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From: Kyle M. <me...@co...> - 2017-05-24 01:16:33
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Also, as an extra incentive, we have pushed back the deadline for late registration for anyone who is going to stay at the University Inn using the booking code below. J Kyle Medley, PhD Student Bioengineering/BPSD, Sauro Lab University of Washington, Seattle skype: jkylemedley On 5/23/17 4:10 PM, Kyle Medley wrote: > > Dear All, > > Two news items for Harmony 2017 here. The first is that we need more > people to book at the University Inn in order to secure our special > group rate. If you have not booked yet, please book at the University > Inn <http://www.universityinnseattle.com/> this week using our special > group code 170625UWDE. After this week, the code expires. More details > on booking are available at the Harmony website > <http://co.mbine.org/events/HARMONY_2017#Accommodation>. > > The second is that while Harmony is a hackathon-type meeting, we do > allow attendees to submit poster abstracts. If you plan on bringing a > poster, please submit an abstract here > <https://docs.google.com/forms/d/e/1FAIpQLScaI2TLfnPE-VaaW-yBRzuHo1ArjYf7ugzn6PdVGw0y6vQxZQ/viewform?usp=sf_link>. > > Regards on behalf of the HARMONY 2017 local organizers, > > Herbert Sauro > > Kyle Medley > > Kiri Choi > > -- > J Kyle Medley, PhD Student > Bioengineering/BPSD, Sauro Lab > University of Washington, Seattle |
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From: Kyle M. <me...@co...> - 2017-05-23 23:11:26
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Dear All, Two news items for Harmony 2017 here. The first is that we need more people to book at the University Inn in order to secure our special group rate. If you have not booked yet, please book at the University Inn <http://www.universityinnseattle.com/> this week using our special group code 170625UWDE. After this week, the code expires. More details on booking are available at the Harmony website <http://co.mbine.org/events/HARMONY_2017#Accommodation>. The second is that while Harmony is a hackathon-type meeting, we do allow attendees to submit poster abstracts. If you plan on bringing a poster, please submit an abstract here <https://docs.google.com/forms/d/e/1FAIpQLScaI2TLfnPE-VaaW-yBRzuHo1ArjYf7ugzn6PdVGw0y6vQxZQ/viewform?usp=sf_link>. Regards on behalf of the HARMONY 2017 local organizers, Herbert Sauro Kyle Medley Kiri Choi -- J Kyle Medley, PhD Student Bioengineering/BPSD, Sauro Lab University of Washington, Seattle |
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From: David N. <dav...@gm...> - 2017-05-20 21:09:07
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Hi all, This is a call for nominations for two SED-ML editors to replace Sven Sahle and Ion Moraru, whose terms ended on the 31st of December 2016. The length of a SED-ML Editor's term is 3 years, belatedly starting from the 1st of January 2017. The current editors are Ion Moraru (to be replaced), Sven Sahle (to be replaced), Brett Olivier (until 2017), David Nickerson (until 2017), and Lucian Smith (until 2018). We would like to ask you to nominate suitable candidates. You may nominate anyone (including yourself) who you think is qualified to act as an editor. You can fill out this survey multiple times in order to nominate multiple candidates. The current members of the editorial board can not be nominated. The nomination page is at: https://goo.gl/forms/jh6GGU5grUG0Bnv42 The call for nomination is open from now until the 4th of June 2017. After the nomination phase, we will issue a call for voting. Thanks, David. |
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From: Herbert S. <uw....@gm...> - 2017-05-16 23:35:52
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Agree with both of you. HARMONY would be a good place to sort out what to do. Herbert On Tue, May 16, 2017 at 4:17 PM, David Nickerson <dav...@gm...> wrote: > Just to follow on from Lucian, the L1V3 draft only defines linking to > data via NuML - no work has been done with the updates discussed at > COMBINE last year. I'm pretty sure that JWS crafted their own code for > linking to data (which also uses the seek services). > > As I understand it, libSEDML currently doesn't actually link to the > data directly, it simply provides access to the XML data structures > that define that linkage - so you'd need to take that information and > use libNuML to actually retrieve the data. How to actually implement > linkage to CSV or Excel data directly in SED-ML and libSEDML is > something that would be good to work on at HARMONY. I'll add a session > for that. > > Cheers, > David. > > On 17 May 2017 at 10:40, Lucian Smith <luc...@gm...> wrote: >> To be clear, there has been no SED-ML activity on the editors' side since >> COMBINE, so, no spec work nor anything else has been done. Nobody else has >> mentioned any work being done on SED-ML on the discussion lists, either. I >> had hoped to have some time to work on a new version of the spec myself >> (since I've done a lot of spec work for SBML), but have had to focus my time >> elsewhere. I believe that Frank has been in a similar situation with >> libsedml--none of his official duties involve working on the library. I >> think he is also reluctant to work on libsedml without there being an >> official spec backing him up--if the spec was officially released, I think >> he'd probably be able to find the time to incorporate that into the library. >> >> Ideally, work on the spec could be justified by a grant, but in the absence >> of that, the whole effort is living on time borrowed from other projects. >> >> -Lucian >> >> On Tue, May 16, 2017 at 3:31 PM, Herbert Sauro <uw....@gm...> wrote: >>> >>> So does the current L1V3 specify how data can be referenced from >>> spreadsheets? Is there support for this in libSEDML or I wonder if JWS >>> has hand crafted their own code? >>> >>> Herbert >>> >>> On Tue, May 16, 2017 at 3:29 PM, David Nickerson >>> <dav...@gm...> wrote: >>> > yes, we decided at COMBINE 2016 to move to something more in line with >>> > CSV or Excel rather than NuML. But this has not yet been written up in >>> > the specification. Part of the problem we currently have is that the >>> > "current state" of SED-ML is only captured across a couple of google >>> > docs, some email treads, and the draft L1V3 specification. Hopefully >>> > this will be something we can address during HARMONY. >>> > >>> > Also, while JWS does make use of L1V3 to link to data, they are using >>> > data from Excel spreadsheets - one of the main driving use-cases for >>> > the move away from NuML. >>> > >>> > Cheers, >>> > David. >>> > >>> > >>> > On 17 May 2017 at 08:01, Herbert Sauro <uw....@gm...> wrote: >>> >> I see. Wasn't it decidedin COMBINE 2016 that we wouldn't be using NuML >>> >> or at least priority had moved to using Excel like data sources? >>> >> Something like that. >>> >> >>> >> On another note: >>> >> >>> >> Might be worth adding a summary of changes in the main spec document >>> >> as new versions are released. >>> >> >>> >> Herbert >>> >> >>> >> >>> >> On Tue, May 16, 2017 at 12:55 PM, Frank T. Bergmann >>> >> <fbe...@ca...> wrote: >>> >>> Hello Herbert >>> >>> >>> >>> Version 3 extends the SED-ML language to include addressing of >>> >>> external data files, by introducing the datasource construct ... the >>> >>> summary is here: >>> >>> >>> >>> https://github.com/fbergmann/sedml-data-proposal >>> >>> >>> >>> cheers >>> >>> Frank >>> >>> >>> >>> On Tue, May 16, 2017 at 9:48 PM, Herbert Sauro <uw....@gm...> >>> >>> wrote: >>> >>>> I just noticed that JWS Online uses Level 1 Version 3 of SED-ML. >>> >>>> >>> >>>> What's the difference between Version 2 and 3? I couldn't find a >>> >>>> summary of the differences in the draft document for Version 3. >>> >>>> >>> >>>> Herbert >>> >>>> >>> >>>> >>> >>>> ------------------------------------------------------------------------------ >>> >>>> Check out the vibrant tech community on one of the world's most >>> >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> >>>> _______________________________________________ >>> >>>> SED-ML-discuss mailing list >>> >>>> SED...@li... >>> >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> Check out the vibrant tech community on one of the world's most >>> >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> >>> _______________________________________________ >>> >>> SED-ML-discuss mailing list >>> >>> SED...@li... >>> >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >> >>> >> >>> >> ------------------------------------------------------------------------------ >>> >> Check out the vibrant tech community on one of the world's most >>> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> >> _______________________________________________ >>> >> SED-ML-discuss mailing list >>> >> SED...@li... >>> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> > >>> > >>> > >>> > -- >>> > >>> > >>> > David Nickerson >>> > about.me/david.nickerson >>> > >>> > >>> > ------------------------------------------------------------------------------ >>> > Check out the vibrant tech community on one of the world's most >>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> > _______________________________________________ >>> > SED-ML-discuss mailing list >>> > SED...@li... >>> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > > > > -- > > > David Nickerson > about.me/david.nickerson > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: David N. <dav...@gm...> - 2017-05-16 23:17:48
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Just to follow on from Lucian, the L1V3 draft only defines linking to data via NuML - no work has been done with the updates discussed at COMBINE last year. I'm pretty sure that JWS crafted their own code for linking to data (which also uses the seek services). As I understand it, libSEDML currently doesn't actually link to the data directly, it simply provides access to the XML data structures that define that linkage - so you'd need to take that information and use libNuML to actually retrieve the data. How to actually implement linkage to CSV or Excel data directly in SED-ML and libSEDML is something that would be good to work on at HARMONY. I'll add a session for that. Cheers, David. On 17 May 2017 at 10:40, Lucian Smith <luc...@gm...> wrote: > To be clear, there has been no SED-ML activity on the editors' side since > COMBINE, so, no spec work nor anything else has been done. Nobody else has > mentioned any work being done on SED-ML on the discussion lists, either. I > had hoped to have some time to work on a new version of the spec myself > (since I've done a lot of spec work for SBML), but have had to focus my time > elsewhere. I believe that Frank has been in a similar situation with > libsedml--none of his official duties involve working on the library. I > think he is also reluctant to work on libsedml without there being an > official spec backing him up--if the spec was officially released, I think > he'd probably be able to find the time to incorporate that into the library. > > Ideally, work on the spec could be justified by a grant, but in the absence > of that, the whole effort is living on time borrowed from other projects. > > -Lucian > > On Tue, May 16, 2017 at 3:31 PM, Herbert Sauro <uw....@gm...> wrote: >> >> So does the current L1V3 specify how data can be referenced from >> spreadsheets? Is there support for this in libSEDML or I wonder if JWS >> has hand crafted their own code? >> >> Herbert >> >> On Tue, May 16, 2017 at 3:29 PM, David Nickerson >> <dav...@gm...> wrote: >> > yes, we decided at COMBINE 2016 to move to something more in line with >> > CSV or Excel rather than NuML. But this has not yet been written up in >> > the specification. Part of the problem we currently have is that the >> > "current state" of SED-ML is only captured across a couple of google >> > docs, some email treads, and the draft L1V3 specification. Hopefully >> > this will be something we can address during HARMONY. >> > >> > Also, while JWS does make use of L1V3 to link to data, they are using >> > data from Excel spreadsheets - one of the main driving use-cases for >> > the move away from NuML. >> > >> > Cheers, >> > David. >> > >> > >> > On 17 May 2017 at 08:01, Herbert Sauro <uw....@gm...> wrote: >> >> I see. Wasn't it decidedin COMBINE 2016 that we wouldn't be using NuML >> >> or at least priority had moved to using Excel like data sources? >> >> Something like that. >> >> >> >> On another note: >> >> >> >> Might be worth adding a summary of changes in the main spec document >> >> as new versions are released. >> >> >> >> Herbert >> >> >> >> >> >> On Tue, May 16, 2017 at 12:55 PM, Frank T. Bergmann >> >> <fbe...@ca...> wrote: >> >>> Hello Herbert >> >>> >> >>> Version 3 extends the SED-ML language to include addressing of >> >>> external data files, by introducing the datasource construct ... the >> >>> summary is here: >> >>> >> >>> https://github.com/fbergmann/sedml-data-proposal >> >>> >> >>> cheers >> >>> Frank >> >>> >> >>> On Tue, May 16, 2017 at 9:48 PM, Herbert Sauro <uw....@gm...> >> >>> wrote: >> >>>> I just noticed that JWS Online uses Level 1 Version 3 of SED-ML. >> >>>> >> >>>> What's the difference between Version 2 and 3? I couldn't find a >> >>>> summary of the differences in the draft document for Version 3. >> >>>> >> >>>> Herbert >> >>>> >> >>>> >> >>>> ------------------------------------------------------------------------------ >> >>>> Check out the vibrant tech community on one of the world's most >> >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >>>> _______________________________________________ >> >>>> SED-ML-discuss mailing list >> >>>> SED...@li... >> >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >>> >> >>> >> >>> ------------------------------------------------------------------------------ >> >>> Check out the vibrant tech community on one of the world's most >> >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >>> _______________________________________________ >> >>> SED-ML-discuss mailing list >> >>> SED...@li... >> >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> Check out the vibrant tech community on one of the world's most >> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >> _______________________________________________ >> >> SED-ML-discuss mailing list >> >> SED...@li... >> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > >> > >> > >> > -- >> > >> > >> > David Nickerson >> > about.me/david.nickerson >> > >> > >> > ------------------------------------------------------------------------------ >> > Check out the vibrant tech community on one of the world's most >> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> > _______________________________________________ >> > SED-ML-discuss mailing list >> > SED...@li... >> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > -- David Nickerson about.me/david.nickerson |
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From: Lucian S. <luc...@gm...> - 2017-05-16 22:40:27
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To be clear, there has been no SED-ML activity on the editors' side since COMBINE, so, no spec work nor anything else has been done. Nobody else has mentioned any work being done on SED-ML on the discussion lists, either. I had hoped to have some time to work on a new version of the spec myself (since I've done a lot of spec work for SBML), but have had to focus my time elsewhere. I believe that Frank has been in a similar situation with libsedml--none of his official duties involve working on the library. I think he is also reluctant to work on libsedml without there being an official spec backing him up--if the spec was officially released, I think he'd probably be able to find the time to incorporate that into the library. Ideally, work on the spec could be justified by a grant, but in the absence of that, the whole effort is living on time borrowed from other projects. -Lucian On Tue, May 16, 2017 at 3:31 PM, Herbert Sauro <uw....@gm...> wrote: > So does the current L1V3 specify how data can be referenced from > spreadsheets? Is there support for this in libSEDML or I wonder if JWS > has hand crafted their own code? > > Herbert > > On Tue, May 16, 2017 at 3:29 PM, David Nickerson > <dav...@gm...> wrote: > > yes, we decided at COMBINE 2016 to move to something more in line with > > CSV or Excel rather than NuML. But this has not yet been written up in > > the specification. Part of the problem we currently have is that the > > "current state" of SED-ML is only captured across a couple of google > > docs, some email treads, and the draft L1V3 specification. Hopefully > > this will be something we can address during HARMONY. > > > > Also, while JWS does make use of L1V3 to link to data, they are using > > data from Excel spreadsheets - one of the main driving use-cases for > > the move away from NuML. > > > > Cheers, > > David. > > > > > > On 17 May 2017 at 08:01, Herbert Sauro <uw....@gm...> wrote: > >> I see. Wasn't it decidedin COMBINE 2016 that we wouldn't be using NuML > >> or at least priority had moved to using Excel like data sources? > >> Something like that. > >> > >> On another note: > >> > >> Might be worth adding a summary of changes in the main spec document > >> as new versions are released. > >> > >> Herbert > >> > >> > >> On Tue, May 16, 2017 at 12:55 PM, Frank T. Bergmann > >> <fbe...@ca...> wrote: > >>> Hello Herbert > >>> > >>> Version 3 extends the SED-ML language to include addressing of > >>> external data files, by introducing the datasource construct ... the > >>> summary is here: > >>> > >>> https://github.com/fbergmann/sedml-data-proposal > >>> > >>> cheers > >>> Frank > >>> > >>> On Tue, May 16, 2017 at 9:48 PM, Herbert Sauro <uw....@gm...> > wrote: > >>>> I just noticed that JWS Online uses Level 1 Version 3 of SED-ML. > >>>> > >>>> What's the difference between Version 2 and 3? I couldn't find a > >>>> summary of the differences in the draft document for Version 3. > >>>> > >>>> Herbert > >>>> > >>>> ------------------------------------------------------------ > ------------------ > >>>> Check out the vibrant tech community on one of the world's most > >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >>>> _______________________________________________ > >>>> SED-ML-discuss mailing list > >>>> SED...@li... > >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > >>> > >>> ------------------------------------------------------------ > ------------------ > >>> Check out the vibrant tech community on one of the world's most > >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >>> _______________________________________________ > >>> SED-ML-discuss mailing list > >>> SED...@li... > >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > >> > >> ------------------------------------------------------------ > ------------------ > >> Check out the vibrant tech community on one of the world's most > >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >> _______________________________________________ > >> SED-ML-discuss mailing list > >> SED...@li... > >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > > > > -- > > > > > > David Nickerson > > about.me/david.nickerson > > > > ------------------------------------------------------------ > ------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > _______________________________________________ > > SED-ML-discuss mailing list > > SED...@li... > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > |
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From: Herbert S. <uw....@gm...> - 2017-05-16 22:31:52
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So does the current L1V3 specify how data can be referenced from spreadsheets? Is there support for this in libSEDML or I wonder if JWS has hand crafted their own code? Herbert On Tue, May 16, 2017 at 3:29 PM, David Nickerson <dav...@gm...> wrote: > yes, we decided at COMBINE 2016 to move to something more in line with > CSV or Excel rather than NuML. But this has not yet been written up in > the specification. Part of the problem we currently have is that the > "current state" of SED-ML is only captured across a couple of google > docs, some email treads, and the draft L1V3 specification. Hopefully > this will be something we can address during HARMONY. > > Also, while JWS does make use of L1V3 to link to data, they are using > data from Excel spreadsheets - one of the main driving use-cases for > the move away from NuML. > > Cheers, > David. > > > On 17 May 2017 at 08:01, Herbert Sauro <uw....@gm...> wrote: >> I see. Wasn't it decidedin COMBINE 2016 that we wouldn't be using NuML >> or at least priority had moved to using Excel like data sources? >> Something like that. >> >> On another note: >> >> Might be worth adding a summary of changes in the main spec document >> as new versions are released. >> >> Herbert >> >> >> On Tue, May 16, 2017 at 12:55 PM, Frank T. Bergmann >> <fbe...@ca...> wrote: >>> Hello Herbert >>> >>> Version 3 extends the SED-ML language to include addressing of >>> external data files, by introducing the datasource construct ... the >>> summary is here: >>> >>> https://github.com/fbergmann/sedml-data-proposal >>> >>> cheers >>> Frank >>> >>> On Tue, May 16, 2017 at 9:48 PM, Herbert Sauro <uw....@gm...> wrote: >>>> I just noticed that JWS Online uses Level 1 Version 3 of SED-ML. >>>> >>>> What's the difference between Version 2 and 3? I couldn't find a >>>> summary of the differences in the draft document for Version 3. >>>> >>>> Herbert >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > -- > > > David Nickerson > about.me/david.nickerson > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: David N. <dav...@gm...> - 2017-05-16 22:29:34
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yes, we decided at COMBINE 2016 to move to something more in line with CSV or Excel rather than NuML. But this has not yet been written up in the specification. Part of the problem we currently have is that the "current state" of SED-ML is only captured across a couple of google docs, some email treads, and the draft L1V3 specification. Hopefully this will be something we can address during HARMONY. Also, while JWS does make use of L1V3 to link to data, they are using data from Excel spreadsheets - one of the main driving use-cases for the move away from NuML. Cheers, David. On 17 May 2017 at 08:01, Herbert Sauro <uw....@gm...> wrote: > I see. Wasn't it decidedin COMBINE 2016 that we wouldn't be using NuML > or at least priority had moved to using Excel like data sources? > Something like that. > > On another note: > > Might be worth adding a summary of changes in the main spec document > as new versions are released. > > Herbert > > > On Tue, May 16, 2017 at 12:55 PM, Frank T. Bergmann > <fbe...@ca...> wrote: >> Hello Herbert >> >> Version 3 extends the SED-ML language to include addressing of >> external data files, by introducing the datasource construct ... the >> summary is here: >> >> https://github.com/fbergmann/sedml-data-proposal >> >> cheers >> Frank >> >> On Tue, May 16, 2017 at 9:48 PM, Herbert Sauro <uw....@gm...> wrote: >>> I just noticed that JWS Online uses Level 1 Version 3 of SED-ML. >>> >>> What's the difference between Version 2 and 3? I couldn't find a >>> summary of the differences in the draft document for Version 3. >>> >>> Herbert >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss -- David Nickerson about.me/david.nickerson |
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From: Herbert S. <uw....@gm...> - 2017-05-16 21:41:22
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A more collaborative service would be useful. Please no github if possible, I can't use, when I have, I've screwed up the repository. If you do use github I suppose I could request changes and someone else upload them. Herbert On Tue, May 16, 2017 at 2:28 PM, David Nickerson <dav...@gm...> wrote: > Frank's C++ libSEDML has all the usual bindings, which I'm pretty sure > include C and Java. Not sure what the state of the native Java library > is, but we should make sure we get updates at HARMONY. There is also a > native C library from Akira's group (I think), but again not sure what > the status of that project is. > > The SED-ML specification is currently on SourceForge.net under > subversion. See > https://sourceforge.net/p/sed-ml/code/HEAD/tree/sed-ml/specification/trunk/level-1/version-3/ > for the L1V3. One of the issues the editors will be discussing at > HARMONY is whether we should be moving to some other service. > > Cheers, > David. > > > On 17 May 2017 at 05:31, Herbert Sauro <uw....@gm...> wrote: >> Can the v3 draft be put on something like sharelatex or overleaf so >> everyone has access? >> >> Herbert >> >> On Tue, May 16, 2017 at 9:44 AM, Frank T. Bergmann <fbe...@ca...> wrote: >>> Sounds like a plan, we did discuss the extension for curve styles at >>> COMBINE. I'd be willing to help out if people wanted to work on >>> implementation of the v3 draft. >>> >>> Also as always if you find issues with the C++ library, please let me know: >>> >>> https://github.com/fbergmann/libSEDML/issues >>> >>> or with the C# one / issue with the webtools: >>> >>> https://sourceforge.net/p/libsedml/tickets >>> >>> thanks >>> Frank >>> >>> >>> On Tue, May 16, 2017 at 5:55 PM, Herbert Sauro <uw....@gm...> wrote: >>>> I guess one thing is add the material agreed to last year into the document. >>>> Also a discussion on the state of the libraries would be useful, without >>>> those we cannot easily use sedml. >>>> >>>> Herbert >>>> >>>> On Mon, May 15, 2017 at 9:59 PM David Nickerson <dav...@gm...> >>>> wrote: >>>>> >>>>> Hi all, >>>>> >>>>> HARMONY is rapidly approaching in Seattle this June 26-30 >>>>> (http://co.mbine.org/events/HARMONY_2017). There is a preliminary >>>>> draft agenda available via the website, with sessions rapidly filling >>>>> up. >>>>> >>>>> Are there any specific topics that people would like to see discussed >>>>> or worked on during HARMONY? There have been some offline discussions >>>>> around clarifying some details in the specification, so we'll be >>>>> aiming for at least one session on making sure the SED-ML L1V3 draft >>>>> itself is a clear and unambiguous definition of SED-ML, but otherwise >>>>> the focus for SED-ML will be trying to help get implementations of the >>>>> L1V3 draft up and running so that we can start moving beyond. >>>>> >>>>> Cheers, >>>>> David. >>>>> >>>>> >>>>> -- >>>>> >>>>> >>>>> David Nickerson >>>>> about.me/david.nickerson >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Check out the vibrant tech community on one of the world's most >>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>> _______________________________________________ >>>>> SED-ML-discuss mailing list >>>>> SED...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > -- > > > David Nickerson > about.me/david.nickerson > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: David N. <dav...@gm...> - 2017-05-16 21:28:43
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Frank's C++ libSEDML has all the usual bindings, which I'm pretty sure include C and Java. Not sure what the state of the native Java library is, but we should make sure we get updates at HARMONY. There is also a native C library from Akira's group (I think), but again not sure what the status of that project is. The SED-ML specification is currently on SourceForge.net under subversion. See https://sourceforge.net/p/sed-ml/code/HEAD/tree/sed-ml/specification/trunk/level-1/version-3/ for the L1V3. One of the issues the editors will be discussing at HARMONY is whether we should be moving to some other service. Cheers, David. On 17 May 2017 at 05:31, Herbert Sauro <uw....@gm...> wrote: > Can the v3 draft be put on something like sharelatex or overleaf so > everyone has access? > > Herbert > > On Tue, May 16, 2017 at 9:44 AM, Frank T. Bergmann <fbe...@ca...> wrote: >> Sounds like a plan, we did discuss the extension for curve styles at >> COMBINE. I'd be willing to help out if people wanted to work on >> implementation of the v3 draft. >> >> Also as always if you find issues with the C++ library, please let me know: >> >> https://github.com/fbergmann/libSEDML/issues >> >> or with the C# one / issue with the webtools: >> >> https://sourceforge.net/p/libsedml/tickets >> >> thanks >> Frank >> >> >> On Tue, May 16, 2017 at 5:55 PM, Herbert Sauro <uw....@gm...> wrote: >>> I guess one thing is add the material agreed to last year into the document. >>> Also a discussion on the state of the libraries would be useful, without >>> those we cannot easily use sedml. >>> >>> Herbert >>> >>> On Mon, May 15, 2017 at 9:59 PM David Nickerson <dav...@gm...> >>> wrote: >>>> >>>> Hi all, >>>> >>>> HARMONY is rapidly approaching in Seattle this June 26-30 >>>> (http://co.mbine.org/events/HARMONY_2017). There is a preliminary >>>> draft agenda available via the website, with sessions rapidly filling >>>> up. >>>> >>>> Are there any specific topics that people would like to see discussed >>>> or worked on during HARMONY? There have been some offline discussions >>>> around clarifying some details in the specification, so we'll be >>>> aiming for at least one session on making sure the SED-ML L1V3 draft >>>> itself is a clear and unambiguous definition of SED-ML, but otherwise >>>> the focus for SED-ML will be trying to help get implementations of the >>>> L1V3 draft up and running so that we can start moving beyond. >>>> >>>> Cheers, >>>> David. >>>> >>>> >>>> -- >>>> >>>> >>>> David Nickerson >>>> about.me/david.nickerson >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss -- David Nickerson about.me/david.nickerson |
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From: Herbert S. <uw....@gm...> - 2017-05-16 20:01:54
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I see. Wasn't it decidedin COMBINE 2016 that we wouldn't be using NuML or at least priority had moved to using Excel like data sources? Something like that. On another note: Might be worth adding a summary of changes in the main spec document as new versions are released. Herbert On Tue, May 16, 2017 at 12:55 PM, Frank T. Bergmann <fbe...@ca...> wrote: > Hello Herbert > > Version 3 extends the SED-ML language to include addressing of > external data files, by introducing the datasource construct ... the > summary is here: > > https://github.com/fbergmann/sedml-data-proposal > > cheers > Frank > > On Tue, May 16, 2017 at 9:48 PM, Herbert Sauro <uw....@gm...> wrote: >> I just noticed that JWS Online uses Level 1 Version 3 of SED-ML. >> >> What's the difference between Version 2 and 3? I couldn't find a >> summary of the differences in the draft document for Version 3. >> >> Herbert >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: Frank T. B. <fbe...@ca...> - 2017-05-16 19:55:53
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Hello Herbert Version 3 extends the SED-ML language to include addressing of external data files, by introducing the datasource construct ... the summary is here: https://github.com/fbergmann/sedml-data-proposal cheers Frank On Tue, May 16, 2017 at 9:48 PM, Herbert Sauro <uw....@gm...> wrote: > I just noticed that JWS Online uses Level 1 Version 3 of SED-ML. > > What's the difference between Version 2 and 3? I couldn't find a > summary of the differences in the draft document for Version 3. > > Herbert > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: Herbert S. <uw....@gm...> - 2017-05-16 19:48:44
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I just noticed that JWS Online uses Level 1 Version 3 of SED-ML. What's the difference between Version 2 and 3? I couldn't find a summary of the differences in the draft document for Version 3. Herbert |
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From: Herbert S. <uw....@gm...> - 2017-05-16 17:31:27
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Can the v3 draft be put on something like sharelatex or overleaf so everyone has access? Herbert On Tue, May 16, 2017 at 9:44 AM, Frank T. Bergmann <fbe...@ca...> wrote: > Sounds like a plan, we did discuss the extension for curve styles at > COMBINE. I'd be willing to help out if people wanted to work on > implementation of the v3 draft. > > Also as always if you find issues with the C++ library, please let me know: > > https://github.com/fbergmann/libSEDML/issues > > or with the C# one / issue with the webtools: > > https://sourceforge.net/p/libsedml/tickets > > thanks > Frank > > > On Tue, May 16, 2017 at 5:55 PM, Herbert Sauro <uw....@gm...> wrote: >> I guess one thing is add the material agreed to last year into the document. >> Also a discussion on the state of the libraries would be useful, without >> those we cannot easily use sedml. >> >> Herbert >> >> On Mon, May 15, 2017 at 9:59 PM David Nickerson <dav...@gm...> >> wrote: >>> >>> Hi all, >>> >>> HARMONY is rapidly approaching in Seattle this June 26-30 >>> (http://co.mbine.org/events/HARMONY_2017). There is a preliminary >>> draft agenda available via the website, with sessions rapidly filling >>> up. >>> >>> Are there any specific topics that people would like to see discussed >>> or worked on during HARMONY? There have been some offline discussions >>> around clarifying some details in the specification, so we'll be >>> aiming for at least one session on making sure the SED-ML L1V3 draft >>> itself is a clear and unambiguous definition of SED-ML, but otherwise >>> the focus for SED-ML will be trying to help get implementations of the >>> L1V3 draft up and running so that we can start moving beyond. >>> >>> Cheers, >>> David. >>> >>> >>> -- >>> >>> >>> David Nickerson >>> about.me/david.nickerson >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: Herbert S. <uw....@gm...> - 2017-05-16 17:30:22
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I assume there isn't a C API for libsedml? Are there any docs for libsedml? If the P41 center grant comes in (will know in October) I am hoping we an help with development. Herbert On Tue, May 16, 2017 at 9:44 AM, Frank T. Bergmann <fbe...@ca...> wrote: > Sounds like a plan, we did discuss the extension for curve styles at > COMBINE. I'd be willing to help out if people wanted to work on > implementation of the v3 draft. > > Also as always if you find issues with the C++ library, please let me know: > > https://github.com/fbergmann/libSEDML/issues > > or with the C# one / issue with the webtools: > > https://sourceforge.net/p/libsedml/tickets > > thanks > Frank > > > On Tue, May 16, 2017 at 5:55 PM, Herbert Sauro <uw....@gm...> wrote: >> I guess one thing is add the material agreed to last year into the document. >> Also a discussion on the state of the libraries would be useful, without >> those we cannot easily use sedml. >> >> Herbert >> >> On Mon, May 15, 2017 at 9:59 PM David Nickerson <dav...@gm...> >> wrote: >>> >>> Hi all, >>> >>> HARMONY is rapidly approaching in Seattle this June 26-30 >>> (http://co.mbine.org/events/HARMONY_2017). There is a preliminary >>> draft agenda available via the website, with sessions rapidly filling >>> up. >>> >>> Are there any specific topics that people would like to see discussed >>> or worked on during HARMONY? There have been some offline discussions >>> around clarifying some details in the specification, so we'll be >>> aiming for at least one session on making sure the SED-ML L1V3 draft >>> itself is a clear and unambiguous definition of SED-ML, but otherwise >>> the focus for SED-ML will be trying to help get implementations of the >>> L1V3 draft up and running so that we can start moving beyond. >>> >>> Cheers, >>> David. >>> >>> >>> -- >>> >>> >>> David Nickerson >>> about.me/david.nickerson >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: Chris M. <my...@ec...> - 2017-05-16 16:46:45
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And Java? Any hope to keep that one alive. Chris > On May 16, 2017, at 12:44 PM, Frank T. Bergmann <fbe...@ca...> wrote: > > Sounds like a plan, we did discuss the extension for curve styles at > COMBINE. I'd be willing to help out if people wanted to work on > implementation of the v3 draft. > > Also as always if you find issues with the C++ library, please let me know: > > https://github.com/fbergmann/libSEDML/issues > > or with the C# one / issue with the webtools: > > https://sourceforge.net/p/libsedml/tickets > > thanks > Frank > > > On Tue, May 16, 2017 at 5:55 PM, Herbert Sauro <uw....@gm...> wrote: >> I guess one thing is add the material agreed to last year into the document. >> Also a discussion on the state of the libraries would be useful, without >> those we cannot easily use sedml. >> >> Herbert >> >> On Mon, May 15, 2017 at 9:59 PM David Nickerson <dav...@gm...> >> wrote: >>> >>> Hi all, >>> >>> HARMONY is rapidly approaching in Seattle this June 26-30 >>> (http://co.mbine.org/events/HARMONY_2017). There is a preliminary >>> draft agenda available via the website, with sessions rapidly filling >>> up. >>> >>> Are there any specific topics that people would like to see discussed >>> or worked on during HARMONY? There have been some offline discussions >>> around clarifying some details in the specification, so we'll be >>> aiming for at least one session on making sure the SED-ML L1V3 draft >>> itself is a clear and unambiguous definition of SED-ML, but otherwise >>> the focus for SED-ML will be trying to help get implementations of the >>> L1V3 draft up and running so that we can start moving beyond. >>> >>> Cheers, >>> David. >>> >>> >>> -- >>> >>> >>> David Nickerson >>> about.me/david.nickerson >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: Frank T. B. <fbe...@ca...> - 2017-05-16 16:44:51
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Sounds like a plan, we did discuss the extension for curve styles at COMBINE. I'd be willing to help out if people wanted to work on implementation of the v3 draft. Also as always if you find issues with the C++ library, please let me know: https://github.com/fbergmann/libSEDML/issues or with the C# one / issue with the webtools: https://sourceforge.net/p/libsedml/tickets thanks Frank On Tue, May 16, 2017 at 5:55 PM, Herbert Sauro <uw....@gm...> wrote: > I guess one thing is add the material agreed to last year into the document. > Also a discussion on the state of the libraries would be useful, without > those we cannot easily use sedml. > > Herbert > > On Mon, May 15, 2017 at 9:59 PM David Nickerson <dav...@gm...> > wrote: >> >> Hi all, >> >> HARMONY is rapidly approaching in Seattle this June 26-30 >> (http://co.mbine.org/events/HARMONY_2017). There is a preliminary >> draft agenda available via the website, with sessions rapidly filling >> up. >> >> Are there any specific topics that people would like to see discussed >> or worked on during HARMONY? There have been some offline discussions >> around clarifying some details in the specification, so we'll be >> aiming for at least one session on making sure the SED-ML L1V3 draft >> itself is a clear and unambiguous definition of SED-ML, but otherwise >> the focus for SED-ML will be trying to help get implementations of the >> L1V3 draft up and running so that we can start moving beyond. >> >> Cheers, >> David. >> >> >> -- >> >> >> David Nickerson >> about.me/david.nickerson >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > |
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From: Herbert S. <uw....@gm...> - 2017-05-16 15:55:59
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I guess one thing is add the material agreed to last year into the document. Also a discussion on the state of the libraries would be useful, without those we cannot easily use sedml. Herbert On Mon, May 15, 2017 at 9:59 PM David Nickerson <dav...@gm...> wrote: > Hi all, > > HARMONY is rapidly approaching in Seattle this June 26-30 > (http://co.mbine.org/events/HARMONY_2017). There is a preliminary > draft agenda available via the website, with sessions rapidly filling > up. > > Are there any specific topics that people would like to see discussed > or worked on during HARMONY? There have been some offline discussions > around clarifying some details in the specification, so we'll be > aiming for at least one session on making sure the SED-ML L1V3 draft > itself is a clear and unambiguous definition of SED-ML, but otherwise > the focus for SED-ML will be trying to help get implementations of the > L1V3 draft up and running so that we can start moving beyond. > > Cheers, > David. > > > -- > > > David Nickerson > about.me/david.nickerson > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > |
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From: David N. <dav...@gm...> - 2017-05-16 04:59:00
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Hi all, HARMONY is rapidly approaching in Seattle this June 26-30 (http://co.mbine.org/events/HARMONY_2017). There is a preliminary draft agenda available via the website, with sessions rapidly filling up. Are there any specific topics that people would like to see discussed or worked on during HARMONY? There have been some offline discussions around clarifying some details in the specification, so we'll be aiming for at least one session on making sure the SED-ML L1V3 draft itself is a clear and unambiguous definition of SED-ML, but otherwise the focus for SED-ML will be trying to help get implementations of the L1V3 draft up and running so that we can start moving beyond. Cheers, David. -- David Nickerson about.me/david.nickerson |
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From: David N. <dav...@gm...> - 2017-05-09 04:48:04
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---------- Forwarded message ---------- From: Marco Antoniotti <ma...@gm...> Date: 9 May 2017 at 02:08 Subject: [sbml-discuss] [COMBINE 2017] October 9-13 2017, Milan, Italy To: sbml-discuss <sbm...@go...> Cc: mar...@un... COMBINE 2017: 8th Computational Modeling in Biology Network Workshop ============================================================================== Oct. 9th - 13th, 2017, Università degli Studi di Milano Bicocca, Milan, ITALY http://co.mbine.org/events/COMBINE_2017 ------------------------------------------------------------------------------ The "Computational Modeling in Biology" Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. COMBINE 2017 will be a workshop-style event with oral presentations, posters, and breakout sessions. The five meeting days will include talks about the COMBINE standards and associated or related standardization efforts, as well as presentations of tools using these standards. Oral presentations will be selected from the submitted abstracts. In addition, poster sessions will allow people to inform each other about their software and other projects in a setting that fosters interaction and in-depth discussion. CALL FOR ABSTRACTS ------------------ We solicit high-quality abstracts, to be refereed by the COMBINE Coordinators below, for either oral or poster presentation at the Workshop. Abstracts will appear on the COMBINE website only, there will be no formal publication. Please see the COMBINE website for submission instructions. The submission process is hosted by Easychair. TOPICS OF INTEREST ------------------ Topics include, but are not limited to: - Data exchange, pipelines and model standards for systems biology - Graphical notation standards for systems biology - Standards for sharing and analysing biological pathway data - Standards for computational biological models More on the COMBINE standards at http://co.mbine.org/standards IMPORTANT DATES --------------- Abstract submission: July 1, 2017 Notification: July 23, 2017 COMBINE Workshop: October 9-13 2017 LOCAL CHAIRS ------------ Marco Antoniotti, Alex Graudenzi, Giancarlo Mauri, DISCo), (Università degli Studi di Milano Bicocca) COMBINE COORDINATORS -------------------- Gary Bader (Toronto) Martin Golebiewski (Heidelberg) Michael Hucka (Caltech) Nicolas Le Novère (Babraham) Chris J. Myers (Utah) David Nickerson (Auckland) Falk Schreiber (Monash) Dagmar Waltemath (Rostock) ACKNOWLEDGEMENTS ---------------- COMBINE 2017 is generously supported by: - Department of Informatics, Systems and Communication (DISCo), Università degli Studi di Milano Bicocca (ITALY) - Centre of Systems Biology, Università degli Studi di Milano Bicocca (ITALY) -- You received this message because you are subscribed to the Google Groups "sbml-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to sbm...@go.... To post to this group, send email to sbm...@go.... To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/4be4bbf5-14e3-424b-8196-48fc9d1ddcb9%40googlegroups.com. For more options, visit https://groups.google.com/d/optout. -- David Nickerson about.me/david.nickerson |
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From: Kyle M. <me...@co...> - 2017-04-28 18:27:35
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Dear all, Below, please find the registration details for HARMONY 2017. In order to avoid late fees, please register by May 12th. If you have applied / will apply for a travel scholarship, please do not register until after you hear from us. For those who have already applied for the travel scholarship, thank you for your patience. I am trying to get the travel scholarships sorted out asap. == INFO == HARMONY is a hackathon-type meeting, with a focus on development of the standards, interoperability and infrastructure. There are generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between people focused on practical development of software and standards. == REGISTRATION == Registration is done through Eventbrite. Students enrolled at a university are eligible for a special discount rate. Late registration carries a fee of $50 and starts May 12th. https://www.eventbrite.com/e/harmony-2017-registration-32738694316 == TRAVEL SCHOLARSHIPS == To apply for a travel scholarship, please use the form below. Funds are limited, so please apply as early as possible. https://goo.gl/forms/WUPp41rxKJsm3gVJ2 == ACKNOWLEDGEMENTS == HARMONY 2017 is generously supported by: - The National Science Foundation -- J Kyle Medley, PhD Student Bioengineering/BPSD, Sauro Lab University of Washington, Seattle |
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From: David N. <dav...@gm...> - 2017-04-04 03:42:21
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---------- Forwarded message ---------- From: Jk Medley <me...@co...> Date: 28 March 2017 at 11:32 Subject: [sbml-discuss] HARMONY 2017 Registration and Call for Abstracts To: sbml-discuss <sbm...@go...> Dear all, I just wanted to announce that registration is open for HARMONY 2017. HARMONY 2017 will be held at the University of Washington, Seattle WA (USA) from June 26 to June 30. Please find below the Call for Abstracts - the submission deadline is May 26. We look forward to seeing you in Seattle! Regards, Sauro Lab, Department of Bioengineering, University of Washington, Seattle WA *********************************************************************** == CALL FOR ABSTRACTS == HARMONY is a hackathon-type meeting, with a focus on development of the standards, interoperability and infrastructure. There are generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between people focused on practical development of software and standards. Abstracts will appear on the HARMONY website only, there will be no formal publication. https://goo.gl/forms/g2z9GvItBIABzHFL2 == REGISTRATION == Registration is done through Eventbrite. Students enrolled at a university are eligible for a special discount rate. Late registration carries a fee of $50 and starts May 12th. https://www.eventbrite.com/e/harmony-2017-registration-32738694316 == TRAVEL SCHOLARSHIPS == To apply for a travel scholarship, please use the form below. Funds are limited, so please apply as early as possible. https://goo.gl/forms/WUPp41rxKJsm3gVJ2 == ACKNOWLEDGEMENTS == HARMONY 2017 is generously supported by: - National Science Foundation (USA) *********************************************************************** |
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From: David N. <dav...@gm...> - 2016-12-20 08:26:53
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HI Nisha, You can use annotations in SED-ML, see the "annotation" element in the SED-ML specification. If you are using the C++ libSEDML, you can see an example dealing with annotations in the 'print_sedml` example (https://github.com/fbergmann/libSEDML/blob/master/examples/c%2B%2B/print_sedml.cpp). If you are using a different library providing the getNumChildren() method you'll need to provide some details. As far as I know, the libSBML ASTNode objects and methods are only used by libSEDML to handle the MathML in SED-ML. Cheers, David. On Tue, Dec 20, 2016 at 8:25 PM, Nisha Viswan <ni...@nc...> wrote: > Dear all, > > I would like to know whether custom-annotation-tags can be used in SEDML, > just like in SBML. I found ASTNode functions work well for > custom-annotations in SBML files but not in SEDML(L1V1). > For example, when I use getNumChildren() for custom-annotations, I get a > random number in SEDML (huge number) but it works fine for SBML files. > > I am not sure whether I am missing something very obvious, and I would > really appreciate if somebody could help out with a direct fix or any other > solution to overcome this. > > Regards, > Nisha Viswan > > > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today.http://sdm.link/intel > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > -- David Nickerson about.me/david.nickerson |
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From: Nisha V. <ni...@nc...> - 2016-12-20 07:45:10
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Dear all, I would like to know whether custom-annotation-tags can be used in SEDML, just like in SBML. I found ASTNode functions work well for custom-annotations in SBML files but not in SEDML(L1V1). For example, when I use getNumChildren() for custom-annotations, I get a random number in SEDML (huge number) but it works fine for SBML files. I am not sure whether I am missing something very obvious, and I would really appreciate if somebody could help out with a direct fix or any other solution to overcome this. Regards, Nisha Viswan |
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From: David N. <dav...@gm...> - 2016-09-23 12:32:18
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Hi all, Just starting a breakout on proposed changes/new features for SED-ML. Google doc with notes: https://docs.google.com/document/d/1uNNkjATFUQ78FspKkBTwJ2UmevmCGfovaKI22sr3VF8/edit# BlueJeans link for remote attendance: http://bluejeans.com/702321230 Cheers, David. -- David Nickerson about.me/david.nickerson |
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