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From: crepinau@sb-roscoff.fr (Crepineau florent)
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Subject: Re: which automated BLAST system ?
Date: 1 Mar 2000 10:10:28 GMT
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In article <8946tu$bcf$1@nnrp1.deja.com>, zgudmunt@my-deja.com wrote:

  >     DBWatcher? What is that? Could someone tell me what on earth that
  > thing is? It sounds like a tool that I have much use for....
  > 
  > 
  >                Mummi

DBWatcher is a programm to automat BLAST search, you can use it to locally
search or search at the NCBI. However it is not yet ready for BLAST2 (the
author is working on it).

I have seen another programm that mimics a browser but I have not yet used it.

A+

Florent

-- 
Florent Crépineau
Station Biologique de Roscoff
BP 74
29682 Roscoff cedex


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-----Àb«È±M®a¦øªA¾¹hkserver¤u§@«ÇÀb«È±Ð¾Ç¥úºÐ-----------
89/02/28 
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

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From owner-acedb@hgmp.mrc.ac.uk  Thu Mar  2 21:02:13 2000
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: A little while back, I was browsing through newsgroups, just like you are 
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: No catch, that was it. So after thinking it over, and talking to a few 
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: NOTE: You may want to retain every name and address sent to you, either on 
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: ---DIRECTIONS ---HOW TO POST TO NEWSGROUPS---- 
: Step 1) You do not need to retype this entire letter to do your own 
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: Step 2) Open a blank "notepad" file under accessories in windows and place 
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: Step 3) Save your new notepad file as a txt file. If you want to do your 
postings in different sittings, you'll always have this file to go back to. 

: Step 4) Use Netscape or Internet explorer and try searching for various 
newsgroups (on-line forums, message boards, chat sites, discussions). 

: Step 5) Visit these message boards and post this article as a new message 
by highlighting the text of this letter and selecting paste from the edit 
menu. Fill in the Subject, this will be the header that everyone sees as they 
scroll through the list of postings in a particular group, click the post 
message button. 

: You're done with your first one! Congratulations...THAT'S IT! All you have 
to do is jump to different newsgroups and post away, after you get the hang 
of it, it will take about 30 seconds for each newsgroup! 
: **REMEMBER, THE MORE NEWSGROUPS YOU POST IN, THE MORE MONEY YOU WILL MAKE!! 
BUT YOU HAVE TO POST A MINIMUM OF 200** 

: That's it! You will begin receiving money from around the world within 
days! You may eventually want to rent a P.O.Box due to the large amount of 
mail you will receive. If you wish to stay anonymous, you can invent a name 
to use, as long as the postman will deliver it. **JUST MAKE SURE ALL THE 
ADDRESSES ARE CORRECT.** 
: Now I tell you how this program is virtually impossible to fail....the WHY 
part: 
: Out of 200 postings, say I receive only 5 replies (a very low example). So 
then I made $5.00 with my name at #6 on the letter. Now, each of the 5 
persons who just sent me $1.00 make the MINIMUM 200 postings, each with my 
name at #5 and only 5 persons respond to each of the original 5, that is 
another $25.00 for me, now those 25 each make 200 MINIMUM posts with my name 
at #4 and only 5 replies each, I will bring in an additional $125.00! Now, 
those 125 persons turn around and post the MINIMUM 200 with my name at #3 and 
only receive 5 replies each, I will make an additional $626.00! OK, now here 
is the fun part, each of those 625 persons post a MINIMUM 200 letters with my 
name at #2 and they each only receive 5 replies, that just made me 
$3,125.00!!! Those 3,125 persons will all deliver this message to 200 
newsgroups with my name at #1 and if still 5 persons per 200 newsgroups react 
I will receive $15,625,000! With an original investment of only $6.00! 
AMAZING! 

: When your name is no longer on the list, you just take the latest posting 
in the newsgroups, and send out another $6.00 to names on the list, putting 
your name at number 6 again. And start posting again. The thing to remember 
is, do you realize that thousands of people all over the world are joining 
the Internet and reading these articles everyday, JUST LIKE YOU are now!! So 
can you afford $6.00 and see if it really works?? I think so... People have 
said, "what if the plan is played out and no one sends you the money? So 
what! What are the chances of that happening when there are tons of new 
honest users and new honest people who are joining the Internet and 
newsgroups everyday and are willing to give it a try? Estimates are at 20,000 
to 50,000 new users, every day, with thousands of those joining the actual 
Internet. 

: Remember, play FAIRLY and HONESTLY and this will work. Thanks for 
participating 

---


From owner-acedb@hgmp.mrc.ac.uk  Fri Mar  3 10:34:22 2000
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¸Û¼xºô¸ô°ª¤â¥u­n±z¬Oºô­¶³]­p¡B¬ü¤u¡B¸ê®Æ®wµ{¦¡³]­p¡Bºô¯¸¥ø¹º°ª¤â
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½Ð¾¨³tÁpµ¸

³ß³Í¬ì§Þ³]­p¦³­­¤½¥q
03 524-2819
home@home104.com.tw
¤H¨Æ³¡  ±i¤p©j




From owner-acedb@hgmp.mrc.ac.uk  Fri Mar  3 16:40:23 2000
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From: zgudmunt@my-deja.com
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Date: Fri, 03 Mar 2000 16:29:50 GMT
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  I have some additional questions on the client/server issue. In this
new version, will the write-lock mechanism still be used for writing
operations? Will only one user be able to write at the same time, and
will a user, who want to write after another one has saved while the
first one was reading, have to restart to see the changes?

     This is really an emphasized version of my message to the list a
couple of days ago, about the write-lock issue.


                       Mummi


In article <38BA66FF.71AF4A2E@sanger.ac.uk>,
  Ed Griffiths <edgrif@sanger.ac.uk> wrote:
> Nathaniel,
>
> OK, here are some answers for the 4_7 version of the client/server
> (which uses RPC for communication):
>
> > Also, if someone knows the port number and ip address of a running
AceDB
> > server, is there any way to keep them from connecting to it ?
>
> This version of the server used an ingenious method for restricting
> read/write access which did not require the user to have a password.
The
> basic idea was that the server would write two magic files (one for
> read, one for write) in a  directory(ies) known to the client and
> server. If the client could read and return the contents of the read
> file, it got read access, if it could read/return the contents of the
> write file it got write access. Thus if the client and server were on
> different machines then the directory where these files appeared had
to
> be NFS mounted by the two machines. So the answer to your question is
> that you can restrict access if the client and server can see this
> directory. You can give read access to everybody without them having
to
> see this directory. This is explained in the file wspec/server.wrm.
>
> > Also, in the passwd.wrm file, you're supposed to list user ids with
write
> > access to the database.  I assume this is only for non-remote
clients ?
>
> You assume correctly, passwd.wrm file is used by the program actually
> accessing the database (xace, tace, aceserver etc.).
>
> > another machine.  Surely I don't have to NFS mount directories do I
?
>
> The problem with this method (as you point out in a later note) is
that
> it doesn't allow that much control if NFS mounting is not possible.
With
> ace 4_7 I'm afraid you are just stuck with this.
>
> Now...for ace 4_8 we have rewritten the server to directly use sockets
> instead of RPC (for portability and interfacing reasons). We have also
> taken the opportunity to add a password mechanism for users, so this
> will answer your question. Now you will have a "true" client/server
> setup with control files for restrict access to just the people you
> want. There are new admin commands to manage these control files.
>
> When this all be available ?  Well its available now for Beta-testing.
> The caveat is that a number of other parts of acedb have been changed
> and we are still testing locally to iron out bugs. I can build you a
> binary (we are about to do a monthly build) and you can try it out if
> you like. I am also just doing the documentation because we have added
> some new commands to manage the user stuff and a number of other
> additions to the server.
>
> I hope this answers your questions, please feel free to email me
direct
> or append here if you need more information.
>
> 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  Sat Mar  4 07:24:13 2000
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---


From owner-acedb@hgmp.mrc.ac.uk  Sun Mar  5 08:01:20 2000
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From: dfhk@ms50.url.com.tw
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sorry......¥´ÂZ¤F!!
====================================================================
***½Ð»{©ú¥¿©v¨¾¤îÀb«È'dfhk'(dfhk@ms50.url.com.tw)¥¿©vdfhk¥X«~«e³£¸g¹L5ºØ¼tµP¥úºÐ¾÷´ú¸Õ¹L½T«O«~½è!!

¤£­n¶R¿ù¤F!!¦³°ÝÃDªº¤ù¤l100%¥]´«!!·PÁÂ¤j®aªº¤ä«ù!!
=========================================================

Pretty Park¹q¸£¯f¬r§Ö³tÂX´² 

[Àb«È·s»D]
3/5/2000 
Pretty Park¹q¸£¯f¬r§Ö³tÂX´² 

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®a¥ø·~©M¬F©²ºô¸ô¨ü¨ì·P¬V¡C ¦¹¤@¯f¬r¥¿¦¡¦WºÙ¬°¡¨W32/Pretty.worm.unp¡¨¡C 

 

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From owner-acedb@hgmp.mrc.ac.uk  Sun Mar  5 09:45:36 2000
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cherche belgium
music maker 5
music studio 5
gravure nero
video capture

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  "francis" <francis.jurdan@advalvas.be> a =E9crit dans le message news: =
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  cherche belgium
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From owner-acedb@hgmp.mrc.ac.uk  Thu Mar  9 15:04:41 2000
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In the grand tradition of previous Acedb developer/curator's meetings,
Acedb '2000 will be held from June 12th-16th, 2000 in Vancouver, BC,
Canada. Visit http://www.acedb.org for information.

---


From owner-acedb@hgmp.mrc.ac.uk  Fri Mar 10 00:38:29 2000
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From: janety@u.washington.edu (janety)
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Subject: column configuration and queries
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Hi everybody

I am having trouble with column configuration of the Gmap display and am
hoping someone can tell me what stupid mistake I am making.

I have a query which works fine via the query commands window, but when
I use it to try to configure a column I get nothing displayed.

The query is
Find Chrom_Band Positive_BAC; follow Positive_BAC

The model I am using is based on the chromosome 6 model at Sanger:

?Chrom_Band Map  ?Map XREF Chrom_Band #Map_position  // position on
vertical maps
            Display     Black
                        Dark 
                        NOR
                        Centromere  // special flag for waisted drawing
                        p_Telomere      // special flag for drawing
                        q_Telomere  // special flag for drawing
            Contains ?Chrom_Band XREF Contained_in
            Contained_in ?Chrom_Band XREF Contains
            Contains_breakpoint ?Hybrid XREF Breaks_in_band
            Positive Positive_locus  ?Locus XREF In_situ
                     Positive_sequence      ?Sequence XREF In_situ
                     Positive_clone         ?Clone XREF In_situ
                     Positive_cosmid  ?Cosmid XREF In_situ
                     Positive_fosmid  ?Fosmid XREF In_situ
                     Positive_YAC           ?YAC XREF In_situ
                     Positive_BAC           ?BAC XREF In_situ
                     Positive_PAC           ?PAC XREF In_situ
                     Positive_STS           ?STS XREF In_situ
                     Positive_cDNA          ?cDNA XREF In_situ
                     Positive_probe         ?Probe XREF In_situ
                     Positive_pool_probe ?Pool XREF In_situ
                     Positive_hybrid ?Hybrid XREF Chrom_band
            OMIM   ?OMIM       XREF Chrom_Band

and In_situ is a Positive tag in the BAC class 

I want to be able to enter my Positive In_situ results, and have BACs
displayed on the map according to those results. Am I not getting the
BACs displayed as I haven't specified a map position for them? My
Chrom_bands have a map position (Ends Left and Right) - shouldn't the
BAC acquire these positions via the Positive magic tag? I think there is
something fundamental I've failed to understand about mapping in ace.

thanks for any help

Janet Young

------------------------------------------------------------------- 
                         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  Fri Mar 10 01:42:48 2000
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From: matthews@greengenes.cit.cornell.edu (Dave Matthews)
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Hi Janet,

> From: janety@u.washington.edu (janety)
> Date: 10 Mar 2000 00:38:24 -0000
> 
> Am I not getting the
> BACs displayed as I haven't specified a map position for them? My
> Chrom_bands have a map position (Ends Left and Right) - shouldn't the
> BAC acquire these positions via the Positive magic tag?

I think this may be the problem.  Anything on the map must have its own
Map Position data.  Doesn't inherit it via the Positive tag.  

I believe Positive/Negative is for the purpose of visually checking
(colors) whether the assertion of positivity/negativity is consistent with
the actual position data.

There's some info about this at
http://ars-genome.cornell.edu/acedocs/magic/gmap.html

- Dave
---


From owner-acedb@hgmp.mrc.ac.uk  Fri Mar 10 09:02:58 2000
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From: tandbob@hotmail.com (T & B Associates)
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Subject: FREE! "BYTEBLES" CD w/ 9 Million email addresses.
Date: 10 Mar 2000 09:02:52 -0000
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---


From owner-acedb@hgmp.mrc.ac.uk  Fri Mar 10 16:15:23 2000
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From: "Norman" <dnorm@1coolplace.com>
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</td>
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</table>



</body>
</html>

------=_NextPart_344745117372285477--

---


From owner-acedb@hgmp.mrc.ac.uk  Mon Mar 13 05:35:29 2000
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From owner-acedb@hgmp.mrc.ac.uk  Mon Mar 13 09:38:34 2000
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§A¬Oºô­¶³]­p,¸ê®Æ®wµ{¦¡³]­p,¥ø¹º,¬ü¤u,°ª¤â¶Ü?
Åwªï¥[¤J§Ú­Ìªº¤u§@¦æ¦C.

³ß³Í¬ì§Þºô­¶³]­p¦³­­¤½¥q.
¤H¨Æ³¡±i¤p©j: annmis@ms14.url.com.tw





From owner-acedb@hgmp.mrc.ac.uk  Mon Mar 13 10:04:41 2000
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From: Martin Trick <martin.trick@bbsrc.ac.uk>
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Subject: Bioinformatics position at John Innes Centre, UK
Date: Mon, 13 Mar 2000 09:58:38 +0000
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Applications are invited for a Computational Molecular Biology
specialist to join the John Innes Centre's (JIC)
computing/bioinformatics service. S/he will be responsible for providing
high level scientific and technical support to end-users in the fields
of sequence analysis and database searching.  The successful applicant
will be expected to proactively develop the service to ensure that JIC
scientists will have access to state of the art facilities.

Applicants are likely to have a degree (although a PhD is desirable) in
an appropriate subject and be able to demonstrate 3 or more years of
practical
experience in relevant areas such as UNIX system admin, shell
programming, Perl, HTML authoring and, of course, use of sequence
analysis software. This is a permanent position and salary on
appointment will be within the range £21,800 to £31,500. There is a
non-contributory superannuation scheme.

JIC is an internationally recognised centre of excellence in plant and
microbial sciences, for more details visit us at
http://www.jic.bbsrc.ac.uk  To register your interest or ask for further
details you can in the first instance e-mail me (with PGP if desired) at
mailto:martin.trick@bbsrc.ac.uk


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

Dr Martin Trick
Brassica & Oilseeds Research Department
John Innes Centre, Norwich NR4 7UH, UK
tel: +44/0 1603 450557
fax: +44/0 1603 450014
http://www.jic.bbsrc.ac.uk/staff/martin-trick


From owner-acedb@hgmp.mrc.ac.uk  Wed Mar 15 00:10:16 2000
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When I am retrieving a ?LongText item through AcePerl (using
the ->asString method) the tabs in the stored text are not
preserved (they become ~ 16 spaces).  

Also, if I have a line over 20 characters long, that 
line is wrapped to a new line when retrieved.

The text looks ok using xace (although I do see funny
characters where the tabs are).

Has anyone else seen this problem and have a solution? or
is it just me? (as usual)

Thanks.  Brian
---


From owner-acedb@hgmp.mrc.ac.uk  Wed Mar 15 15:10:55 2000
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From: hkserver@ms52.url.com.tw
X-Newsgroups: bionet.software.acedb
Subject: Àb«È¾i¦¨¥úºÐ±Ð±z¦¨¬°±M·~Àb«È!!!
Date: 15 Mar 2000 15:09:59 GMT
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-----Àb«È±M®a¦øªA¾¹hkserver¤u§@«ÇÀb«È±Ð¾Ç¥úºÐ-----------
89/02/28 
¥»¥úºÐ¬O¬°¤FÀ°§U¦U¦ì¤F¸ÑÀb«È¤J«I¹q¸£ªº¤âªk¤Î§Þ¥©,¨C­Óµ{¦¡³£¦³¸Ô²Óªº¤¤¤å¨Ï¥Î
»¡©úÂ²³æ©ö¾Ç©öÀ´
¾Þ§@®e©ö!!
¦]¥»¥úºÐ¯}Ãa¤O¶W±j!½Ð¤£­n¥Î©ó«Dªk¥Î³~!!

°t³Æ»Ý¨D
========
Intel(Pentium 166MHz)¥H¤W
°O¾ÐÅé 8MB¥H¤W
©Ò»ÝµwºÐªÅ¶¡ §¹¾ã¦w¸Ë300 MB ³Ì¤p¦w¸Ë15 MB
©Ò»Ý§@·~³nÅé WINDOWS NT/WORKSTATION/95/98/2000
¸ÑÀ£³nÅé  ZIP OR RAR FOR WINDOWS


¥úºÐ¥Ø¿ý
========
[A°Ï] ¤J«Iµ{¦¡ #¯S¬¥¥ìµ{¦¡#
      ^^^^^^^^
           A/1 -Back Orifice
           A/2 -NetBus
           A/3 -Netspy (¦w¸Ë«e½Ð§â¨¾¬r³nÅé¨ø¸ü)
           A/4 -¤J«Iµ{¦¡ªº«OÅ@»P°»°£

[B°Ï] ICQ ¤u¨ã
      ^^^^^^^^
           B/1 -ICQ
           B/2 -ICQ IP / PORT /UIN
           B/3 -ICQ §ðÀ»/±K½X/TRO
           B/4 -ICQªº«OÅ@»P°»°£

[C°Ï] §ðÀ»&ÄdºIµ{¦¡
      ^^^^^^^^^^^^^
           C/1 -¶l¥ó¬µ¼u/°Î¦W«Hµ{¦¡
           C/2 -IP·í¾÷
           C/3 -ÄdºIµ{¦¡ºô¸ô«Ê¥]ÄdºIµ{¦¡
           C/4 -¯f¬r²£¥Í¾¹(½Ð¤p¤ß¨Ï¥Î)
           C/5 -§ðÀ»%ÄdºIµ{¦¡ªº«OÅ@»P°»°£

[D°Ï] ¸Ñ±K¤u¨ã
      ^^^^^^^^
           D/1 -¤å¥óÀÉ®×¸Ñ±K
                           +Word¸Ñ±Kµ{¦¡
                           +Excel¸Ñ±Kµ{¦¡
                           +Zip¸Ñ±Kµ{¦¡
           D/2 -UNIX¸Ñ±Kµ{¦¡$¦r¨å¦¡¯}¸Ñ(¥xÆW¦U¤jISP¬Ò¤wUNIX¨t²Î¬°¥D)
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      ^^^^^^^^^^^^^^



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


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[H°Ï] ¯S§Oªº¤å¥ó¦¬¶° ( UNDERGROUND )

============================================================================
===========
¦p·Q¾Ç²ßÀb«È§Þ¥©³o¤ù¥úºÐ¬O±z³Ì¦nªº¿ï¾Ü:
**Àb«È±Ð¾Ç¥úºÐ°â»ù400¤¸¤w¥]§t§Ö±¶¶l¶O(¦¬¨ì­q³æ«á¹j¤Ñ±H¥X¬ù2-3¤Ñ±z·|¦¬¨ì),±Ä
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24hr¤º·|¦^«H¦p¨S¦¬¨ì¦^«H½Ð¦A±H¤@¦¸ thankS!!
============================================================================
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*¥H¤W¸ê®Æ¥»Àb«È±M®a¦øªA¾¹hkserver¤u§@«Ç¦C¬°¾÷±Kµ´¤£¹ï¥~¬ªº|·q½Ð½Ð©ñ¤ß!!~~

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From owner-acedb@hgmp.mrc.ac.uk  Wed Mar 15 17:56:21 2000
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From: Jamie Kincaid <jamie@thale.life.nottingham.ac.uk>
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What are the features which most heavily influence the performance of an
acedb database in the following scenarios, ie:

running an acedb database standalone ie with xace
accessing an acedb database via the web (is acebrowser more memory
intensive than webace?)
writing large amounts of data to the database (reading in ace files)

I ask since I notice that our server can slow down considerably at times,
and wondered how best to serve a large acedb database w.r.t the four
scenarios above. Ie which tasks are CPU intensive, which are memory
intensive etc.

Regards,

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  Fri Mar 17 07:37:39 2000
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From: 958473@aol.com
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Subject: International Identity !!!
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---


From owner-acedb@hgmp.mrc.ac.uk  Sat Mar 18 22:57:02 2000
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hi,

i stumbled over acedb by reading a perl journal.  i was wondering if anybody
had any experience, or has any ideas regarding the use of acedb as an xml
repository.

i am working on a project where there are rather complex, but well
structured xml documents that need to be entered in some searchable database
system.  doing this with a traditional relational dbms seems to become
overly complicated.

the tree structure of the acedb model and that of a document type definition
(dtd) used to define these documents seem rather related.

any hints or ideas are very much appreciated.  thanks in advance,
Jakob.
jakob@free.fr




From owner-acedb@hgmp.mrc.ac.uk  Sun Mar 19 02:08:10 2000
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From: matthews@greengenes.cit.cornell.edu (Dave Matthews)
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Hi Jakob,

I think you're on the right track.  As you say, 

> the tree structure of the acedb model and that of a document type definition
> (dtd) used to define these documents seem rather related.
and 
> doing this with a traditional relational dbms seems to become
> overly complicated.

Right.  The part I see as crucial is the implementation of 1-to-Many
relationships.  xml incorporates this in a natural way.  We need it, no
question.  So xml includes it as an easy just-do-it.  Doesn't try to
implement, it's only a flat file.

When the data gets bigger than manageable for flat files, how to implement?

rdbms: Every 1-to-Many is a "join".  Even if the Many end turns out to be
null, you still took the performance hit to find that out.  My Oracle bible
says five joins is pushing the edge on performance.  The core problem,
integral to the rdbms paradigm and irremediable within it, is that
1-to-Many is actually implemented as Many-to-1, searching all the external
tables for which of their records link to the current item.

acedb: 1-to-Many links are direct, O(1).  Instantaneous regardless of the
size of the data.  As many as you want.   For example my GrainGenes
schema for the Probe entity has 61 one-to-Many links currently.  More 
whenever I want.  No cost.

As for Many-to-Many links, in rdbms these are a separate operation,
creating a relation table.  I'm not sure how these affect performance from
the user side.  Maybe no worse than any other join.  In acedb they're
transparent.  Some or all of my 61 may actually be Many-to-Many, I don't
even have to think about it, they're still O(1) for the user and no
complication for me.

- Dave 


> From: "Jakob Fix" <jakob@free.fr>
> Subject: different use of acedb
> Date: Sat, 18 Mar 2000 22:56:54 GMT
> 
> hi,
> 
> i stumbled over acedb by reading a perl journal.  i was wondering if anybody
> had any experience, or has any ideas regarding the use of acedb as an xml
> repository.
> 
> i am working on a project where there are rather complex, but well
> structured xml documents that need to be entered in some searchable database
> system.  doing this with a traditional relational dbms seems to become
> overly complicated.
> 
> the tree structure of the acedb model and that of a document type definition
> (dtd) used to define these documents seem rather related.
> 
> any hints or ideas are very much appreciated.  thanks in advance,
> Jakob.
> jakob@free.fr
---


From owner-acedb@hgmp.mrc.ac.uk  Sun Mar 19 03:32:37 2000
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From: "francis" <francis.jurdan@advalvas.be>
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From owner-acedb@hgmp.mrc.ac.uk  Sun Mar 19 07:24:07 2000
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From owner-acedb@hgmp.mrc.ac.uk  Thu Mar 23 01:55:44 2000
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When I am retrieving a ?LongText item through AcePerl (using
the ->asString method) the tabs in the stored text are not
preserved (they become ~ 16 spaces).  

Also, if I have a line over 20 characters long, that 
line is wrapped to a new line when retrieved.

The text looks ok using xace (although I do see funny
characters where the tabs are).

Has anyone else seen this problem and have a solution? or
is it just me?

Thanks.  Brian
---


From owner-acedb@hgmp.mrc.ac.uk  Thu Mar 23 04:30:38 2000
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From: gyy@tc.umn.edu
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Subject: linkage utility programs for windows
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Hi,

I am trying to set up a set of programs for linkage analysis on my windows 95 
PC.  Could you please tell me what tool programs work best together with 
linkage?

 I am specially interested in prgrams for management of pedegree, and 
genotyping data (kind of database or DBMS), generation of input files  and 
plot of output files, and possible automation of some steps.  Thank you.

Guoyun Yu
gyy@tc.umn.edu


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Subject: RE: Easy homeowner loans
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---


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From: Search-Magic@saveit.fsnet.co.uk
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Subject: Search Engine Secrets Discovered
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"Amazing Search Engine Secrets Discovered By A Computer
Illiterate Man in Massachusetts Can Practically Hand
You the Top Search Engine Positions...And Add 1,550 
Hits a Day to Web Site Overnight!"

Dear Friend,

Remember the first time you built a web site. You stayed up 
until the early morning working it out so that it would be 
just perfect. Then, you were finally done and you sat back 
and thought, "The World is Good."

After that, you've dreamed of all the visitors your site 
would have, how they would all see your ad and buy your 
product.  Then it hit you, like a ton of bricks....How was 
anyone going to find your web site?

You thought about it for a while and eventually thought you 
had the answer....submit your site to the search engines. 
But after you submitted your site you checked it out and 
couldn't find it.

So you waited a few days.....and still nothing

You couldn't even find your site if you looked up your own 
name!!!

Then, you got discouraged....after all that hard work 
NOTHING?!?!?

And this is where most people give up.....
BUT You Don't Have To...

You can achieve top 20 positioning for your web site...and 
the tens of thousands of hits which come with it...if you 
have the "Right" information available to you.

For Example, did you know:

* Infoseek, Alta Vista, and HotBot ban web sites which break 
their rules (many of the 'insider' techniques most experts
recommend will get you banned faster than you could imagine).

* Many search engines limit the number of pages you can 
submit from your domain (some only allow you to submit one 
page for best results), although we can show you a technique 
we use to get hundreds of our pages listed.

* Yahoo only lists about 1% of the web in their actual 
directory.  To even get your page listed, you may have to 
use the "backdoor".

* Using a so-called search engine submission software that 
submits your site to 1,000 or more search engines could 
actually get your page deleted from the major search engines.

* 95% of Internet traffic originates at one of the 10 major
search engines...If you're not listed, you might as well
not even have a web site!

* Choosing the most effective 'keywords' is one of the major
keys to a successful web site submission...Pick the right 
ones and your web site will look like Grand Central Station 
during rush hour!

It has taken us over 2 years to learn how to consistently and 
without fail place any type of web site in the top 20 of the 
major search engines.

Normally, we charge $500 per keyword that you want a top 
ranking on (plus a monthly fee of $150 for keeping that rank), 
but we have found we just don't have enough time for all of 
the clients that desperately need our services...

So, we have produced a "Search Engine Magic" interactive
CD-ROM that will show you step by step how to create pages
which storm the search engines and lay hold to the precious 
Top 20 positions that millions of people are trying to reach.

The Search Engine Magic CD-ROM consists of 21 interactive 
video and audio lessons that will run on any IBM compatible 
computer showing you the exact step-by-step process we use 
to traffic thousands of visitors to our web sites every 
single day.

You will learn:

* Three Different Methods We Use to Pick the Best Traffic 
Producing Keywords for any web site...and how you can have 
a list of hundreds of popular keywords in only a few minutes.

* How Quick and Easy it is to Create 'Doorway' and 'Hallway' 
pages for the search engines so that you could possibly have 
thousands of different pages on your domain all pulling in 
visitors for your site 24 hours a day 7 days a week.

* The Secret Weapon that gives you an "Unfair Advantage" over 
your competition...and virtually assures you will reach the 
top positions (don't let your competitors hear about this one 
first or you will be in trouble).

* How to Submit Your Pages to the Search Engines and assure 
that every single one of them gets listed. (if you listen to 
one of those amateurs tell you how to list your site,  you 
may just get banned for life).

* How to Use Pay-Per-Click search engines to receive over 
10,000 visitors for only $100

* The Infamous Yahoo backdoor...You can get listed and we 
will show you the quickest and easiest method for doing so!

* And much, much more...

Even Better, You'll Get the Same Results For A Fraction of 
What Everyone Else Had to Pay!

Listen: A lot of people all over the world are gonna be 
furious with me for sharing these "Insider Secrets" with 
you...especially since you won't be paying even part of what 
they had to shell out for one top positioning page!

That's just too bad.  It's been a secret for too long.  So,
let me tell you what the deal is....

Contact us today using the below Risk-Free Response Form 
and you can have all of our secrets for only $139.00.

This price wouldn't even buy you 10 minutes of our time at
our regular submission fees, but you can own the top search
engine positions for less than the cost of a few classified
ads!  You will be learning everything we know about top 
positioning!

That, my friend, is the bargain of a lifetime for a serious
Internet marketer like yourself.  What’s more, the money is
actually irrelevant, because...

You Also Get a 90 Day No-Risk 100% Money-Back Guarantee!

Here's how it works.  Order your personal copy of this
CD-ROM, and use it like you own it.  If...For any reason
or no reason at all, you aren't completely satisfied after
90 days (by which I had over 47 Top 20 positions for my
own web site), just send the CD-ROM back in any condition,
and I personally guarantee you to get a complete refund
of your purchase price.  No questions asked.  No problems
or forms to fill out.  No problems at all.

PLUS, You Will Also Receive What is Considered to be by
most experts as the "Ultimate Bonus!"

For the first 50 people who fill out the below response
form and send it in, you will also receive UNLIMITED
REPRINT AND REPRODUCTION RIGHTS to this 
CD-ROM for LIFE!

I am not going to allow this CD-ROM to become like many
of those over-advertised products you see out there,
so only the first 50 will receive these rights.

This means that you will be able to use this exact same
sales letter, copy the CD-ROM yourself, and sell it

For $139.00 a copy, one sell will have breaking even.  Sell 
two copies and you will be in profit.This isn't even 
counting what the CD-ROM package will do for you!

Since only 50 people are going to have these rights...
you must take action today!

Yours in Success,
Michael Burgess


To rush order this "Search Engine Magic CD-ROM" simply fill 
out the order form below and fax it to our 24 hour  order 
line at:

FAX ORDER LINE:
1 (212) 504-8032

Regular Mail to:
Financial Systems
P.O. Box 301
Orange, Ma 01364


ORDER FORM     ID#SP325
--------------------------------------------------------
Please send to:


Your Name: _____________________________________________


Your Address: __________________________________________


Your City: _____________________________________________


State / Zip: ___________________________________________


Your Country: __________________________________________


Phone #: _______________________________________________
(For problems with your order only. No salesmen will call.)


Email Address: ___________________________________________


We Accept Checks or Money Orders along with all Major Credit 
Cards including Visa, MasterCard, American Express and 
Discover. (NOTE - We only ship to the address listed on the 
credit card)


(Please Fill Out Below Section and Make sure that the above 
name and address are listed as it appears on the card) for 
$144 ($139 + 5.00 Shipping)


Credit Card Number:________________________________


Expiration Date:___________________________


Signature:_________________________


Date:____________________


* Please check one of the following payment options:


[  ] I am faxing a check (Do not send original, we will make 
     a draft from the faxed check)

[  ] I am faxing or mailing my credit card number. (Note your 
     card will be charged for $144.00 and we only ship to the
     address on the card)

[  ] I am enclosing a check or money order for $144.00!


Note - If ordering outside continental US, please add 
$5 to S&H


P.S. If you send in your order and you are not one of the
first 50 to receive the Reprint and Reproduction Rights,
I will notify you immediately and give you the opportunity
to cancel your order.



_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
If you have received this message in error and would
like to be removed from future mailings, please reply
with the word remove in the subject. 
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/

---


From owner-acedb@hgmp.mrc.ac.uk  Mon Mar 27 22:22:17 2000
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From: "Webdesigns" <puat30@hotmail.com>
X-Newsgroups: bionet.software.acedb
Subject: get traffic on your site
Date: Mon, 27 Mar 2000 23:15:52 +0200
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--
Webposition Gold, a great tool to get traffic on your site without
advertising cost.

Go here:
http://www.web-submit.itgo.com





From owner-acedb@hgmp.mrc.ac.uk  Tue Mar 28 03:20:12 2000
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From: zgudmunt@my-deja.com
X-Newsgroups: bionet.software.acedb
Subject: ACeDB 4.8: availability???
Date: Tue, 28 Mar 2000 02:08:22 GMT
Organization: Deja.com - Before you buy.
Lines: 58
Message-ID: <8bp46c$g50$1@nnrp1.deja.com>
References: <895t9m$m3v$1@news.uky.edu> <38BA66FF.71AF4A2E@sanger.ac.uk>
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  Where can I obtain the most recent version of 4.8? I was looking for this
monthly build the other day on the FTP-site but did not see anything changed
from a version I tested several months ago. That was actually a precompiled
4.8 beta, straight  from one of the developers. Is there a better source for
me out there than the official site?

  I am primarily interested in the new client/server socket setup. I am
having trouble managing multiple local databases along with a couple of
servers. I think that a better solution would be a total client/server
system. But would I be able to set up Windows-clients that access
Unix-server(s)?


                 Thanks

                             Mummi

>
> Now...for ace 4_8 we have rewritten the server to directly use sockets
> instead of RPC (for portability and interfacing reasons). We have also
> taken the opportunity to add a password mechanism for users, so this
> will answer your question. Now you will have a "true" client/server
> setup with control files for restrict access to just the people you
> want. There are new admin commands to manage these control files.
>
> When this all be available ? Well its available now for Beta-testing.
> The caveat is that a number of other parts of acedb have been changed
> and we are still testing locally to iron out bugs. I can build you a
> binary (we are about to do a monthly build) and you can try it out if
> you like. I am also just doing the documentation because we have added
> some new commands to manage the user stuff and a number of other
> additions to the server.
>
> I hope this answers your questions, please feel free to email me direct
> or append here if you need more information.
>
> 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  Tue Mar 28 15:21:19 2000
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From: kristoff@hgmp.mrc.ac.uk
X-Newsgroups: bionet.software.acedb
Subject: cmsg newgroup bionet.software.acedb moderated
Control: newgroup bionet.software.acedb moderated
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 This newgroup message changes bionet.software.acedb to moderated
 as discussed in the group.

bionet.software.acedb is a moderated newsgroup.

Group submission address:   acedb@net.bio.net

For your newsgroups file:
bionet.software.acedb		Use of genome DBs using ACEDB. (Moderated)

 NOTE: the moderated bionet newsgroups follow the convention that
 articles can be delivered to the moderator by forming an address
 consisting of the newsgroup name with the dots changed to dashes
 @net.bio.net (i.e., bionet.software.www articles go to
 bionet-software-www@net.bio.net.) If you run INN, you can
 add "bionet.*:%s@net.bio.net" to /usr/lib/news/moderators to
 achieve the same effect.

This newsgroup will be moderated by:

	Ed Griffiths <edgrif@sanger.ac.uk>

Unapproved posts and posts with forged approval are subject to
cancellation without notice.

The guidelines for proper use of the Usenet News System as stated in the
rules of netiquette posted to news.announce.newgroups are to be followed
in the bionet newsgroups.  In particular, the following rules apply:

  *  No commercial advertising.
  *  No Excessive Multiple Posting and Excessive Cross-Posting (EMP/ECP,
     also known as "spam") involving these newsgroups.
  *  No pyramid or Ponzi schemes (including chain letters).
  *  No binary posts.

Violations of these specific rules may result in article cancellation
without notice even if cross-posted to groups outside the bionet
hierarchy.



From owner-acedb@hgmp.mrc.ac.uk  Tue Mar 28 17:55:06 2000
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From: Ed Griffiths <edgrif@sanger.ac.uk>
Newsgroups: bionet.software.acedb
Subject: moderation of acedb news group
Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre
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>From today Simon Kelley and I (both acedb developers at the Sanger
Centre) will be moderating the acedb newsgroup. (Richard Durbin and Mike
Cherry also have moderator access)

This is in response to a number of requests in this newsgroup and
several private requests sent direct to me.

Mail to this newsgroup falls mainly into three groups:

1) genuine acedb questions
2) bioinformatics job adverts
3) spam (usually porn, money, software type stuff)

I would suggest that items 1) & 2) are allowed through still, but if
people feel strongly about also rejecting item 2) then we will filter
out those items as well.

I hope this will produce a newsgroup that is much nicer to use, comments
and
suggestions welcome.

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 Mar 28 17:55:07 2000
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>From today Simon Kelley and I (both acedb developers at the Sanger
Centre) will be moderating the acedb newsgroup. (Richard Durbin and Mike
Cherry also have moderator access)

This is in response to a number of requests in this newsgroup and
several private requests sent direct to me.

Mail to this newsgroup falls mainly into three groups:

1) genuine acedb questions
2) bioinformatics job adverts
3) spam (usually porn, money, software type stuff)

I would suggest that items 1) & 2) are allowed through still, but if
people feel strongly about also rejecting item 2) then we will filter
out those items as well.

I hope this will produce a newsgroup that is much nicer to use, comments
and
suggestions welcome.

Ed.
-- 

------------------------------------------------------------------------------
| Ed Griffiths, Informatics
Group,                                             |
|               The Sanger Centre, Wellcome Trust Genome
Campus,               |
|               Hinxton, Cambridge CB10 1SA,
UK                                |
|                                                                      