaring this both shows the
subsequence objects in the appropriate column AND provides text display
of the 'Visible' information.

The 'Brief_identification' tag need not be used.

I am testing this further, but ... so far, so good ...

PS I tried this after noting a reference in the ACEDB article
in the Baxevanis 'Bioinformatics' book to NALUSDA 'magic tag' documentation,
which, although out of date, suggests that Subsequence column info is displayed
via 'Properties' tags ...



I now have another problem perhaps someone has experienced:

in displaying BLASTN homology data, the objects are displayed appropriately.
BUT with each manipulation that requires redrawing of the display, the
homology objects move to the right ... and thereby walk across the screen
to disappear into the sunset, never to be seen again ...

The BLASTN Method I am using, patterned after the Celegans method, is as
follows:

-----
Method : "BLASTN"
Colour	 "LIGHTBLUE"
Score_by_width
Score_bounds	 100 1000
Cluster
Right_priority	 5.2
Show_text
Blastn
Blixem_N
-----

any suggestions?

Thanks
  -Doug


---


From owner-acedb@hgmp.mrc.ac.uk  Thu Feb 10 13:30:18 2000
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   I have noticed the same thing, requiring a total shutdown of the
program which is quite annoying (didn't have to reboot though). I have
however not experiences this for quite a while now. It may be due to the
fact that I upgraded to the most recent version a few months ago. I
don't know, what do the programmers have to say about this.. ?



               Mummi

In article <389FFBBE.38F6@hgu.mrc.ac.uk>,
  Philippe.Gautier@hgu.mrc.ac.uk wrote:
> Hi everybody,
>
> I just started to create a new database with the 4.7 version on
solaris.
> I have a strange bug which seems to appear randomly, possibly
everytime
> I use a map display: the mouse right-button menu (the one with "quit,
> help, print, preserve ...) becomes completely inactive and I cannot
> select items from that menu anymore. I have no idea what causes this
> problem. This is specific to acedb, the right button menu on the sun
> desktop is working fine.
>
> The only way to restore this function is to exit acedb AND log out
/log
> in, which of course is really a pain.
>
> Has anybody heard of such a problem? any solution?
>
> Cheers
> --
> Philippe Gautier
>
> MRC Human Genetics Unit
> Western General Hospital
> Crewe Road
> Edinburgh EH4 2XU
> United Kingdom
>
> Phone: +44 (0)131 332 2471
> Fax:   +44 (0)131 343 2620
>


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


From owner-acedb@hgmp.mrc.ac.uk  Thu Feb 10 14:02:33 2000
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> don't know, what do the programmers have to say about this.. ?


Did you see mine & Richards appends about the CAPS LOCK problem ??  Is
this the problem or are you seeing another problem ??
 
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: Jamie Kincaid <jamie@thale.life.nottingham.ac.uk>
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Hello,
Glad to see I am not the only one working on blastn stuff today!
My only suggestion about the missing objects would be to try changing the
Score_bounds value.

My question is:
With the Blastn tag specified ACEDB can calculate percent from score.
How does it do this?
Does it work for both gapped and ungapped blast?
The percent shown when I read in my blast results does not match the
percentage in the blast output. (I'm reading in results from gapped blast
jobs).
In addition if a blast hit is to the negative strand how does ACEDB
display this. I note there is a tag Strand_sensitive which if specified
only shows positive strand boxes. 
Finally  how can I display the name of the blast hit sequence on the Fmap
display.

Many thanks for any help,

Jamie
_______________________________________________________________________________

Jamie Kincaid 
Nottingham Arabidopsis Stock Centre (NASC)
School of Biological Sciences
University of Nottingham, Nottingham, NG7 2RD 

Phone: 0115 951 3091
Fax: 0115 951 3297

NASC website:	nasc.nott.ac.uk





From owner-acedb@hgmp.mrc.ac.uk  Thu Feb 10 23:13:49 2000
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> Does it work for both gapped and ungapped blast?

No.  It only works with ungapped blast, and hence is becoming irrelevant
in the modern world of gapped alignments.
---


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From owner-acedb@hgmp.mrc.ac.uk  Fri Feb 11 05:44:24 2000
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From owner-acedb@hgmp.mrc.ac.uk  Mon Feb 14 08:27:04 2000
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From owner-acedb@hgmp.mrc.ac.uk  Mon Feb 14 16:00:20 2000
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From: zgudmunt@my-deja.com
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Date: Mon, 14 Feb 2000 15:48:05 GMT
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References: <389FFBBE.38F6@hgu.mrc.ac.uk> <87ue1a$843$1@nnrp1.deja.com> <38A2C4F4.8353B362@sanger.ac.uk>
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   Hehe.... (blushing) no, I did not. Tried putting CAPS LOCK on and,
voila, bug reproduced. Perhaps I've simply not been accidentally hitting
CAPS recently...Thanks. Bug Xterminated pronto :)



                       Mummi


In article <38A2C4F4.8353B362@sanger.ac.uk>,
  Ed Griffiths <edgrif@sanger.ac.uk> wrote:
>
> > don't know, what do the programmers have to say about this.. ?
>
> Did you see mine & Richards appends about the CAPS LOCK problem ??  Is
> this the problem or are you seeing another problem ??
>
> 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        |
>
>
------------------------------------------------------------------------
------
>


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


From owner-acedb@hgmp.mrc.ac.uk  Mon Feb 14 16:29:59 2000
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From: "Faramarz Valafar" <faramarz@cns.bu.edu>
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o Any application of computers in Medicine and biological sciences (protein
structure-function analysis, drug and protein design, molecular modeling and
simulation, etc.)
o Application of information technology in biomedicine (e.g. medical
database management, information retrieval and use of computers in
hospitals)
o Application of Computational Intelligence (artificial neural networks,
fuzzy logic, and evolutionary computing) in medicine and biological sciences
o Medical and bio-computing.
o Computer-based medical systems (automation in medicine, etc.)
o Recent history (1990-1999) of Mathematics and engineering techniques in
medicine and biological sciences, and what to expect during the next decade
(2000-2009); New horizons. Review articles)
o Other aspects and applications relating to technological advancements in
medicine and biological sciences.



SUBMISSION OF PAPERS

Prospective authors are invited to submit three copies of their draft paper
(about 4 pages) to F. Valafar (address is given below) by February 28, 2000.
E-mail and Fax submissions are also acceptable.  The length of the
Camera-Ready papers (if accepted) will be limited to 7 pages.  Papers must
not have been previously published or currently submitted for publication
elsewhere.

The first page of the draft paper should include: title of the paper, name,
affiliation, postal address, E-mail address, telephone number, and Fax
number for each author.  The first page should also include the name of the
author who will be presenting the paper (if accepted) and a maximum of 5
keywords.


PROPOSAL FOR ORGANIZING TECHNICAL SESSIONS

Each technical session will have  at least 6 paper presentations.  The
session chairs will be responsible for all aspects of their sessions,
including soliciting papers, reviewing, selecting, ...

The names of session chairs will appear as Associate Editors in the
conference proceedings.  After the conference, some sessions will be
considered for publication in appropriate journals as Special Issues with
the session proposer as the Guest Editor of the journal.

Proposals to organize technical sessions should include the following
information: name and address (+ E-mail) of the proposer, title of session,
a 100-word description of the topic of the session, and a short description
on how the session will be advertised (in most cases, session proposers
solicit papers from colleagues and researchers whose work is known to the
session proposer).

Mail your proposal to F. Valafar (address is given below); E-mail
submissions are preferred.


EVALUATION PROCESS

Papers will be evaluated for originality, significance, clarity, and
soundness.  Two researchers in the topical area will referee each paper.
The Camera-Ready papers will be reviewed by one person.


PUBLICATION

The conference proceedings will be published by CSREA Press (ISBN).  The
proceedings will be available at the conference.  Some accepted papers will
also be considered for journal publication (soon after the conference).


ORGANIZERS/SPONSORS

A number of university faculty members and their staff, in cooperation with
the Monte Carlo Resort (Conference Division, Las Vegas), will be organizing
the conference.  The conference will be sponsored by Computer Science
Research, Education, & Applications Press (CSREA: USA Federal EIN #
58-2171953) in cooperation with research centers, international
associations, international research groups, and developers of
high-performance machines and systems.  The complete list of sponsors and
co-sponsors will be available at a later time.

The last conference's sponsors included: CSREA, the National Supercomputing
Center for Energy and the Environment - DOE, The International Association
for Mathematics and Computers in Simulation, The International Technology
Institute (ITI), The Java High Performance Computing research group, Korea
Information Processing Society, World Scientific and Engineering Society,
Sundance Digital Signal Processing Inc., the Computer Vision Research and
Applications Tech., and more.


LOCATION OF CONFERENCE

The conference will be held in the Monte Carlo Resort Hotel, Las Vegas,
Nevada, USA.  This is a mega hotel with excellent conference facilities and
over 3000 rooms.  The hotel is minutes from the Las Vegas airport with free
shuttles to and from the airport.  This hotel has many vacation and
recreational attractions, including: waterfalls, casino, spa, pools & kiddie
pools, sunning decks, Easy River water ride, wave pool with cascades,
lighted tennis courts, health spa (with workout equipment, whirlpool, sauna,
...), arcade virtual reality game rooms, nightly shows, snack bars, a number
of restaurants, shopping area, bars, ...  Many of these attractions are open
24 hours a day and most are suitable for families and children.  The
negotiated hotel's room rate for conference attendees is very reasonable
($79 + tax) per night (no extra charge for double occupancy) for the
duration of the conference.

The hotel is within walking distance from most other Las Vegas attractions
(major shopping areas, recreational destinations, fine dining and night
clubs, free street shows, and more).

For the benefit of our international colleagues: the state of Nevada
neighbors with the states of California, Oregon, Idaho, Utah, and Arizona.
Las Vegas is only a few driving hours away from other major cities and
attractions, including: Los Angeles, San Diego, Phoenix, the Grand Canyon,
and more.


EXHIBITION

An exhibit is planned for the duration of the conference.  We have reserved
20+ exhibit spaces.  Interested parties should contact F. Valafar (address
is given below).  All exhibitors will be considered to be the co-sponsors of
the conference.


IMPORTANT DATES

February 28, 2000 (Monday): Draft papers (about 4 pages) due
April 3, 2000 (Monday):  Notification of acceptance
May 1, 2000 (Monday):  Camera-Ready papers & Prereg. due
June 26 - 29, 2000:  PDPTA'2000 Conference

Proposals to organize technical sessions should be submitted as soon as
possible.  All accepted papers are expected to be presented at the
conference.


MEMBERS OF PROGRAM & ORGANIZING COMMITTEES

The Program Committee is currently being formed.  Those interested in
joining the Program Committee should e-mail F. Valafar (faramarz@cns.bu.edu
<mailto:faramarz@cns.bu.edu>) the following information: Name, affiliation
and position, complete mailing address, e-mail address, tel/fax numbers, a
short biography together with research interests.


OTHER INFORMATION

Last year PDPTA, CISST, and IC-AI had research contributions from over 44
countries (over 900 participants from all over the world.)  To make this a
more complete suite of conferences, we have added METMBS.  METMBS will also
have a strong international flavor and offers its participants an
introduction to a wide range of related interdisciplinary subjects through
the other three conferences.


CONFERENCE CONTACT:

          Faramarz Valafar
          Cognitive and Neural Systems
          Boston University
          677 Beacon Street
          Boston, MA 02215

          Tel: (617) 353-5134
          Fax: (617) 353-7755
          E-mail: Faramarz@cns.bu.edu <mailto:Faramarz@cns.bu.edu>

















---









From owner-acedb@hgmp.mrc.ac.uk  Mon Feb 14 17:02:14 2000
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Per esempio: essere collegati ad una home page di un qualche provider e
riuscire a vedere le email delle persone che sono collegate in quel momento.
Questo chiaramente è solo un esempio.
a me interessa avere un elenco di indirizzi il piu ampio possibile.
Ringrazio tutti coloro che mi vorranno aiutare.





From owner-acedb@hgmp.mrc.ac.uk  Mon Feb 14 18:45:56 2000
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Subject: Hi !
Date: 14 Feb 2000 18:45:19 -0000
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From owner-acedb@hgmp.mrc.ac.uk  Tue Feb 15 07:06:30 2000
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From owner-acedb@hgmp.mrc.ac.uk  Tue Feb 15 10:35:32 2000
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Subject: Are subclasses mutually exclusive?
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A quick question...

Should members of any particular subclass be unique to that subclass,
i.e. can they belong to more than one subclass?

In our Arabidopsis database we already have several Sequence subclasses
(genomic, mitochondrial, etc.) and I would possibly like to include a new
subclass for Sequences derived from one particular ecotype of Arabidopsis.
It is possible though, that these sequences might also satisfy the
requirements of another subclass and so I would like to know whether this
might cause problems.

Thanks in advance,

Keith


~  Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR)
~  Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/
~  University Park, University of Nottingham, NG7 2RD, UK
~  Tel: (0115) 951 3091 




From owner-acedb@hgmp.mrc.ac.uk  Thu Feb 17 00:40:19 2000
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From: schwartz@uclink4.berkeley.edu
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Subject: Sequence Contig Display?
Date: Thu, 17 Feb 2000 00:32:02 GMT
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Hi All,

I use the Sequence map display for annotation.  I am now annotating a
contiguous megabase which I broke into 10 pieces for acedb.

I was wondering if there is anyway to connect the pieces and annotate
the overlap regions.  I see under the Sequence object that there is an
overlap right and left.  I tried to add a Sequence to see if it would
show the overlap region, but nothing happened.  I didn't know what the
integer was for, the overlap or ???

Does anyone know how to connect sequences and what that enables me to
do?  Am I on the right track?

Thank you.
Jody





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


From owner-acedb@hgmp.mrc.ac.uk  Thu Feb 17 01:05:30 2000
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From: rd@sanger.ac.uk (Richard Durbin)
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Subject: Re:  Sequence Contig Display?
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You need to create a new sequence object (conventionally called "LINK<xxx>")
with subsequences your 10 fragments.  You will have to give these fragments
coordinates in the parent, which will automatically tie them together.

e.g. 

Sequence LINK
Subsequence FRAGMENT1 1 100000
Subsequence FRAGMENT2 100001 200000
Subsequence FRAGMENT3 200001 300000
etc.

You don't have to give DNA for the link.  The subsequences can overlap, but
where they do so must agree exactly.

Richard
---


From owner-acedb@hgmp.mrc.ac.uk  Thu Feb 17 20:51:22 2000
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From: krazy_ass_russian@hotmail.com ("V.i. Kats")
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From owner-acedb@hgmp.mrc.ac.uk  Sat Feb 19 00:51:18 2000
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From owner-acedb@hgmp.mrc.ac.uk  Sun Feb 20 13:36:32 2000
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Subject: Your Platinum Free Vacation and Airline Tickets~.
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Subject: HOW TO MAKE $100,000 SENDING E-MAILS
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