From gregghelt at gmail.com Fri Sep 12 20:36:48 2008 From: gregghelt at gmail.com (Gregg Helt) Date: Sat, 13 Sep 2008 01:36:48 +0100 Subject: [DAS2] Merging DAS and DAS2 discussion lists Message-ID: <50158cb00809121736v73d2d2dfn9429f1ee490b7cd4@mail.gmail.com> Hi all, I've been out at the Hinxton genome center this week talking to other DAS developers about spec evolution etc. In the interest of reviving activity on the lists, it was proposed that the DAS and DAS2 discussion lists be merged. Which makes sense to me. So unless there's major objection, the DAS2 list will soon be merged back into the DAS list ( das at biodas.org), hopefully within a week or two. I'll be posting more about my recent DAS & DAS2 work soon. sincerely, Gregg Helt From aloraine at gmail.com Sat Sep 13 18:25:14 2008 From: aloraine at gmail.com (Ann Loraine) Date: Sat, 13 Sep 2008 18:25:14 -0400 Subject: [DAS2] Merging DAS and DAS2 discussion lists In-Reply-To: <50158cb00809121736v73d2d2dfn9429f1ee490b7cd4@mail.gmail.com> References: <50158cb00809121736v73d2d2dfn9429f1ee490b7cd4@mail.gmail.com> Message-ID: <83722dde0809131525t3b4a99ap9c6706e79b861116@mail.gmail.com> That sounds like a good idea to me. -Ann On Fri, Sep 12, 2008 at 8:36 PM, Gregg Helt wrote: > Hi all, I've been out at the Hinxton genome center this week talking to > other DAS developers about spec evolution etc. In the interest of reviving > activity on the lists, it was proposed that the DAS and DAS2 discussion > lists be merged. Which makes sense to me. So unless there's major > objection, the DAS2 list will soon be merged back into the DAS list ( > das at biodas.org), hopefully within a week or two. > > I'll be posting more about my recent DAS & DAS2 work soon. > > sincerely, > Gregg Helt > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > From ch-das at bobobeach.com Sat Sep 13 21:22:44 2008 From: ch-das at bobobeach.com (Cyrus Harmon) Date: Sat, 13 Sep 2008 18:22:44 -0700 Subject: [DAS2] Merging DAS and DAS2 discussion lists In-Reply-To: <83722dde0809131525t3b4a99ap9c6706e79b861116@mail.gmail.com> References: <50158cb00809121736v73d2d2dfn9429f1ee490b7cd4@mail.gmail.com> <83722dde0809131525t3b4a99ap9c6706e79b861116@mail.gmail.com> Message-ID: not as good of an idea as merging the two specs, but I step in the right direction I suppose... On Sep 13, 2008, at 3:25 PM, Ann Loraine wrote: > That sounds like a good idea to me. > > -Ann > > On Fri, Sep 12, 2008 at 8:36 PM, Gregg Helt > wrote: >> Hi all, I've been out at the Hinxton genome center this week >> talking to >> other DAS developers about spec evolution etc. In the interest of >> reviving >> activity on the lists, it was proposed that the DAS and DAS2 >> discussion >> lists be merged. Which makes sense to me. So unless there's major >> objection, the DAS2 list will soon be merged back into the DAS list ( >> das at biodas.org), hopefully within a week or two. >> >> I'll be posting more about my recent DAS & DAS2 work soon. >> >> sincerely, >> Gregg Helt >> _______________________________________________ >> DAS2 mailing list >> DAS2 at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das2 >> > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 From gregghelt at gmail.com Tue Sep 16 10:36:03 2008 From: gregghelt at gmail.com (Gregg Helt) Date: Tue, 16 Sep 2008 07:36:03 -0700 Subject: [DAS2] Fwd: [DAS] Spec review In-Reply-To: <48CFA3F2.8060509@ebi.ac.uk> References: <48CFA3F2.8060509@ebi.ac.uk> Message-ID: <50158cb00809160736h75528e76pd1f9e9e3edcecf06@mail.gmail.com> ---------- Forwarded message ---------- From: Andy Jenkinson Date: Tue, Sep 16, 2008 at 5:17 AM Subject: [DAS] Spec review To: das at biodas.org Hi all, Over the last couple of weeks there have been a few meetings on the Hinxton campus aimed at exploring options for reconciling the two versions of the DAS spec. Involved were myself, Gregg Helt, Jonathan Warren, Felix Kokocinski, Phil Jones, Henning Hermjakob and Tim Hubbard. As a first step we have conducted a review of the current 1.53 spec with a view to updating it. The aim is to make the document more consistent with common usage, add official support for the "sources" metadata command (from 1.53E and DAS/2) and to reduce complexity and confusion by removing unused features. Another mail will be sent out soon with the conclusions so that they can be discussed before any changes are made. Cheers, Andy _______________________________________________ DAS mailing list DAS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/das From lincoln.stein at gmail.com Tue Sep 16 15:51:41 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 16 Sep 2008 15:51:41 -0400 Subject: [DAS2] Fwd: [DAS] Spec review In-Reply-To: <50158cb00809160736h75528e76pd1f9e9e3edcecf06@mail.gmail.com> References: <48CFA3F2.8060509@ebi.ac.uk> <50158cb00809160736h75528e76pd1f9e9e3edcecf06@mail.gmail.com> Message-ID: <6dce9a0b0809161251t76a3cf3qc2cf4f7209e929ce@mail.gmail.com> Great! Keep me in the loop. Lincoln On Tue, Sep 16, 2008 at 10:36 AM, Gregg Helt wrote: > ---------- Forwarded message ---------- > From: Andy Jenkinson > Date: Tue, Sep 16, 2008 at 5:17 AM > Subject: [DAS] Spec review > To: das at biodas.org > > > Hi all, > > Over the last couple of weeks there have been a few meetings on the Hinxton > campus aimed at exploring options for reconciling the two versions of the > DAS spec. Involved were myself, Gregg Helt, Jonathan Warren, Felix > Kokocinski, Phil Jones, Henning Hermjakob and Tim Hubbard. > > As a first step we have conducted a review of the current 1.53 spec with a > view to updating it. The aim is to make the document more consistent with > common usage, add official support for the "sources" metadata command (from > 1.53E and DAS/2) and to reduce complexity and confusion by removing unused > features. Another mail will be sent out soon with the conclusions so that > they can be discussed before any changes are made. > > Cheers, > Andy > > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Quinn Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From gregghelt at gmail.com Mon Sep 29 17:27:30 2008 From: gregghelt at gmail.com (Gregg Helt) Date: Mon, 29 Sep 2008 14:27:30 -0700 Subject: [DAS2] Restarting DAS/2 teleconferences? Message-ID: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> Hello again everybody! After taking an eight month sabbatical, I'm back to work (currently as a free agent). In the last two months I've focused mainly on distributed annotation and DAS/2 in particular. And although traffic on the list has been light/nonexistent, I know there are a number of others now actively working on DAS/2 servers and clients. I'm hoping we can move the offline discussions we've been having back onto the list. I would also like to restart the DAS/2 teleconferences as soon as possible. Ann, is the offer to host these on your teleconference line still good? Would people be up for this Thursday morning (Pacific time) for the first one? If not please propose a different time. I think we should plan to devote most of the teleconference to a specific topic each time. For the first one I'd like to do an overview of the current state of DAS/2 -- spec, client/server/validator/registry implementations, deployments, who's working on what, etc. After that here's my shortlist, please chime in with other possibilities: Proposed spec changes -- DAS/2.1 Integration of DAS1 and DAS/2 Security / Authorization issues Server implementations (Genometry, Biopackages, HapMap, Trellis (my new stuff)) Client implementations (IGB, ???) Current state of distributed annotation in general Integration of DAS/2 with GMOD Hope to talk with everyone soon, Gregg From gregghelt at gmail.com Mon Sep 29 17:30:42 2008 From: gregghelt at gmail.com (Gregg Helt) Date: Mon, 29 Sep 2008 14:30:42 -0700 Subject: [DAS2] Restarting DAS/2 teleconferences? In-Reply-To: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> References: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> Message-ID: <50158cb00809291430k34eab050ib74b9893427237ac@mail.gmail.com> Oh yeah, another topic for the teleconference schedule: the DAS/2 paper! On Mon, Sep 29, 2008 at 2:27 PM, Gregg Helt wrote: > > Hello again everybody! > > After taking an eight month sabbatical, I'm back to work (currently as a > free agent). In the last two months I've focused mainly on distributed > annotation and DAS/2 in particular. And although traffic on the list has > been light/nonexistent, I know there are a number of others now actively > working on DAS/2 servers and clients. I'm hoping we can move the offline > discussions we've been having back onto the list. > > I would also like to restart the DAS/2 teleconferences as soon as > possible. Ann, is the offer to host these on your teleconference line still > good? Would people be up for this Thursday morning (Pacific time) for the > first one? If not please propose a different time. I think we should plan > to devote most of the teleconference to a specific topic each time. For the > first one I'd like to do an overview of the current state of DAS/2 -- spec, > client/server/validator/registry implementations, deployments, who's working > on what, etc. After that here's my shortlist, please chime in with other > possibilities: > > Proposed spec changes -- DAS/2.1 > Integration of DAS1 and DAS/2 > Security / Authorization issues > Server implementations (Genometry, Biopackages, HapMap, Trellis (my > new stuff)) > Client implementations (IGB, ???) > Current state of distributed annotation in general > Integration of DAS/2 with GMOD > > Hope to talk with everyone soon, > Gregg > > > From aloraine at gmail.com Mon Sep 29 19:53:30 2008 From: aloraine at gmail.com (Ann Loraine) Date: Mon, 29 Sep 2008 19:53:30 -0400 Subject: [DAS2] Restarting DAS/2 teleconferences? In-Reply-To: <50158cb00809291430k34eab050ib74b9893427237ac@mail.gmail.com> References: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> <50158cb00809291430k34eab050ib74b9893427237ac@mail.gmail.com> Message-ID: <83722dde0809291653y718daf6cxd1f6deb3d94d78dd@mail.gmail.com> My department business officer set up the paperwork for a conference call about a month after I got to Charlotte. I'll get back in touch with her about the details and let you know the specifics. Our best time for this is going to be any time on Wed or Thur. Best, Ann On Mon, Sep 29, 2008 at 5:30 PM, Gregg Helt wrote: > Oh yeah, another topic for the teleconference schedule: the DAS/2 paper! > > On Mon, Sep 29, 2008 at 2:27 PM, Gregg Helt wrote: > >> >> Hello again everybody! >> >> After taking an eight month sabbatical, I'm back to work (currently as a >> free agent). In the last two months I've focused mainly on distributed >> annotation and DAS/2 in particular. And although traffic on the list has >> been light/nonexistent, I know there are a number of others now actively >> working on DAS/2 servers and clients. I'm hoping we can move the offline >> discussions we've been having back onto the list. >> >> I would also like to restart the DAS/2 teleconferences as soon as >> possible. Ann, is the offer to host these on your teleconference line still >> good? Would people be up for this Thursday morning (Pacific time) for the >> first one? If not please propose a different time. I think we should plan >> to devote most of the teleconference to a specific topic each time. For the >> first one I'd like to do an overview of the current state of DAS/2 -- spec, >> client/server/validator/registry implementations, deployments, who's working >> on what, etc. After that here's my shortlist, please chime in with other >> possibilities: >> >> Proposed spec changes -- DAS/2.1 >> Integration of DAS1 and DAS/2 >> Security / Authorization issues >> Server implementations (Genometry, Biopackages, HapMap, Trellis (my >> new stuff)) >> Client implementations (IGB, ???) >> Current state of distributed annotation in general >> Integration of DAS/2 with GMOD >> >> Hope to talk with everyone soon, >> Gregg >> >> >> > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > From lincoln.stein at gmail.com Tue Sep 30 12:00:57 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 30 Sep 2008 12:00:57 -0400 Subject: [DAS2] Restarting DAS/2 teleconferences? In-Reply-To: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> References: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> Message-ID: <6dce9a0b0809300900o411fcd38n3bdda34fe775fe4e@mail.gmail.com> I'm free most thursday after 12 noon eastern time, so that works for me. Lincoln On Mon, Sep 29, 2008 at 5:27 PM, Gregg Helt wrote: > Hello again everybody! > > After taking an eight month sabbatical, I'm back to work (currently as a > free agent). In the last two months I've focused mainly on distributed > annotation and DAS/2 in particular. And although traffic on the list has > been light/nonexistent, I know there are a number of others now actively > working on DAS/2 servers and clients. I'm hoping we can move the offline > discussions we've been having back onto the list. > > I would also like to restart the DAS/2 teleconferences as soon as possible. > Ann, is the offer to host these on your teleconference line still good? > Would people be up for this Thursday morning (Pacific time) for the first > one? If not please propose a different time. I think we should plan to > devote most of the teleconference to a specific topic each time. For the > first one I'd like to do an overview of the current state of DAS/2 -- spec, > client/server/validator/registry implementations, deployments, who's > working > on what, etc. After that here's my shortlist, please chime in with other > possibilities: > > Proposed spec changes -- DAS/2.1 > Integration of DAS1 and DAS/2 > Security / Authorization issues > Server implementations (Genometry, Biopackages, HapMap, Trellis (my new > stuff)) > Client implementations (IGB, ???) > Current state of distributed annotation in general > Integration of DAS/2 with GMOD > > Hope to talk with everyone soon, > Gregg > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Quinn Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From suzi at berkeleybop.org Tue Sep 30 12:15:49 2008 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Tue, 30 Sep 2008 10:15:49 -0600 Subject: [DAS2] Restarting DAS/2 teleconferences? In-Reply-To: <6dce9a0b0809300900o411fcd38n3bdda34fe775fe4e@mail.gmail.com> References: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> <6dce9a0b0809300900o411fcd38n3bdda34fe775fe4e@mail.gmail.com> Message-ID: Thursday morning works for me as well. On Sep 30, 2008, at 10:00 AM, Lincoln Stein wrote: > I'm free most thursday after 12 noon eastern time, so that works for > me. > > Lincoln > > On Mon, Sep 29, 2008 at 5:27 PM, Gregg Helt > wrote: > >> Hello again everybody! >> >> After taking an eight month sabbatical, I'm back to work (currently >> as a >> free agent). In the last two months I've focused mainly on >> distributed >> annotation and DAS/2 in particular. And although traffic on the >> list has >> been light/nonexistent, I know there are a number of others now >> actively >> working on DAS/2 servers and clients. I'm hoping we can move the >> offline >> discussions we've been having back onto the list. >> >> I would also like to restart the DAS/2 teleconferences as soon as >> possible. >> Ann, is the offer to host these on your teleconference line still >> good? >> Would people be up for this Thursday morning (Pacific time) for the >> first >> one? If not please propose a different time. I think we should >> plan to >> devote most of the teleconference to a specific topic each time. >> For the >> first one I'd like to do an overview of the current state of DAS/2 >> -- spec, >> client/server/validator/registry implementations, deployments, who's >> working >> on what, etc. After that here's my shortlist, please chime in with >> other >> possibilities: >> >> Proposed spec changes -- DAS/2.1 >> Integration of DAS1 and DAS/2 >> Security / Authorization issues >> Server implementations (Genometry, Biopackages, HapMap, Trellis >> (my new >> stuff)) >> Client implementations (IGB, ???) >> Current state of distributed annotation in general >> Integration of DAS/2 with GMOD >> >> Hope to talk with everyone soon, >> Gregg >> _______________________________________________ >> DAS2 mailing list >> DAS2 at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das2 >> > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Stacey Quinn > > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 USA > (516) 367-8380 > Assistant: Sandra Michelsen > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > From gregghelt at gmail.com Sat Sep 13 00:36:48 2008 From: gregghelt at gmail.com (Gregg Helt) Date: Sat, 13 Sep 2008 01:36:48 +0100 Subject: [DAS2] Merging DAS and DAS2 discussion lists Message-ID: <50158cb00809121736v73d2d2dfn9429f1ee490b7cd4@mail.gmail.com> Hi all, I've been out at the Hinxton genome center this week talking to other DAS developers about spec evolution etc. In the interest of reviving activity on the lists, it was proposed that the DAS and DAS2 discussion lists be merged. Which makes sense to me. So unless there's major objection, the DAS2 list will soon be merged back into the DAS list ( das at biodas.org), hopefully within a week or two. I'll be posting more about my recent DAS & DAS2 work soon. sincerely, Gregg Helt From aloraine at gmail.com Sat Sep 13 22:25:14 2008 From: aloraine at gmail.com (Ann Loraine) Date: Sat, 13 Sep 2008 18:25:14 -0400 Subject: [DAS2] Merging DAS and DAS2 discussion lists In-Reply-To: <50158cb00809121736v73d2d2dfn9429f1ee490b7cd4@mail.gmail.com> References: <50158cb00809121736v73d2d2dfn9429f1ee490b7cd4@mail.gmail.com> Message-ID: <83722dde0809131525t3b4a99ap9c6706e79b861116@mail.gmail.com> That sounds like a good idea to me. -Ann On Fri, Sep 12, 2008 at 8:36 PM, Gregg Helt wrote: > Hi all, I've been out at the Hinxton genome center this week talking to > other DAS developers about spec evolution etc. In the interest of reviving > activity on the lists, it was proposed that the DAS and DAS2 discussion > lists be merged. Which makes sense to me. So unless there's major > objection, the DAS2 list will soon be merged back into the DAS list ( > das at biodas.org), hopefully within a week or two. > > I'll be posting more about my recent DAS & DAS2 work soon. > > sincerely, > Gregg Helt > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > From ch-das at bobobeach.com Sun Sep 14 01:22:44 2008 From: ch-das at bobobeach.com (Cyrus Harmon) Date: Sat, 13 Sep 2008 18:22:44 -0700 Subject: [DAS2] Merging DAS and DAS2 discussion lists In-Reply-To: <83722dde0809131525t3b4a99ap9c6706e79b861116@mail.gmail.com> References: <50158cb00809121736v73d2d2dfn9429f1ee490b7cd4@mail.gmail.com> <83722dde0809131525t3b4a99ap9c6706e79b861116@mail.gmail.com> Message-ID: not as good of an idea as merging the two specs, but I step in the right direction I suppose... On Sep 13, 2008, at 3:25 PM, Ann Loraine wrote: > That sounds like a good idea to me. > > -Ann > > On Fri, Sep 12, 2008 at 8:36 PM, Gregg Helt > wrote: >> Hi all, I've been out at the Hinxton genome center this week >> talking to >> other DAS developers about spec evolution etc. In the interest of >> reviving >> activity on the lists, it was proposed that the DAS and DAS2 >> discussion >> lists be merged. Which makes sense to me. So unless there's major >> objection, the DAS2 list will soon be merged back into the DAS list ( >> das at biodas.org), hopefully within a week or two. >> >> I'll be posting more about my recent DAS & DAS2 work soon. >> >> sincerely, >> Gregg Helt >> _______________________________________________ >> DAS2 mailing list >> DAS2 at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das2 >> > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 From gregghelt at gmail.com Tue Sep 16 14:36:03 2008 From: gregghelt at gmail.com (Gregg Helt) Date: Tue, 16 Sep 2008 07:36:03 -0700 Subject: [DAS2] Fwd: [DAS] Spec review In-Reply-To: <48CFA3F2.8060509@ebi.ac.uk> References: <48CFA3F2.8060509@ebi.ac.uk> Message-ID: <50158cb00809160736h75528e76pd1f9e9e3edcecf06@mail.gmail.com> ---------- Forwarded message ---------- From: Andy Jenkinson Date: Tue, Sep 16, 2008 at 5:17 AM Subject: [DAS] Spec review To: das at biodas.org Hi all, Over the last couple of weeks there have been a few meetings on the Hinxton campus aimed at exploring options for reconciling the two versions of the DAS spec. Involved were myself, Gregg Helt, Jonathan Warren, Felix Kokocinski, Phil Jones, Henning Hermjakob and Tim Hubbard. As a first step we have conducted a review of the current 1.53 spec with a view to updating it. The aim is to make the document more consistent with common usage, add official support for the "sources" metadata command (from 1.53E and DAS/2) and to reduce complexity and confusion by removing unused features. Another mail will be sent out soon with the conclusions so that they can be discussed before any changes are made. Cheers, Andy _______________________________________________ DAS mailing list DAS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/das From lincoln.stein at gmail.com Tue Sep 16 19:51:41 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 16 Sep 2008 15:51:41 -0400 Subject: [DAS2] Fwd: [DAS] Spec review In-Reply-To: <50158cb00809160736h75528e76pd1f9e9e3edcecf06@mail.gmail.com> References: <48CFA3F2.8060509@ebi.ac.uk> <50158cb00809160736h75528e76pd1f9e9e3edcecf06@mail.gmail.com> Message-ID: <6dce9a0b0809161251t76a3cf3qc2cf4f7209e929ce@mail.gmail.com> Great! Keep me in the loop. Lincoln On Tue, Sep 16, 2008 at 10:36 AM, Gregg Helt wrote: > ---------- Forwarded message ---------- > From: Andy Jenkinson > Date: Tue, Sep 16, 2008 at 5:17 AM > Subject: [DAS] Spec review > To: das at biodas.org > > > Hi all, > > Over the last couple of weeks there have been a few meetings on the Hinxton > campus aimed at exploring options for reconciling the two versions of the > DAS spec. Involved were myself, Gregg Helt, Jonathan Warren, Felix > Kokocinski, Phil Jones, Henning Hermjakob and Tim Hubbard. > > As a first step we have conducted a review of the current 1.53 spec with a > view to updating it. The aim is to make the document more consistent with > common usage, add official support for the "sources" metadata command (from > 1.53E and DAS/2) and to reduce complexity and confusion by removing unused > features. Another mail will be sent out soon with the conclusions so that > they can be discussed before any changes are made. > > Cheers, > Andy > > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Quinn Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From gregghelt at gmail.com Mon Sep 29 21:27:30 2008 From: gregghelt at gmail.com (Gregg Helt) Date: Mon, 29 Sep 2008 14:27:30 -0700 Subject: [DAS2] Restarting DAS/2 teleconferences? Message-ID: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> Hello again everybody! After taking an eight month sabbatical, I'm back to work (currently as a free agent). In the last two months I've focused mainly on distributed annotation and DAS/2 in particular. And although traffic on the list has been light/nonexistent, I know there are a number of others now actively working on DAS/2 servers and clients. I'm hoping we can move the offline discussions we've been having back onto the list. I would also like to restart the DAS/2 teleconferences as soon as possible. Ann, is the offer to host these on your teleconference line still good? Would people be up for this Thursday morning (Pacific time) for the first one? If not please propose a different time. I think we should plan to devote most of the teleconference to a specific topic each time. For the first one I'd like to do an overview of the current state of DAS/2 -- spec, client/server/validator/registry implementations, deployments, who's working on what, etc. After that here's my shortlist, please chime in with other possibilities: Proposed spec changes -- DAS/2.1 Integration of DAS1 and DAS/2 Security / Authorization issues Server implementations (Genometry, Biopackages, HapMap, Trellis (my new stuff)) Client implementations (IGB, ???) Current state of distributed annotation in general Integration of DAS/2 with GMOD Hope to talk with everyone soon, Gregg From gregghelt at gmail.com Mon Sep 29 21:30:42 2008 From: gregghelt at gmail.com (Gregg Helt) Date: Mon, 29 Sep 2008 14:30:42 -0700 Subject: [DAS2] Restarting DAS/2 teleconferences? In-Reply-To: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> References: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> Message-ID: <50158cb00809291430k34eab050ib74b9893427237ac@mail.gmail.com> Oh yeah, another topic for the teleconference schedule: the DAS/2 paper! On Mon, Sep 29, 2008 at 2:27 PM, Gregg Helt wrote: > > Hello again everybody! > > After taking an eight month sabbatical, I'm back to work (currently as a > free agent). In the last two months I've focused mainly on distributed > annotation and DAS/2 in particular. And although traffic on the list has > been light/nonexistent, I know there are a number of others now actively > working on DAS/2 servers and clients. I'm hoping we can move the offline > discussions we've been having back onto the list. > > I would also like to restart the DAS/2 teleconferences as soon as > possible. Ann, is the offer to host these on your teleconference line still > good? Would people be up for this Thursday morning (Pacific time) for the > first one? If not please propose a different time. I think we should plan > to devote most of the teleconference to a specific topic each time. For the > first one I'd like to do an overview of the current state of DAS/2 -- spec, > client/server/validator/registry implementations, deployments, who's working > on what, etc. After that here's my shortlist, please chime in with other > possibilities: > > Proposed spec changes -- DAS/2.1 > Integration of DAS1 and DAS/2 > Security / Authorization issues > Server implementations (Genometry, Biopackages, HapMap, Trellis (my > new stuff)) > Client implementations (IGB, ???) > Current state of distributed annotation in general > Integration of DAS/2 with GMOD > > Hope to talk with everyone soon, > Gregg > > > From aloraine at gmail.com Mon Sep 29 23:53:30 2008 From: aloraine at gmail.com (Ann Loraine) Date: Mon, 29 Sep 2008 19:53:30 -0400 Subject: [DAS2] Restarting DAS/2 teleconferences? In-Reply-To: <50158cb00809291430k34eab050ib74b9893427237ac@mail.gmail.com> References: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> <50158cb00809291430k34eab050ib74b9893427237ac@mail.gmail.com> Message-ID: <83722dde0809291653y718daf6cxd1f6deb3d94d78dd@mail.gmail.com> My department business officer set up the paperwork for a conference call about a month after I got to Charlotte. I'll get back in touch with her about the details and let you know the specifics. Our best time for this is going to be any time on Wed or Thur. Best, Ann On Mon, Sep 29, 2008 at 5:30 PM, Gregg Helt wrote: > Oh yeah, another topic for the teleconference schedule: the DAS/2 paper! > > On Mon, Sep 29, 2008 at 2:27 PM, Gregg Helt wrote: > >> >> Hello again everybody! >> >> After taking an eight month sabbatical, I'm back to work (currently as a >> free agent). In the last two months I've focused mainly on distributed >> annotation and DAS/2 in particular. And although traffic on the list has >> been light/nonexistent, I know there are a number of others now actively >> working on DAS/2 servers and clients. I'm hoping we can move the offline >> discussions we've been having back onto the list. >> >> I would also like to restart the DAS/2 teleconferences as soon as >> possible. Ann, is the offer to host these on your teleconference line still >> good? Would people be up for this Thursday morning (Pacific time) for the >> first one? If not please propose a different time. I think we should plan >> to devote most of the teleconference to a specific topic each time. For the >> first one I'd like to do an overview of the current state of DAS/2 -- spec, >> client/server/validator/registry implementations, deployments, who's working >> on what, etc. After that here's my shortlist, please chime in with other >> possibilities: >> >> Proposed spec changes -- DAS/2.1 >> Integration of DAS1 and DAS/2 >> Security / Authorization issues >> Server implementations (Genometry, Biopackages, HapMap, Trellis (my >> new stuff)) >> Client implementations (IGB, ???) >> Current state of distributed annotation in general >> Integration of DAS/2 with GMOD >> >> Hope to talk with everyone soon, >> Gregg >> >> >> > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > From lincoln.stein at gmail.com Tue Sep 30 16:00:57 2008 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 30 Sep 2008 12:00:57 -0400 Subject: [DAS2] Restarting DAS/2 teleconferences? In-Reply-To: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> References: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> Message-ID: <6dce9a0b0809300900o411fcd38n3bdda34fe775fe4e@mail.gmail.com> I'm free most thursday after 12 noon eastern time, so that works for me. Lincoln On Mon, Sep 29, 2008 at 5:27 PM, Gregg Helt wrote: > Hello again everybody! > > After taking an eight month sabbatical, I'm back to work (currently as a > free agent). In the last two months I've focused mainly on distributed > annotation and DAS/2 in particular. And although traffic on the list has > been light/nonexistent, I know there are a number of others now actively > working on DAS/2 servers and clients. I'm hoping we can move the offline > discussions we've been having back onto the list. > > I would also like to restart the DAS/2 teleconferences as soon as possible. > Ann, is the offer to host these on your teleconference line still good? > Would people be up for this Thursday morning (Pacific time) for the first > one? If not please propose a different time. I think we should plan to > devote most of the teleconference to a specific topic each time. For the > first one I'd like to do an overview of the current state of DAS/2 -- spec, > client/server/validator/registry implementations, deployments, who's > working > on what, etc. After that here's my shortlist, please chime in with other > possibilities: > > Proposed spec changes -- DAS/2.1 > Integration of DAS1 and DAS/2 > Security / Authorization issues > Server implementations (Genometry, Biopackages, HapMap, Trellis (my new > stuff)) > Client implementations (IGB, ???) > Current state of distributed annotation in general > Integration of DAS/2 with GMOD > > Hope to talk with everyone soon, > Gregg > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 > -- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Quinn Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen From suzi at berkeleybop.org Tue Sep 30 16:15:49 2008 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Tue, 30 Sep 2008 10:15:49 -0600 Subject: [DAS2] Restarting DAS/2 teleconferences? In-Reply-To: <6dce9a0b0809300900o411fcd38n3bdda34fe775fe4e@mail.gmail.com> References: <50158cb00809291427o43de54b7ra26c2ca6fc63fbb1@mail.gmail.com> <6dce9a0b0809300900o411fcd38n3bdda34fe775fe4e@mail.gmail.com> Message-ID: Thursday morning works for me as well. On Sep 30, 2008, at 10:00 AM, Lincoln Stein wrote: > I'm free most thursday after 12 noon eastern time, so that works for > me. > > Lincoln > > On Mon, Sep 29, 2008 at 5:27 PM, Gregg Helt > wrote: > >> Hello again everybody! >> >> After taking an eight month sabbatical, I'm back to work (currently >> as a >> free agent). In the last two months I've focused mainly on >> distributed >> annotation and DAS/2 in particular. And although traffic on the >> list has >> been light/nonexistent, I know there are a number of others now >> actively >> working on DAS/2 servers and clients. I'm hoping we can move the >> offline >> discussions we've been having back onto the list. >> >> I would also like to restart the DAS/2 teleconferences as soon as >> possible. >> Ann, is the offer to host these on your teleconference line still >> good? >> Would people be up for this Thursday morning (Pacific time) for the >> first >> one? If not please propose a different time. I think we should >> plan to >> devote most of the teleconference to a specific topic each time. >> For the >> first one I'd like to do an overview of the current state of DAS/2 >> -- spec, >> client/server/validator/registry implementations, deployments, who's >> working >> on what, etc. After that here's my shortlist, please chime in with >> other >> possibilities: >> >> Proposed spec changes -- DAS/2.1 >> Integration of DAS1 and DAS/2 >> Security / Authorization issues >> Server implementations (Genometry, Biopackages, HapMap, Trellis >> (my new >> stuff)) >> Client implementations (IGB, ???) >> Current state of distributed annotation in general >> Integration of DAS/2 with GMOD >> >> Hope to talk with everyone soon, >> Gregg >> _______________________________________________ >> DAS2 mailing list >> DAS2 at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das2 >> > > > > -- > Lincoln D. Stein > > Ontario Institute for Cancer Research > 101 College St., Suite 800 > Toronto, ON, Canada M5G0A3 > 416 673-8514 > Assistant: Stacey Quinn > > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 USA > (516) 367-8380 > Assistant: Sandra Michelsen > _______________________________________________ > DAS2 mailing list > DAS2 at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das2 >