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

[David N. <dav...@gm...>]

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
>> >>>>
>> >>>>
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>> >
>> > --
>> >
>> >
>> > David Nickerson
>> > about.me/david.nickerson
>> >
>> >
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David Nickerson
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