Re: [SED-ML-discuss] Level 1 Version 3?

[Herbert S. <uw....@gm...>]

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