From suzi at fruitfly.org  Tue Aug  2 13:09:50 2005
From: suzi at fruitfly.org (Suzanna Lewis)
Date: Tue, 2 Aug 2005 13:09:50 -0400
Subject: [DAS2] revised specific aims
Message-ID: <79d703a511efeb11e4c74a568a873460@fruitfly.org>

More tightening of the specific aims.

Suzi, Andrew, Gregg, and Lincoln (all visiting Rutgers)

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From Gregg_Helt at affymetrix.com  Mon Aug  8 19:09:44 2005
From: Gregg_Helt at affymetrix.com (Helt,Gregg)
Date: Mon, 8 Aug 2005 16:09:44 -0700
Subject: [DAS2] getting mail delivery failures when commiting to sourceforge
Message-ID: <C71929195D04BF48BAECD499AF717B48B6F8E4@msex02.affymetrix.com>


I just tried to do a number of commits to the genoviz sourceforge
repository, and got a whole bunch of bounced back mail about delivery
failures.  As far as I can tell, the commits themselves went through.
Steve or Ed, any idea what's going on?

	thanks,
	gregg

> -----Original Message-----
> From: Mail Delivery System
[mailto:Mailer-Daemon at users.sourceforge.net]
> Sent: Monday, August 08, 2005 3:46 PM
> To: gregghelt2 at users.sourceforge.net
> Subject: Mail delivery failed: returning message to sender
> 
> This message was created automatically by mail delivery software.
> 
> A message that you sent could not be delivered to one or more of its
> recipients. This is a permanent error. The following address(es)
failed:
> 
>   genoviz-cmts at lists.sourceforge.net
>     SMTP error from remote mailer after RCPT TO:<genoviz-
> cmts at lists.sourceforge.net>:
>     host externalmx-1.sourceforge.net [12.152.184.25]:
>     550-Verification failed for <gregghelt2 at users.sourceforge.net>
>     550-Called:   206.173.192.170
>     550-Sent:     RCPT TO:<postmaster at affymetrix.com>
>     550-Response: 550 5.7.1 <postmaster at affymetrix.com>... User
unknown
>     550 Sender verify failed
> 
> ------ This is a copy of the message, including all the headers.
------
> 
> Return-path: <gregghelt2 at users.sourceforge.net>
> Received: from localhost.localdomain ([127.0.0.1]
> helo=projects.sourceforge.net)
> 	by sc8-pr-cvs1.sourceforge.net with esmtp (Exim 4.20)
> 	id 1E2GNV-0001mX-He
> 	for genoviz-cmts at lists.sourceforge.net; Mon, 08 Aug 2005
15:45:53 -
> 0700
> From: Gregg Helt <gregghelt2 at users.sourceforge.net>
> To: genoviz-cmts at lists.sourceforge.net
> Subject: genoviz/igb/src/com/affymetrix/igb/genometry
> AnnotatedSeqGroup.java,1.3,1.4
> Date: Mon, 08 Aug 2005 22:45:43 +0000
> X-Mailer: Python syncmail $Revision: 1.2 $
<http://sf.net/projects/cvs-
> syncmail>
> Message-Id: <E1E2GNV-0001mX-He at sc8-pr-cvs1.sourceforge.net>
> 
> Update of
/cvsroot/genoviz/genoviz/igb/src/com/affymetrix/igb/genometry
> In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6828
> 
> Modified Files:
> 	AnnotatedSeqGroup.java
> Log Message:
> Changed AnnotatedSeqGroup.addSeq() method to throw a RuntimeException
is
> try to add a sequence whose id matches that of a sequence that's
already
> in the group.
> 
> Index: AnnotatedSeqGroup.java
> ===================================================================
> RCS file:
>
/cvsroot/genoviz/genoviz/igb/src/com/affymetrix/igb/genometry/AnnotatedS
eq
> Group.java,v
> retrieving revision 1.3
> retrieving revision 1.4
> diff -C2 -d -r1.3 -r1.4
> *** AnnotatedSeqGroup.java	26 Jul 2005 18:51:45 -0000	1.3
> --- AnnotatedSeqGroup.java	8 Aug 2005 22:45:40 -0000	1.4
> ***************
> *** 1,10 ****
>   /**
>   *   Copyright (c) 2001-2004 Affymetrix, Inc.
> ! *
>   *   Licensed under the Common Public License, Version 1.0 (the
> "License").
>   *   A copy of the license must be included with any distribution of
>   *   this source code.
>   *   Distributions from Affymetrix, Inc., place this in the
> ! *   IGB_LICENSE.html file.
>   *
>   *   The license is also available at
> --- 1,10 ----
>   /**
>   *   Copyright (c) 2001-2004 Affymetrix, Inc.
> ! *
>   *   Licensed under the Common Public License, Version 1.0 (the
> "License").
>   *   A copy of the license must be included with any distribution of
>   *   this source code.
>   *   Distributions from Affymetrix, Inc., place this in the
> ! *   IGB_LICENSE.html file.
>   *
>   *   The license is also available at
> ***************
> *** 38,43 ****
> 
>     public MutableAnnotatedBioSeq getSeq(int index) {
> !     if (index < seqlist.size()) {
> !       return (MutableAnnotatedBioSeq)seqlist.get(index);
>       }
>       else { return null; }
> --- 38,43 ----
> 
>     public MutableAnnotatedBioSeq getSeq(int index) {
> !     if (index < seqlist.size()) {
> !       return (MutableAnnotatedBioSeq)seqlist.get(index);
>       }
>       else { return null; }
> ***************
> *** 102,106 ****
>       }
>     }
> !
>     public MutableAnnotatedBioSeq addSeq(String seqid, int length) {
>       MutableAnnotatedBioSeq aseq = new SmartAnnotBioSeq(seqid,
> this.getID(), length);
> --- 102,106 ----
>       }
>     }
> !
>     public MutableAnnotatedBioSeq addSeq(String seqid, int length) {
>       MutableAnnotatedBioSeq aseq = new SmartAnnotBioSeq(seqid,
> this.getID(), length);
> ***************
> *** 110,117 ****
> 
>     public void addSeq(MutableAnnotatedBioSeq seq) {
> !     id2seq.put(seq.getID(), seq);
> !     seqlist.add(seq);
> !     if (seq instanceof SmartAnnotBioSeq) {
> !       ((SmartAnnotBioSeq)seq).setSeqGroup(this);
>       }
>     }
> --- 110,124 ----
> 
>     public void addSeq(MutableAnnotatedBioSeq seq) {
> !     MutableAnnotatedBioSeq oldseq =
> (MutableAnnotatedBioSeq)id2seq.get(seq.getID());
> !     if (oldseq == null) {
> !       id2seq.put(seq.getID(), seq);
> !       seqlist.add(seq);
> !       if (seq instanceof SmartAnnotBioSeq) {
> ! 	((SmartAnnotBioSeq)seq).setSeqGroup(this);
> !       }
> !     }
> !     else {
> !       throw new RuntimeException("ERROR! tried to add seq: " +
> seq.getID() + " to AnnotatedSeqGroup: " +
> ! 				 this.getID() + ", but seq with same id
is already
> in group");
>       }
>     }




From Gregg_Helt at affymetrix.com  Tue Aug  9 13:38:15 2005
From: Gregg_Helt at affymetrix.com (Helt,Gregg)
Date: Tue, 9 Aug 2005 10:38:15 -0700
Subject: [DAS2] More sourceforge trouble
Message-ID: <C71929195D04BF48BAECD499AF717B48B6F8F0@msex02.affymetrix.com>

I just tried to commit to sourceforge, and got a message that says "The
module genoviz was not found in the repository".  Checking my CVS
settings everything looks fine, I haven't changed anything recently.  My
CVSROOT is set  to :ext:gregghelt2 at cvs.sourceforge.net:/cvsroot/genoviz
.  Steve or Ed, any idea what's going on?  Could this be related to
cvs-commit email problems yesterday?
 
I don't like being cut off from the repository...
 
            gregg



From Steve_Chervitz at affymetrix.com  Tue Aug  9 13:53:39 2005
From: Steve_Chervitz at affymetrix.com (Chervitz, Steve)
Date: Tue, 09 Aug 2005 10:53:39 -0700
Subject: [DAS2] More sourceforge trouble
In-Reply-To: <C71929195D04BF48BAECD499AF717B48B6F8F0@msex02.affymetrix.com>
Message-ID: <BF1E3BB3.124A6%Steve_Chervitz@affymetrix.com>

Sourceforge is upgrading their CVS server right now. Here's the report from
their site status page:

( 2005-08-04 10:34:06 - Project CVS Service )   Starting on 2005-08-09 at
09:00 Pacific, developer CVS service will be offline for a expected period
of up to 36 hours to facilitate significant hardware upgrades. Developer CVS
service is moving from its current home on a 4 x 700MHz PIII, 500GB RAID5,
4GB RAM host to a new host that has roughly quadruple the I/O performance: a
2 x 2.8GHz Xeon, 1TB RAID5 striped, 8GB RAM host. Further announcements of
CVS service improvements will occur in the weeks following this hardware
upgrade (CVS sync delay is not yet eliminated, but that is on our list to
complete).

http://sourceforge.net/docman/display_doc.php?group_id=1&docid=2352

Steve


> From: "Helt,Gregg" <Gregg_Helt at affymetrix.com>
> Date: Tue, 9 Aug 2005 10:38:15 -0700
> To: <das2 at portal.open-bio.org>
> Subject: [DAS2] More sourceforge trouble
> 
> I just tried to commit to sourceforge, and got a message that says "The
> module genoviz was not found in the repository".  Checking my CVS
> settings everything looks fine, I haven't changed anything recently.  My
> CVSROOT is set  to :ext:gregghelt2 at cvs.sourceforge.net:/cvsroot/genoviz
> .  Steve or Ed, any idea what's going on?  Could this be related to
> cvs-commit email problems yesterday?
>  
> I don't like being cut off from the repository...
>  
>             gregg
> 
> _______________________________________________
> DAS2 mailing list
> DAS2 at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/das2



From dalke at dalkescientific.com  Wed Aug 10 00:13:32 2005
From: dalke at dalkescientific.com (Andrew Dalke)
Date: Wed, 10 Aug 2005 06:13:32 +0200
Subject: [DAS2] I'll be in Cambridge
Message-ID: <9993e4f2b4b7a20aad4b9fdfdacb025b@dalkescientific.com>

Hi DAS/2-ers,

   and more specifically the Cambridge area contingent.

I'm going to be at a conference in Scotland on the 4th October
(likely) and another in Cambridge 5-7 October 2005.  I
would like to stop by Hinxton and visit for a day or so,
most likely on the 28th-30th September time period.  Is
that a good time to drop by?

   Also, any recommendations on an inexpensive place to
stay around then?

					Andrew
					dalke at dalkescientific.com



From edgrif at sanger.ac.uk  Wed Aug 10 01:57:23 2005
From: edgrif at sanger.ac.uk (Ed Griffiths)
Date: Wed, 10 Aug 2005 06:57:23 +0100 (BST)
Subject: [DAS2] I'll be in Cambridge
In-Reply-To: <9993e4f2b4b7a20aad4b9fdfdacb025b@dalkescientific.com>
References: <9993e4f2b4b7a20aad4b9fdfdacb025b@dalkescientific.com>
Message-ID: <Pine.OSF.4.58.0508100654270.327009@griffin2.internal.sanger.ac.uk>

Andrew,

> I'm going to be at a conference in Scotland on the 4th October
> (likely) and another in Cambridge 5-7 October 2005.  I
> would like to stop by Hinxton and visit for a day or so,
> most likely on the 28th-30th September time period.  Is
> that a good time to drop by?

Yes, I will be around then for sure.

>    Also, any recommendations on an inexpensive place to
> stay around then?

I don't have ideas of the top of my head but I'll ask around and see if anyone
has any good suggestions.

Ed
-- 
             ** PLEASE NOTE NEW ADDRESS/PHONE NUMBER **

 ------------------------------------------------------------------------
| Ed Griffiths, Acedb development, Informatics Group,                    |
|  The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus   |
|  Hinxton, Cambridge CB10 1HH                                           |
|                                                                        |
| email: edgrif at sanger.ac.uk  Tel: +44-1223-496844  Fax: +44-1223-494919 |
 ------------------------------------------------------------------------


From suzi at fruitfly.org  Tue Aug 30 19:06:02 2005
From: suzi at fruitfly.org (Suzanna Lewis)
Date: Tue, 30 Aug 2005 16:06:02 -0700
Subject: [DAS2] Re: BioCyc pathway database sharing
In-Reply-To: <BF01A737.10FBF%Steve_Chervitz@affymetrix.com>
References: <BF01A737.10FBF%Steve_Chervitz@affymetrix.com>
Message-ID: <194173cc8184409fbaa21425505aa370@fruitfly.org>

Hmm, too bad this is one of the specific aims we are dropping. But that 
doesn't mean we can't work on it if we have the chance.

-S

On Jul 18, 2005, at 6:36 PM, Chervitz, Steve wrote:

> Cool. And speaking of interactions, I interacted with some of the
> biopathways folks at the ISMB in Detroit and mentioned our vision of 
> the
> pathways extension to DAS for the continuation grant. They seemed very
> interested and eager to have some way to enable distributed pathway
> annotation.
>
> They also were interested in helping contribute ideas/verbiage for the
> pathways section of the continuation grant. They recommended that we 
> post a
> blurb about what we are doing to the Biopax wiki, then send a message 
> to
> their discussion list with a pointer to this wiki entry. Sound 
> reasonable?
>
> Steve
>
>
>> From: Suzanna Lewis <suzi at fruitfly.org>
>> Date: Sun, 17 Jul 2005 13:53:20 -0700
>> To: "Chervitz, Steve" <Steve_Chervitz at affymetrix.com>
>> Cc: DAS/2 <das2 at portal.open-bio.org>
>> Subject: Re: [DAS2] Re: BioCyc pathway database sharing
>>
>> Here is a little bit of additional information. Lincoln has just
>> submitted a renewal application for the Reactome grant and it includes
>> a collaboration with Peter K and Paul Thomas (ABI) to regularly
>> exchange pathways. The plan is to use bioPax and I would guess that
>> this can be DAS-ified without too much difficulty.
>>
>> It is interesting to see the migration of interaction sets (as this
>> data gets refined) transmogrified into full-out pathway data, and all
>> the intermediate forms in between.
>>
>> -S
>>
>> On Jul 13, 2005, at 2:22 PM, Chervitz, Steve wrote:
>>
>>> My earlier message got sent prematurely. Here's the link to the
>>> BioInform
>>> article:
>>> http://www.bioinform.com/articles/view-sl.asp?Article=200578124042
>>>
>>> The reason I mention it is that it would be instructive to look into
>>> BioCyc's pathway tools in light of the pathway DAS extension being
>>> proposed
>>> in the DAS/2 continuation grant. This community may also be ideal
>>> candidate
>>> beta testers of pathway DAS prototypes.
>>>
>>> Steve
>>>
>>>> From: <Chervitz>, Steve <Steve_Chervitz at affymetrix.com>
>>>> Date: Wed, 13 Jul 2005 14:09:43 -0700
>>>> To: DAS/2 <das2 at portal.open-bio.org>
>>>> Subject: BioCyc pathway database sharing
>>>>
>>>> The current BioInform has an article about SRI's database adoption
>>>> program for
>>>> the computationally generated pathway databases. He says they are
>>>> making
>>>> available "peer-to-peer database sharing techniques":
>>>>
>>>>
>>>>
>>>> http://biocyc.org/intro.shtml#adopt
>>>
>>> _______________________________________________
>>> DAS2 mailing list
>>> DAS2 at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/das2
>>
>



From suzi at fruitfly.org  Tue Aug  2 17:09:50 2005
From: suzi at fruitfly.org (Suzanna Lewis)
Date: Tue, 2 Aug 2005 13:09:50 -0400
Subject: [DAS2] revised specific aims
Message-ID: <79d703a511efeb11e4c74a568a873460@fruitfly.org>

More tightening of the specific aims.

Suzi, Andrew, Gregg, and Lincoln (all visiting Rutgers)

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From Gregg_Helt at affymetrix.com  Mon Aug  8 23:09:44 2005
From: Gregg_Helt at affymetrix.com (Helt,Gregg)
Date: Mon, 8 Aug 2005 16:09:44 -0700
Subject: [DAS2] getting mail delivery failures when commiting to sourceforge
Message-ID: <C71929195D04BF48BAECD499AF717B48B6F8E4@msex02.affymetrix.com>


I just tried to do a number of commits to the genoviz sourceforge
repository, and got a whole bunch of bounced back mail about delivery
failures.  As far as I can tell, the commits themselves went through.
Steve or Ed, any idea what's going on?

	thanks,
	gregg

> -----Original Message-----
> From: Mail Delivery System
[mailto:Mailer-Daemon at users.sourceforge.net]
> Sent: Monday, August 08, 2005 3:46 PM
> To: gregghelt2 at users.sourceforge.net
> Subject: Mail delivery failed: returning message to sender
> 
> This message was created automatically by mail delivery software.
> 
> A message that you sent could not be delivered to one or more of its
> recipients. This is a permanent error. The following address(es)
failed:
> 
>   genoviz-cmts at lists.sourceforge.net
>     SMTP error from remote mailer after RCPT TO:<genoviz-
> cmts at lists.sourceforge.net>:
>     host externalmx-1.sourceforge.net [12.152.184.25]:
>     550-Verification failed for <gregghelt2 at users.sourceforge.net>
>     550-Called:   206.173.192.170
>     550-Sent:     RCPT TO:<postmaster at affymetrix.com>
>     550-Response: 550 5.7.1 <postmaster at affymetrix.com>... User
unknown
>     550 Sender verify failed
> 
> ------ This is a copy of the message, including all the headers.
------
> 
> Return-path: <gregghelt2 at users.sourceforge.net>
> Received: from localhost.localdomain ([127.0.0.1]
> helo=projects.sourceforge.net)
> 	by sc8-pr-cvs1.sourceforge.net with esmtp (Exim 4.20)
> 	id 1E2GNV-0001mX-He
> 	for genoviz-cmts at lists.sourceforge.net; Mon, 08 Aug 2005
15:45:53 -
> 0700
> From: Gregg Helt <gregghelt2 at users.sourceforge.net>
> To: genoviz-cmts at lists.sourceforge.net
> Subject: genoviz/igb/src/com/affymetrix/igb/genometry
> AnnotatedSeqGroup.java,1.3,1.4
> Date: Mon, 08 Aug 2005 22:45:43 +0000
> X-Mailer: Python syncmail $Revision: 1.2 $
<http://sf.net/projects/cvs-
> syncmail>
> Message-Id: <E1E2GNV-0001mX-He at sc8-pr-cvs1.sourceforge.net>
> 
> Update of
/cvsroot/genoviz/genoviz/igb/src/com/affymetrix/igb/genometry
> In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6828
> 
> Modified Files:
> 	AnnotatedSeqGroup.java
> Log Message:
> Changed AnnotatedSeqGroup.addSeq() method to throw a RuntimeException
is
> try to add a sequence whose id matches that of a sequence that's
already
> in the group.
> 
> Index: AnnotatedSeqGroup.java
> ===================================================================
> RCS file:
>
/cvsroot/genoviz/genoviz/igb/src/com/affymetrix/igb/genometry/AnnotatedS
eq
> Group.java,v
> retrieving revision 1.3
> retrieving revision 1.4
> diff -C2 -d -r1.3 -r1.4
> *** AnnotatedSeqGroup.java	26 Jul 2005 18:51:45 -0000	1.3
> --- AnnotatedSeqGroup.java	8 Aug 2005 22:45:40 -0000	1.4
> ***************
> *** 1,10 ****
>   /**
>   *   Copyright (c) 2001-2004 Affymetrix, Inc.
> ! *
>   *   Licensed under the Common Public License, Version 1.0 (the
> "License").
>   *   A copy of the license must be included with any distribution of
>   *   this source code.
>   *   Distributions from Affymetrix, Inc., place this in the
> ! *   IGB_LICENSE.html file.
>   *
>   *   The license is also available at
> --- 1,10 ----
>   /**
>   *   Copyright (c) 2001-2004 Affymetrix, Inc.
> ! *
>   *   Licensed under the Common Public License, Version 1.0 (the
> "License").
>   *   A copy of the license must be included with any distribution of
>   *   this source code.
>   *   Distributions from Affymetrix, Inc., place this in the
> ! *   IGB_LICENSE.html file.
>   *
>   *   The license is also available at
> ***************
> *** 38,43 ****
> 
>     public MutableAnnotatedBioSeq getSeq(int index) {
> !     if (index < seqlist.size()) {
> !       return (MutableAnnotatedBioSeq)seqlist.get(index);
>       }
>       else { return null; }
> --- 38,43 ----
> 
>     public MutableAnnotatedBioSeq getSeq(int index) {
> !     if (index < seqlist.size()) {
> !       return (MutableAnnotatedBioSeq)seqlist.get(index);
>       }
>       else { return null; }
> ***************
> *** 102,106 ****
>       }
>     }
> !
>     public MutableAnnotatedBioSeq addSeq(String seqid, int length) {
>       MutableAnnotatedBioSeq aseq = new SmartAnnotBioSeq(seqid,
> this.getID(), length);
> --- 102,106 ----
>       }
>     }
> !
>     public MutableAnnotatedBioSeq addSeq(String seqid, int length) {
>       MutableAnnotatedBioSeq aseq = new SmartAnnotBioSeq(seqid,
> this.getID(), length);
> ***************
> *** 110,117 ****
> 
>     public void addSeq(MutableAnnotatedBioSeq seq) {
> !     id2seq.put(seq.getID(), seq);
> !     seqlist.add(seq);
> !     if (seq instanceof SmartAnnotBioSeq) {
> !       ((SmartAnnotBioSeq)seq).setSeqGroup(this);
>       }
>     }
> --- 110,124 ----
> 
>     public void addSeq(MutableAnnotatedBioSeq seq) {
> !     MutableAnnotatedBioSeq oldseq =
> (MutableAnnotatedBioSeq)id2seq.get(seq.getID());
> !     if (oldseq == null) {
> !       id2seq.put(seq.getID(), seq);
> !       seqlist.add(seq);
> !       if (seq instanceof SmartAnnotBioSeq) {
> ! 	((SmartAnnotBioSeq)seq).setSeqGroup(this);
> !       }
> !     }
> !     else {
> !       throw new RuntimeException("ERROR! tried to add seq: " +
> seq.getID() + " to AnnotatedSeqGroup: " +
> ! 				 this.getID() + ", but seq with same id
is already
> in group");
>       }
>     }




From Gregg_Helt at affymetrix.com  Tue Aug  9 17:38:15 2005
From: Gregg_Helt at affymetrix.com (Helt,Gregg)
Date: Tue, 9 Aug 2005 10:38:15 -0700
Subject: [DAS2] More sourceforge trouble
Message-ID: <C71929195D04BF48BAECD499AF717B48B6F8F0@msex02.affymetrix.com>

I just tried to commit to sourceforge, and got a message that says "The
module genoviz was not found in the repository".  Checking my CVS
settings everything looks fine, I haven't changed anything recently.  My
CVSROOT is set  to :ext:gregghelt2 at cvs.sourceforge.net:/cvsroot/genoviz
.  Steve or Ed, any idea what's going on?  Could this be related to
cvs-commit email problems yesterday?
 
I don't like being cut off from the repository...
 
            gregg



From Steve_Chervitz at affymetrix.com  Tue Aug  9 17:53:39 2005
From: Steve_Chervitz at affymetrix.com (Chervitz, Steve)
Date: Tue, 09 Aug 2005 10:53:39 -0700
Subject: [DAS2] More sourceforge trouble
In-Reply-To: <C71929195D04BF48BAECD499AF717B48B6F8F0@msex02.affymetrix.com>
Message-ID: <BF1E3BB3.124A6%Steve_Chervitz@affymetrix.com>

Sourceforge is upgrading their CVS server right now. Here's the report from
their site status page:

( 2005-08-04 10:34:06 - Project CVS Service )   Starting on 2005-08-09 at
09:00 Pacific, developer CVS service will be offline for a expected period
of up to 36 hours to facilitate significant hardware upgrades. Developer CVS
service is moving from its current home on a 4 x 700MHz PIII, 500GB RAID5,
4GB RAM host to a new host that has roughly quadruple the I/O performance: a
2 x 2.8GHz Xeon, 1TB RAID5 striped, 8GB RAM host. Further announcements of
CVS service improvements will occur in the weeks following this hardware
upgrade (CVS sync delay is not yet eliminated, but that is on our list to
complete).

http://sourceforge.net/docman/display_doc.php?group_id=1&docid=2352

Steve


> From: "Helt,Gregg" <Gregg_Helt at affymetrix.com>
> Date: Tue, 9 Aug 2005 10:38:15 -0700
> To: <das2 at portal.open-bio.org>
> Subject: [DAS2] More sourceforge trouble
> 
> I just tried to commit to sourceforge, and got a message that says "The
> module genoviz was not found in the repository".  Checking my CVS
> settings everything looks fine, I haven't changed anything recently.  My
> CVSROOT is set  to :ext:gregghelt2 at cvs.sourceforge.net:/cvsroot/genoviz
> .  Steve or Ed, any idea what's going on?  Could this be related to
> cvs-commit email problems yesterday?
>  
> I don't like being cut off from the repository...
>  
>             gregg
> 
> _______________________________________________
> DAS2 mailing list
> DAS2 at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/das2



From dalke at dalkescientific.com  Wed Aug 10 04:13:32 2005
From: dalke at dalkescientific.com (Andrew Dalke)
Date: Wed, 10 Aug 2005 06:13:32 +0200
Subject: [DAS2] I'll be in Cambridge
Message-ID: <9993e4f2b4b7a20aad4b9fdfdacb025b@dalkescientific.com>

Hi DAS/2-ers,

   and more specifically the Cambridge area contingent.

I'm going to be at a conference in Scotland on the 4th October
(likely) and another in Cambridge 5-7 October 2005.  I
would like to stop by Hinxton and visit for a day or so,
most likely on the 28th-30th September time period.  Is
that a good time to drop by?

   Also, any recommendations on an inexpensive place to
stay around then?

					Andrew
					dalke at dalkescientific.com



From edgrif at sanger.ac.uk  Wed Aug 10 05:57:23 2005
From: edgrif at sanger.ac.uk (Ed Griffiths)
Date: Wed, 10 Aug 2005 06:57:23 +0100 (BST)
Subject: [DAS2] I'll be in Cambridge
In-Reply-To: <9993e4f2b4b7a20aad4b9fdfdacb025b@dalkescientific.com>
References: <9993e4f2b4b7a20aad4b9fdfdacb025b@dalkescientific.com>
Message-ID: <Pine.OSF.4.58.0508100654270.327009@griffin2.internal.sanger.ac.uk>

Andrew,

> I'm going to be at a conference in Scotland on the 4th October
> (likely) and another in Cambridge 5-7 October 2005.  I
> would like to stop by Hinxton and visit for a day or so,
> most likely on the 28th-30th September time period.  Is
> that a good time to drop by?

Yes, I will be around then for sure.

>    Also, any recommendations on an inexpensive place to
> stay around then?

I don't have ideas of the top of my head but I'll ask around and see if anyone
has any good suggestions.

Ed
-- 
             ** PLEASE NOTE NEW ADDRESS/PHONE NUMBER **

 ------------------------------------------------------------------------
| Ed Griffiths, Acedb development, Informatics Group,                    |
|  The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus   |
|  Hinxton, Cambridge CB10 1HH                                           |
|                                                                        |
| email: edgrif at sanger.ac.uk  Tel: +44-1223-496844  Fax: +44-1223-494919 |
 ------------------------------------------------------------------------


From suzi at fruitfly.org  Tue Aug 30 23:06:02 2005
From: suzi at fruitfly.org (Suzanna Lewis)
Date: Tue, 30 Aug 2005 16:06:02 -0700
Subject: [DAS2] Re: BioCyc pathway database sharing
In-Reply-To: <BF01A737.10FBF%Steve_Chervitz@affymetrix.com>
References: <BF01A737.10FBF%Steve_Chervitz@affymetrix.com>
Message-ID: <194173cc8184409fbaa21425505aa370@fruitfly.org>

Hmm, too bad this is one of the specific aims we are dropping. But that 
doesn't mean we can't work on it if we have the chance.

-S

On Jul 18, 2005, at 6:36 PM, Chervitz, Steve wrote:

> Cool. And speaking of interactions, I interacted with some of the
> biopathways folks at the ISMB in Detroit and mentioned our vision of 
> the
> pathways extension to DAS for the continuation grant. They seemed very
> interested and eager to have some way to enable distributed pathway
> annotation.
>
> They also were interested in helping contribute ideas/verbiage for the
> pathways section of the continuation grant. They recommended that we 
> post a
> blurb about what we are doing to the Biopax wiki, then send a message 
> to
> their discussion list with a pointer to this wiki entry. Sound 
> reasonable?
>
> Steve
>
>
>> From: Suzanna Lewis <suzi at fruitfly.org>
>> Date: Sun, 17 Jul 2005 13:53:20 -0700
>> To: "Chervitz, Steve" <Steve_Chervitz at affymetrix.com>
>> Cc: DAS/2 <das2 at portal.open-bio.org>
>> Subject: Re: [DAS2] Re: BioCyc pathway database sharing
>>
>> Here is a little bit of additional information. Lincoln has just
>> submitted a renewal application for the Reactome grant and it includes
>> a collaboration with Peter K and Paul Thomas (ABI) to regularly
>> exchange pathways. The plan is to use bioPax and I would guess that
>> this can be DAS-ified without too much difficulty.
>>
>> It is interesting to see the migration of interaction sets (as this
>> data gets refined) transmogrified into full-out pathway data, and all
>> the intermediate forms in between.
>>
>> -S
>>
>> On Jul 13, 2005, at 2:22 PM, Chervitz, Steve wrote:
>>
>>> My earlier message got sent prematurely. Here's the link to the
>>> BioInform
>>> article:
>>> http://www.bioinform.com/articles/view-sl.asp?Article=200578124042
>>>
>>> The reason I mention it is that it would be instructive to look into
>>> BioCyc's pathway tools in light of the pathway DAS extension being
>>> proposed
>>> in the DAS/2 continuation grant. This community may also be ideal
>>> candidate
>>> beta testers of pathway DAS prototypes.
>>>
>>> Steve
>>>
>>>> From: <Chervitz>, Steve <Steve_Chervitz at affymetrix.com>
>>>> Date: Wed, 13 Jul 2005 14:09:43 -0700
>>>> To: DAS/2 <das2 at portal.open-bio.org>
>>>> Subject: BioCyc pathway database sharing
>>>>
>>>> The current BioInform has an article about SRI's database adoption
>>>> program for
>>>> the computationally generated pathway databases. He says they are
>>>> making
>>>> available "peer-to-peer database sharing techniques":
>>>>
>>>>
>>>>
>>>> http://biocyc.org/intro.shtml#adopt
>>>
>>> _______________________________________________
>>> DAS2 mailing list
>>> DAS2 at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/das2
>>
>