From dlondon at ebi.ac.uk  Wed Mar  3 16:06:52 2004
From: dlondon at ebi.ac.uk (Darin London)
Date: Wed Mar  3 16:27:44 2004
Subject: [DAS] BOSC 2004 Announcement and Call for Papers
Message-ID: <Pine.LNX.4.44.0403032044280.31442-100000@parrot.ebi.ac.uk>

 {Please pass the word!}
 
 MEETING ANNOUNCEMENT & CALL FOR SPEAKERS
 
 The 5th annual Bioinformatics Open Source Conference (BOSC'2004) is 
 organized by the not-for-profit Open Bioinformatics Foundation. The 
 meeting will take place July 29-30, 2004 in Glasgow, Scotland, and is 
 one of several Special Interest Group (SIG) meetings occurring in 
 conjunction with the 12th International Conference on Intelligent 
 Systems for Molecular Biology.

 see http://www.iscb.org/ismb2004/ for more information.

 The focus of the meeting will be on current and emerging Open Source** 
 informatics tools and toolkits. BOSC provides a forum for developers, 
 project groups, users and interested parties to meet personally, exchange ideas and 
 collaborate together.

 In addition, keynote speeches from well known Open Source Bioinformatics 
 leaders are being planned.
 
 BOSC PROGRAM & CONTACT INFO
 
 * Web: http://www.open-bio.org/bosc2004/
 * Email: bosc@open-bio.org
 * Online registration: https://www.cteusa.com/iscb3/
 
 
 FEES
 
 * Corporate :GBP ?165.00 british pounds sterling
 * Academic : GBP ?120.00 british pounds sterling
 * Student : GBP ?90.00 british pounds sterling
 
 A 17.5% Valued Added Tax(VAT) will be added to all fees.

 Note: We have tried to set our fees as low as possible without risking 
 the chance that the foundation will lose money on the event. We budget 
 with the goal of breaking even on costs or realizing a small profit.
 
 REGISTER ONLINE FOR BOSC'2004 & ISMB AT:
 https://www.cteusa.com/iscb3/
 
 SPEAKERS & ABSTRACTS WANTED
 
 The program committee is currently seeking abstracts for talks at BOSC 
 2004. BOSC is a great opportunity for you to tell the community about 
 your use, development, or philosophy of open source software development 
 in bioinformatics. The committee will select several submitted abstracts 
 for 25-minute talks and others for shorter "lightning" talks. Accepted 
 abstracts will be published on the BOSC web site.
 
 If you are interested in speaking at BOSC 2004, 
 please send us:

 * an abstract (no more than a few paragraphs)
 * a URL for the project page, if applicable  
 * information about the open source license used for your software or
   your release plans.
 
 LIGHTNING-TALK SPEAKERS WANTED!
 
 The program committee is currently seeking speakers for the lightning 
 talks at BOSC 2004. Lightning talks are quick - only five minutes 
 long - and a great opportunity for you to give people a quick 
 summary of your open source project, code, idea, or vision of the future.

 If you are interested in giving a lightning talk at BOSC 2004, 
 please send us:

 * a brief title and summary (one or two lines)
 * a URL for the project page, if applicable
 * information about the open source license used for your software or 
   your release plans.

 We will accept entries on-line until BOSC starts, but
 space for demos and lightning talks is limited.<br/>
    
 SOFTWARE DEMONSTRATIONS WANTED!

 If you are involved in the development of Open Source Bioinformatics 
 Software, you are invited to provide a short demonstration to attendees 
 of BOSC 2004.

 If you are interested in giving a software demonstration at BOSC 2004,
 please send us:

 * a brief title and summary (one or two lines)
 * a URL for the project page, if applicable
 * Internet connectivity requirements (e.g. website Application served on 
   the world wide web, or web based client application).

   We will accept entries on-line until the BOSC starts, but
   space for demos and lightning talks is limited.  

 ** Because the mission of the OBF is to promote Open Source software, we 
 will favor submissions for projects that apply a recognized Open Source 
 License, or adhere to the general Open Source Philosophy.

 See the following websites for further details:
 href="http://www.opensource.org/licenses/
 href="http://www.opensource.org/docs/definition.php




From dag at sonsorol.org  Wed Mar 10 21:30:13 2004
From: dag at sonsorol.org (Chris Dagdigian)
Date: Wed Mar 10 21:35:54 2004
Subject: [DAS] O|B|F mail update -- making progress on anti-spam issues with
 our mailing lists
Message-ID: <404FCF35.5010705@sonsorol.org>


Hi folks,

Apologies for the cross-posting but I just wanted to give our list 
members and admins an update on some new anti-spam measures we have 
(re)enabled. Good news to report basically...

The most annoying spams recently have been the simple plain text 
messages without any HTML, attachments or mime-encoding that just slip 
right by our filters.  Some lists have been forced to switch over to 
"only members can post" while other lists (like bioperl) have 
consistantly voted to stay as open as possible.

I'll update you on our current efforts as well as a new effort that is 
about 24 hours old but already working really well so far.

Until yesterday we had three main lines of defense against spam:

1. The mailserver itself (rejects mail from nonexistant domains, etc.)

2. The sendmail Mail::Milter extention (MIMEDefang+SpamAssassin are used 
to scan all incoming messages. Anything that scores higher than 8.0 is 
simply discarded automatically. MIMEDefang also strips dangerous 
attachments like .exe and .pif)

3. Our mailing list moderation queue (emails with attachments, odd MIME 
encodings and spamassassin scores from 0.0 - 7.9 are held in a moderator 
queue for a human to make an accept/discard decision)

Here are some stats on how this system worked over the past few days:

  o 138 attempts to relay mail through our server blocked
  o 192 emails blocked due to forged or unresolvable sender domain
  o 577 emails discarded automatically by SpamAssassin+MIMEDefang

This system worked *ok* but put a lot of work onto the shoulders of our 
list admins who constantly had to weed out the spam caught up in the 
mailing list moderator system.

Yesterday I brought online another system that seems to be already 
working really well. It catches spam before we even accept it on our 
server which makes the load easier on both our scanning software and our 
  human list moderators.

The system is the RBL+ blackhole list from http://www.mail-abuse.org and 
the way it works is that we now query (via DNS) the RBL+ database each 
time someone connects to our mail server. If the RBL check against the 
sender IP address comes back as "positive" we reject the incoming email.

RBL+ is a combination of four constantly updated databases:

  1. RBL -- IP addresses of known, documented spammers and spam machines
  2. RSS -- IP addresses of documented/tested unsecured email relays
  3. OPS -- IP addresses of documented open proxy servers w/ spam history
  3. DUL -- IP addresses belonging to ISP dialup and DHCP customers

We have already blocked 137 email attempts in the last 24 hours from 
machines that were listed in one or more of the RBL databases.

It is too soon to tell but if the RBL+ system plus our existing 
anti-spam measures work well enough we may be in a position where our 
"closed" mailing lists could revert back to being 'anyone can post'.

Feedback appreciated. Especially if you get a "reject" message from us 
saying that you are listed in the RBL+ blackhole database!


Regards,
Chris
O|B|F




From avilella at ebi.ac.uk  Wed Mar 31 08:03:51 2004
From: avilella at ebi.ac.uk (avilella)
Date: Wed Mar 31 08:09:21 2004
Subject: [DAS] entry_points query
Message-ID: <1080738230.3527.4.camel@localhost.localdomain>

Hi all,

I have been trying to get the grips with biodas the last couple of days,
and playing around with the several servers that are listed by Dr. F.
Cheung.

Any there is something that I don't understand about entry_points query:

If I query any of the databases for something like:

PREFIX/das/DSN/entry_points

Which is what you would query according to the specification (1.5),
you don't get anything.

Now if instead you query with lowecase dsn:

PREFIX/das/dsn/entry_points

you get:

(1) the same result as dsn query for some sites, like for example:

http://genome.cse.ucsc.edu/cgi-bin/das/dsn/entry_points
http://www.wormbase.org/db/das/dsn/entry_points
http://www.tigr.org/docs/tigr-scripts/tgi/das/dsn/entry_points

(2) You don't get anything, like for example:

http://servlet.sanger.ac.uk:8080/das/dsn/entry_points
http://tomcat.molgen.mpg.de:8080/das/dsn/entry_points
http://supfam.org/SUPERFAMILY/cgi-bin/das/dsn/entry_points

(3) You get an error 402 Bad command arguments (arguments invalid):
------------------------------
DAS Error 402

 Path is dsn/entry_points?
------------------------------

like for example in:

http://genome.ornl.gov/das/das.cgi/dsn/entry_points

This is the list that I have checked:

http://servlet.sanger.ac.uk:8080/das
http://genome.cse.ucsc.edu/cgi-bin/das/dsn
http://www.wormbase.org/db/das/dsn
http://genome.ornl.gov/das/das.cgi/dsn
http://tomcat.molgen.mpg.de:8080/das
http://eugenes.org/cgi-bin/srsdas/dsn
http://supfam.org/SUPERFAMILY/cgi-bin/das/dsn
http://www.tigr.org/docs/tigr-scripts/tgi/das/dsn

*http://stash.mrc-lmb.cam.ac.uk:8080/das
*http://das.bcgsc.ca:8080/das
*http://gadfly.gen.cam.ac.uk:8080/das
*http://ensembl.gsc.riken.go.jp/cgi-bin/das/dsn

*Not there anymore.

Any hint of what may be happening?

Thanks in advance,

    Albert.

From td2 at sanger.ac.uk  Wed Mar 31 08:24:03 2004
From: td2 at sanger.ac.uk (Thomas Down)
Date: Wed Mar 31 08:29:13 2004
Subject: [DAS] entry_points query
In-Reply-To: <1080738230.3527.4.camel@localhost.localdomain>
References: <1080738230.3527.4.camel@localhost.localdomain>
Message-ID: <AE0237DE-8316-11D8-B15F-000A95C8B056@sanger.ac.uk>


On 31 Mar 2004, at 14:03, avilella wrote:

> Hi all,

Hi.

> I have been trying to get the grips with biodas the last couple of 
> days,
> and playing around with the several servers that are listed by Dr. F.
> Cheung.
>
> Any there is something that I don't understand about entry_points 
> query:
>
> If I query any of the databases for something like:
>
> PREFIX/das/DSN/entry_points

You're not literally meant to put the string "DSN" in that kind of 
query -- you should substitute in a data source ID (DSN).  For example, 
try:

     http://servlet.sanger.ac.uk:8080/das/vega40/entry_points

> Which is what you would query according to the specification (1.5),
> you don't get anything.
>
> Now if instead you query with lowecase dsn:
>
> PREFIX/das/dsn/entry_points

In this case, most server implementations are interpreting your query 
as the standard DAS `dsn' command.  The differences you're seeing 
between server implementations just reflects the fact that some of them 
are more tolerant that others about having extra text after the command 
name.

        Thomas

From ianl at ebi.ac.uk  Wed Mar 31 08:29:11 2004
From: ianl at ebi.ac.uk (ian Longden)
Date: Wed Mar 31 08:34:21 2004
Subject: [DAS] entry_points query
In-Reply-To: <1080738230.3527.4.camel@localhost.localdomain>
References: <1080738230.3527.4.camel@localhost.localdomain>
Message-ID: <406AC7A7.3040102@ebi.ac.uk>

avilella wrote:

>Hi all,
>
>I have been trying to get the grips with biodas the last couple of days,
>and playing around with the several servers that are listed by Dr. F.
>Cheung.
>
>Any there is something that I don't understand about entry_points query:
>
>If I query any of the databases for something like:
>
>PREFIX/das/DSN/entry_points
>
>Which is what you would query according to the specification (1.5),
>you don't get anything.
>
>Now if instead you query with lowecase dsn:
>
>PREFIX/das/dsn/entry_points
>
>you get:
>
>(1) the same result as dsn query for some sites, like for example:
>
>http://genome.cse.ucsc.edu/cgi-bin/das/dsn/entry_points
>http://www.wormbase.org/db/das/dsn/entry_points
>http://www.tigr.org/docs/tigr-scripts/tgi/das/dsn/entry_points
>
>(2) You don't get anything, like for example:
>
>http://servlet.sanger.ac.uk:8080/das/dsn/entry_points
>http://tomcat.molgen.mpg.de:8080/das/dsn/entry_points
>http://supfam.org/SUPERFAMILY/cgi-bin/das/dsn/entry_points
>  
>
Okay so lets take the servlet example.
Use the
http://servlet.sanger.ac.uk:8080/das/dsn
to get the valid dsn's
which will give you something like:-
-
<DASDSN>
-
<DSN>
<SOURCE id="ens1431cds" version="14">Ensembl 14.31 CDS</SOURCE>
<MAPMASTER>http://das.ensembl.org/das/ensembl1431/</MAPMASTER>
<DESCRIPTION>Ensembl CDS</DESCRIPTION>
</DSN>
-
<DSN>
<SOURCE id="ens1431snp" version="14.31">snps</SOURCE>
<MAPMASTER>http://das.ensembl.org/das/ensembl1431/</MAPMASTER>
<DESCRIPTION>Human genome SNPs from Ensembl</DESCRIPTION>
</DSN>

And then to get the entry points for that dsn replace dsn with the dsn name.
 e.g.  for the first dsn ensembl1431


http://servlet.sanger.ac.uk:8080/das/ensembl1431/entry_points

should be used to obtain the entry points.
The documentation does not know what valid dsn's are hence dsn is written.


Hope this clears it up.

>(3) You get an error 402 Bad command arguments (arguments invalid):
>------------------------------
>DAS Error 402
>
> Path is dsn/entry_points?
>------------------------------
>
>like for example in:
>
>http://genome.ornl.gov/das/das.cgi/dsn/entry_points
>
>This is the list that I have checked:
>
>http://servlet.sanger.ac.uk:8080/das
>http://genome.cse.ucsc.edu/cgi-bin/das/dsn
>http://www.wormbase.org/db/das/dsn
>http://genome.ornl.gov/das/das.cgi/dsn
>http://tomcat.molgen.mpg.de:8080/das
>http://eugenes.org/cgi-bin/srsdas/dsn
>http://supfam.org/SUPERFAMILY/cgi-bin/das/dsn
>http://www.tigr.org/docs/tigr-scripts/tgi/das/dsn
>
>*http://stash.mrc-lmb.cam.ac.uk:8080/das
>*http://das.bcgsc.ca:8080/das
>*http://gadfly.gen.cam.ac.uk:8080/das
>*http://ensembl.gsc.riken.go.jp/cgi-bin/das/dsn
>
>*Not there anymore.
>
>Any hint of what may be happening?
>
>Thanks in advance,
>
>    Albert.
>
>_______________________________________________
>DAS mailing list
>DAS@biodas.org
>http://biodas.org/mailman/listinfo/das
>  
>


From avilella at ebi.ac.uk  Wed Mar 31 08:20:16 2004
From: avilella at ebi.ac.uk (avilella)
Date: Wed Apr  7 23:36:15 2004
Subject: [DAS] little typo in the spec.html document
Message-ID: <1080739216.3527.7.camel@localhost.localdomain>

There is a 'format format' typo.

Find diff and modified file attached,

    Albert.
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From lstein at cshl.edu  Fri Mar  5 12:26:16 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Thu Apr  8 07:05:28 2004
Subject: [DAS] Re: LDAS makefile problem
In-Reply-To: <200403040756.i247ugH05723@mhost2.ucalgary.ca>
References: <200403040756.i247ugH05723@mhost2.ucalgary.ca>
Message-ID: <200403051220.16472.lstein@cshl.edu>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi,

I've seen this problem with faulty Perl installations.  The easiest 
way out of this is to build Perl from source and reinstall.  It won't 
take you more than 10 minutes.

Lincoln

On Thursday 04 March 2004 02:56 am, hili@ucalgary.ca wrote:
> Hi,
>
> I am trying to intall the LDAS on my Redhat Linux 9.0 server, but I
> constantly have a problem with the makefile generated by
> Makefile.PL. My Linux server has Apache 2 and Mysql server 3.23
> installed by default. Also, it has built-in perl-DBI and
> perl-DBD-mysql. I have installed bioperl-live using cpan shell,
> which I had got some testing failed, but not many. When I tried
> 'perl Makefile.PL', I gave the configuaration directory as
> /etc/httpd/conf, the CGI script directory as /var/www/cgi-bin, and
> load script directory as /usr/bin. Then I got warning that pod2man
> program could be located. I made a softlink in the LDAS directory
> to the /usr/bin/pod2man. When I tried make, I got error message
> like this: Makefile:81: *** missing separator. Stop. What have I
> done wrong? This is the beggining of my term project. Please help!
>
> Thank you.
>
> Irene

- -- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
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From hili at ucalgary.ca  Thu Mar  4 03:02:34 2004
From: hili at ucalgary.ca (hili@ucalgary.ca)
Date: Thu Apr  8 13:31:29 2004
Subject: [DAS] LDAS makefile problem
Message-ID: <200403040756.i247ugH05723@mhost2.ucalgary.ca>

Hi,

I am trying to intall the LDAS on my Redhat Linux 9.0 server, but I constantly
have a problem with the makefile generated by Makefile.PL. My Linux server has
Apache 2 and Mysql server 3.23 installed by default. Also, it has built-in
perl-DBI and perl-DBD-mysql. I have installed bioperl-live using cpan shell,
which I had got some testing failed, but not many. When I tried 'perl
Makefile.PL', I gave the configuaration directory as /etc/httpd/conf, the CGI
script directory as /var/www/cgi-bin, and load script directory as /usr/bin.
Then I got warning that pod2man program could be located. I made a softlink in
the LDAS directory to the /usr/bin/pod2man. When I tried make, I got error
message like this: Makefile:81: *** missing separator. Stop. What have I done
wrong? This is the beggining of my term project. Please help!

Thank you.

Irene