sbml-groups — The SBML L3 Groups package discussion list

Re: [sbml-groups] Flux of branched amino acids in bacillus subtilis

[Lucian S. <luc...@gm...>]

On Thu, Apr 1, 2021 at 6:43 AM caroline Fukuda <car...@gm...>
wrote:

> Hi,
>
> I'm a beginner student at metabolic engineering, and I'm analysing the
> valine production of bacillus subtilis on optflux. But when I do the wild
> type simulation, the values of valine, leucine and isoleucine fluxes are
> null. I think that's because the reactions on SBML files are incomplete,
> but I don't know what to do about it. Can someone give me a guidance?
>

 Hi, Caroline!  Happy to answer your questions, though we might need some
more information.  Also, you managed to find the 'sbml-groups' list, which
technically is about the 'groups' package for SBML, not general SBML
questions like yours.  That's better suited to 'sbml-discuss', which I've
copied on this message, and should get you more responses.

So, I haven't used OptFlux before, but a cursory glance makes it look like
it's a flux balance analysis (FBA) tool.  Models used in FBA have
constraints on the reaction rates, but do not set the reaction rates
themselves--the idea is to perform your analysis and discover particular
possible values of reaction rates that would satisfy the given conditions.
These values are then the likely values of the system at steady state in
whatever condition the FBA constraints were set to (often 'max growth').

I'm not sure if the 'simulation' you want to perform is a time-course
simulation, but if so, the flux values you obtained from an FBA analysis
would not be appropriate, since those values would apply at steady state
only.  So if you do want a time course analysis, here are the options I can
think of:

* Find another non-FBA type model of the system you're using.
* Find out what the reaction rates are from the literature.
* Put in 'default' reaction rates based on mass action (or similar).  You
might be able to fill in the rate constants with values that make the model
match an FBA analysis?  I haven't tried this myself, but if (for example)
the FBA tells you that a given reaction rate is X, and that the
concentrations of the reactants are S1 and S2, if you assume mass action
kinetics, you know that X = k*S1*S2, and you can solve for k.

There are a variety of tools out there to help you manipulate the model; I
know COPASI is popular, and our own lab produces the Tellurium suite of
python packages that might also work for you.  Other people here might
suggest their own tools.

Good luck, and let us know if you have any other questions!

-Lucian Smith

[sbml-groups] Flux of branched amino acids in bacillus subtilis

[caroline F. <car...@gm...>]

Hi,

I'm a beginner student at metabolic engineering, and I'm analysing the
valine production of bacillus subtilis on optflux. But when I do the wild
type simulation, the values of valine, leucine and isoleucine fluxes are
nule. I think that's because the reactions on SBML files are incomplete,
but I don't know what to do about it. Can someone give me a guidance?


att. Caroline Fukuda

Re: [sbml-groups] [sbml-discuss] Manuscript describing SBML

[Sarah K. <ske...@ca...>]

Please note the current SBML Editors will continue to work on this 
publication and it will proceed as planned.

SBML Editors

Re: [sbml-groups] [sbml-discuss] Manuscript describing SBML

[Sarah K. <ske...@ca...>]

Sorry I was perhaps not completely clear.

Nicolas Le Novere has withdrawn from the paper and has handed over all 
notes/comments etc to the remaining SBML Editors.

There will be a slight hiatus in the timing, but we are close to having 
a manuscript for submission, and we will proceed with this.

Thank you to everyone who has commented so far and I hope this 
completely clarifies the situation.

Sarah
Coordinator of SBML Editors

On 18/09/2018 09:04, Sarah Keating wrote:
> Please note the current SBML Editors will continue to work on this
> publication and it will proceed as planned.
> 
> SBML Editors
> 

[sbml-groups] Manuscript describing SBML

[Nicolas Le N. <n.l...@gm...>]

Dear Colleagues,

We are in the process of submitting a manuscript describing SBML Level 3 for publication in Molecular Systems Biology as a perspective (current version attached). The manuscript has been written by past and current SBML editors and both its content and structure discussed with MSB editors.

Although the structure and the main messages of the paper have been settled, we would welcome any suggestion you would have in relation with the manuscript.

Best regards

The SBML editors.

Re: [sbml-groups] python snippet to write and read sbml files with groups

[Harsha R. <ran...@gm...>]

Thank you Brett,

For helping me out with xmlns syntax it works and for clarifying
*groups: listofGroups.*
I am able to do a round trip with read and write sbml files with groups.

Regards

On Tue, Feb 21, 2017 at 6:59 PM, Brett G. Olivier <b.g...@vu...> wrote:

> Hi Harsha
>
> I'm not sure it's the best way, but I would do it is as follows:
>
> xmlns = SBMLNamespaces(3, 1)
> xmlns.addNamespace("http://www.w3.org/1999/xhtml"
> <http://www.w3.org/1999/xhtml>, "xhtml")
> xmlns.addNamespace("http://www.myproject.com" <http://www.myproject.com>,
> "myproject")
> xmlns.addNamespace("http://www.sbml.org/sbml/level3/
> version1/groups/version1"
> <http://www.sbml.org/sbml/level3/version1/groups/version1>, "groups")
>
> sbmlDoc = SBMLDocument(xmlns)
> model = sbmlDoc.createModel()
>
> As far as *groups: listofGroups* goes, this is as it should be. All
> package elements use a qualified namespace that differentiates them from
> SBML core.
> HTH
> Brett
>
>
> On 21/02/2017 13:38, Harsha Rani wrote:
>
> Can someone help me to write and read sbml file with groups in python
> along with
> annotation which is specific to project.
> I am attaching file in which I tried to add groups, I am unable to do, I
> am sure I am missing some syntax.
>
> sbmlns = SBMLNamespaces(3,1,"groups",1);
> sbmlDoc = SBMLDocument(sbmlns)
>
> mplugin = model.getPlugin("groups");
> group = mplugin.createGroup();
> group.setId("ATPS");
> group.setKind("classification");
>
> I get this
> <groups:listOfGroups>
>       <groups:group groups:id="ATPS" groups:kind="classification">
>         <groups:listOfMembers>
>           <groups:member groups:idRef="ATPc"/>
>           <groups:member groups:idRef="ATPm"/>
>         </groups:listOfMembers>
>       </groups:group>
>     </groups:listOfGroups>
>
> why *groups: listofGroups *I was expecting
>
> *listOfGroups *
> I also have xmlns namespace as I need to add annotation specific to project
>
>
> Thank you
>
>
> --
> Brett G. Olivier PhD
> Systems Bioinformatics
> Vrije Universiteit Amsterdam
> Tel: +31 20 5987248 <+31%2020%20598%207248>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> sbml-groups mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-groups
>
>

Re: [sbml-groups] python snippet to write and read sbml files with groups

[Brett G. O. <b.g...@vu...>]

Hi Harsha

I'm not sure it's the best way, but I would do it is as follows:

xmlns = SBMLNamespaces(3, 1)
xmlns.addNamespace("http://www.w3.org/1999/xhtml", "xhtml")
xmlns.addNamespace("http://www.myproject.com", "myproject")
xmlns.addNamespace("http://www.sbml.org/sbml/level3/version1/groups/version1", 
"groups")

sbmlDoc = SBMLDocument(xmlns)
model = sbmlDoc.createModel()

As far as *groups: listofGroups* goes, this is as it should be. All 
package elements use a qualified namespace that differentiates them from 
SBML core.

HTH
Brett

On 21/02/2017 13:38, Harsha Rani wrote:
> Can someone help me to write and read sbml file with groups in python 
> along with
> annotation which is specific to project.
> I am attaching file in which I tried to add groups, I am unable to do, 
> I am sure I am missing some syntax.
>
> sbmlns = SBMLNamespaces(3,1,"groups",1);
> sbmlDoc = SBMLDocument(sbmlns)
>
> mplugin = model.getPlugin("groups");
> group = mplugin.createGroup();
> group.setId("ATPS");
> group.setKind("classification");
>
> I get this
> <groups:listOfGroups>
>       <groups:group groups:id="ATPS" groups:kind="classification">
>         <groups:listOfMembers>
>           <groups:member groups:idRef="ATPc"/>
>           <groups:member groups:idRef="ATPm"/>
>         </groups:listOfMembers>
>       </groups:group>
>     </groups:listOfGroups>
>
> why *groups: listofGroups *I was expecting *listOfGroups
>
> *
> I also have xmlns namespace as I need to add annotation specific to 
> project
>
>
> Thank you
>

-- 
Brett G. Olivier PhD
Systems Bioinformatics
Vrije Universiteit Amsterdam
Tel: +31 20 5987248

[sbml-groups] python snippet to write and read sbml files with groups

[Harsha R. <ran...@gm...>]

Can someone help me to write and read sbml file with groups in python along
with
annotation which is specific to project.
I am attaching file in which I tried to add groups, I am unable to do, I am
sure I am missing some syntax.

sbmlns = SBMLNamespaces(3,1,"groups",1);
sbmlDoc = SBMLDocument(sbmlns)

mplugin = model.getPlugin("groups");
group = mplugin.createGroup();
group.setId("ATPS");
group.setKind("classification");

I get this
<groups:listOfGroups>
      <groups:group groups:id="ATPS" groups:kind="classification">
        <groups:listOfMembers>
          <groups:member groups:idRef="ATPc"/>
          <groups:member groups:idRef="ATPm"/>
        </groups:listOfMembers>
      </groups:group>
    </groups:listOfGroups>

why *groups: listofGroups *I was expecting

*listOfGroups*
I also have xmlns namespace as I need to add annotation specific to project


Thank you

[sbml-groups] JIB Special issue COMBINE standards

[Sarah K. <ske...@ca...>]

Hi Groups PWG

Since the groups package reached acceptance this year the specification 
would be eligible to publish in the JIB Special issue this year.

May I ask the authors of the specification to take responsibility for 
the submission OR let the SBML Editors know if no one has available 
time. Guidelines are below.

Thanks

Sarah

on behalf of SBML Editors

================

Call for standard papers in Journal of Integrative Bioinformatics (JIB)
(http://journal.imbio.de) for - promoting COMBINE standards (and
sub-standards such as SBML packages)
- listing them as publications in PubMed
- having a collection of all standards in a way easy to cite

Procedure:

1. Prepare a PDF of the standard 1.1 The normal PDF you already have for
your standard could be used
1.2 Prepare a cover page for your PDF which you attach as first page of
your PDF Use the JIB template for this cover page (the template is
available here: http://journal.imbio.de/instructions.php,Please not: the
Latex template works with latex, not with pdflatex)
The aim is to have the title page of each paper (standard) in the
journal format, but the journal would be flexible enough to allow the
remaining pages to be in the existing format.

2. Submit your standard
2.1. go to submission
http://journal.imbio.de/login.php
2.2. set up your account
2.3. submit new article
(click on link)
2.4. accept the conditions. Please note: ignore ‘... the manuscript is
original, has not already been published and is not currently under
consideration by another journal.' This refers to research articles, you
can later select the special issue for ‘COMBINE standards'
- add all authors with email und affiliation (I know, this is boring
work, but the journal needs this information to produce entries for
Pubmed and other index services automatically)
- add title
- choose article type: ‘Special issue: COMBINE standards'
2.5. upload
your PDF as well as the source file for your title page

Important: Deadline Friday, October 28th, 2016 Please make sure that you
meet this deadline!

[sbml-groups] Groups package accepted

[Sarah K. <ske...@ca...>]

Dear SBML community,

We are pleased to announce the availability of the final Version 1 
specification for Groups in SBML Level 3.  You can find the document at 
its resolvable URI

http://identifiers.org/combine.specifications/sbml.level-3.version-1.groups.version-1.release-1

This specification has been approved by the editors who have confirmed 
there are two working implementations.

The Groups ('groups') specification activity page is

http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/groups

The next libSBML release will include groups as part of the stable 
release, with full validation available.

Please report any errors, issues or questions to the Package Working 
Group for 'groups' (sbm...@li...).

SBML Editors

Re: [sbml-groups] Release Candidate 4!

[Brett G. O. <b.g...@vu...>]

I'll join Mike, great work Lucian.

Cheers
Brett

On 25/03/2016 00:36, Michael Hucka wrote:
> I just wanted it to be known that I'm clapping my hands.  You can't hear me, but the applause is there.
>
> MH
>
> On Mon, 21 Mar 2016 13:14:30 -0700, Lucian Smith wrote:
>> Release Candidate 4, which fixes a small handful of things, is now
>> available:
>>
>> https://sourceforge.net/p/sbml/code/HEAD/tree//trunk/specifications/sbml-level-3/version-1/groups/specification/groups-rc4.pdf
>>
>> The issues addressed in this release candidate are:
>>
>> https://sourceforge.net/p/sbml/sbml-specifications/search/?q=labels%3A%22Level+3+Version+1+Package%3A+groups%22+%26%26+status%3A%22pending%22
>>
>> in brief:  updated acknowledgements, fixed typos, validation rule to say
>> nested loops can't loop, and a couple wording clarifications.
>>
>> If nobody has any issues, I think this will end up becoming the final
>> version!
>>
>> Thanks to everyone for your input; it was quite helpful.
>>
>> -Lucian
>> ------------------------------------------------------------------------------
>> Transform Data into Opportunity.
>> Accelerate data analysis in your applications with
>> Intel Data Analytics Acceleration Library.
>> Click to learn more.
>> http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140_______________________________________________
>> sbml-groups mailing list
>> sbm...@li...
>> https://lists.sourceforge.net/lists/listinfo/sbml-groups
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140
> _______________________________________________
> sbml-groups mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-groups

-- 
Brett G. Olivier PhD

Systems Bioinformatics
VU University Amsterdam
Amsterdam, The Netherlands

Email: b.g.olivier[AT]vu[dot]nl
Tel (office) +31 20 5987248

Re: [sbml-groups] Release Candidate 4!

[Michael H. <mh...@ca...>]

I just wanted it to be known that I'm clapping my hands.  You can't hear me, but the applause is there.

MH

On Mon, 21 Mar 2016 13:14:30 -0700, Lucian Smith wrote:
> Release Candidate 4, which fixes a small handful of things, is now
> available:
> 
> https://sourceforge.net/p/sbml/code/HEAD/tree//trunk/specifications/sbml-level-3/version-1/groups/specification/groups-rc4.pdf
> 
> The issues addressed in this release candidate are:
> 
> https://sourceforge.net/p/sbml/sbml-specifications/search/?q=labels%3A%22Level+3+Version+1+Package%3A+groups%22+%26%26+status%3A%22pending%22
> 
> in brief:  updated acknowledgements, fixed typos, validation rule to say
> nested loops can't loop, and a couple wording clarifications.
> 
> If nobody has any issues, I think this will end up becoming the final
> version!
> 
> Thanks to everyone for your input; it was quite helpful.
> 
> -Lucian
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140_______________________________________________
> sbml-groups mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-groups

[sbml-groups] Release Candidate 4!

[Lucian S. <luc...@gm...>]

Release Candidate 4, which fixes a small handful of things, is now
available:

https://sourceforge.net/p/sbml/code/HEAD/tree//trunk/specifications/sbml-level-3/version-1/groups/specification/groups-rc4.pdf

The issues addressed in this release candidate are:

https://sourceforge.net/p/sbml/sbml-specifications/search/?q=labels%3A%22Level+3+Version+1+Package%3A+groups%22+%26%26+status%3A%22pending%22

in brief:  updated acknowledgements, fixed typos, validation rule to say
nested loops can't loop, and a couple wording clarifications.

If nobody has any issues, I think this will end up becoming the final
version!

Thanks to everyone for your input; it was quite helpful.

-Lucian

Re: [sbml-groups] Anyone else implement 'Groups' support that we can mention in the acknowledgements?

[Lucian S. <luc...@gm...>]

Hey, Brett--did you manage to confirm this?  I don't suppose Neil and
Kieran would mind being acknowledged either way, but it'd be nice to know
for sure if they were involved.

-Lucian

On Mon, Feb 29, 2016 at 1:13 PM, Brett G. Olivier <b.g...@vu...> wrote:

> People are fine, as far as I remember Kieran Smallbone and Neil Swainston
> were involved in the discussions but I can confirm that tomorrow.
>
> Cheers
> b.
>
>
> On 29/02/2016 22:09, Lucian Smith wrote:
>
> Thanks!  Is there a person there you know is responsible for that
> implementation, or should I move to mentioning actual tools?  (Right now, I
> only mention Brett and Anna by name for supporting groups 'in their
> software tools'; I could be more specific, if that was appropriate.)
>
> -Lucian
>
> On Mon, Feb 29, 2016 at 1:03 PM, Brett G. Olivier <b.g...@vu...>
> wrote:
>
>> You could consider the Yeast Consensus Reconstruction as it supports
>> groups as well (yeast 7.6 at least)  http://yeast.sourceforge.net
>>
>> Brett
>>
>>
>> On 29/02/2016 20:41, Lucian Smith wrote:
>>
>> Thus far, in the acknowledgements, I mention Brett and Anna as people
>> that have implemented 'groups' support.  I now know Andreas also has Groups
>> support in BiGG--is there anyone else?
>>
>> -Lucian
>>
>>
>> --
>> Brett G. Olivier PhD
>>
>> Systems Bioinformatics
>> VU University Amsterdam
>> Amsterdam, The Netherlands
>>
>> Email: b.g.olivier[AT]vu[dot]nl
>> Tel (office) +31 20 5987248
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> sbml-groups mailing list
>> sbm...@li...
>> https://lists.sourceforge.net/lists/listinfo/sbml-groups
>>
>>
>
> --
> Brett G. Olivier PhD
>
> Systems Bioinformatics
> VU University Amsterdam
> Amsterdam, The Netherlands
>
> Email: b.g.olivier[AT]vu[dot]nl
> Tel (office) +31 20 5987248
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> sbml-groups mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-groups
>
>

Re: [sbml-groups] Anyone else implement 'Groups' support that we can mention in the acknowledgements?

[Michael H. <mh...@ca...>]

On Mon, 29 Feb 2016 22:13:28 +0100, Brett G. Olivier wrote:
> People are fine, as far as I remember Kieran Smallbone and Neil 
> Swainston were involved in the discussions but I can confirm that 
> tomorrow.

BTW, Kieran is on family leave AFAIK, and so may be difficult to reach.

MH

Re: [sbml-groups] Anyone else implement 'Groups' support that we can mention in the acknowledgements?

[Brett G. O. <b.g...@vu...>]

People are fine, as far as I remember Kieran Smallbone and Neil 
Swainston were involved in the discussions but I can confirm that tomorrow.

Cheers
b.

On 29/02/2016 22:09, Lucian Smith wrote:
> Thanks!  Is there a person there you know is responsible for that 
> implementation, or should I move to mentioning actual tools?  (Right 
> now, I only mention Brett and Anna by name for supporting groups 'in 
> their software tools'; I could be more specific, if that was 
> appropriate.)
>
> -Lucian
>
> On Mon, Feb 29, 2016 at 1:03 PM, Brett G. Olivier <b.g...@vu... 
> <mailto:b.g...@vu...>> wrote:
>
>     You could consider the Yeast Consensus Reconstruction as it
>     supports groups as well (yeast 7.6 at least)
>     http://yeast.sourceforge.net
>
>     Brett
>
>
>     On 29/02/2016 20:41, Lucian Smith wrote:
>>     Thus far, in the acknowledgements, I mention Brett and Anna as
>>     people that have implemented 'groups' support.  I now know
>>     Andreas also has Groups support in BiGG--is there anyone else?
>>
>>     -Lucian
>
>     -- 
>     Brett G. Olivier PhD
>
>     Systems Bioinformatics
>     VU University Amsterdam
>     Amsterdam, The Netherlands
>
>     Email: b.g.olivier[AT]vu[dot]nl
>     Tel (office)+31 20 5987248 <tel:%2B31%2020%205987248>  
>
>
>     ------------------------------------------------------------------------------
>     Site24x7 APM Insight: Get Deep Visibility into Application Performance
>     APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>     Monitor end-to-end web transactions and take corrective actions now
>     Troubleshoot faster and improve end-user experience. Signup Now!
>     http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>     _______________________________________________
>     sbml-groups mailing list
>     sbm...@li...
>     <mailto:sbm...@li...>
>     https://lists.sourceforge.net/lists/listinfo/sbml-groups
>
>

-- 
Brett G. Olivier PhD

Systems Bioinformatics
VU University Amsterdam
Amsterdam, The Netherlands

Email: b.g.olivier[AT]vu[dot]nl
Tel (office) +31 20 5987248

Re: [sbml-groups] Anyone else implement 'Groups' support that we can mention in the acknowledgements?

[Lucian S. <luc...@gm...>]

Thanks!  Is there a person there you know is responsible for that
implementation, or should I move to mentioning actual tools?  (Right now, I
only mention Brett and Anna by name for supporting groups 'in their
software tools'; I could be more specific, if that was appropriate.)

-Lucian

On Mon, Feb 29, 2016 at 1:03 PM, Brett G. Olivier <b.g...@vu...> wrote:

> You could consider the Yeast Consensus Reconstruction as it supports
> groups as well (yeast 7.6 at least)  http://yeast.sourceforge.net
>
> Brett
>
>
> On 29/02/2016 20:41, Lucian Smith wrote:
>
> Thus far, in the acknowledgements, I mention Brett and Anna as people that
> have implemented 'groups' support.  I now know Andreas also has Groups
> support in BiGG--is there anyone else?
>
> -Lucian
>
>
> --
> Brett G. Olivier PhD
>
> Systems Bioinformatics
> VU University Amsterdam
> Amsterdam, The Netherlands
>
> Email: b.g.olivier[AT]vu[dot]nl
> Tel (office) +31 20 5987248
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> sbml-groups mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-groups
>
>

Re: [sbml-groups] Anyone else implement 'Groups' support that we can mention in the acknowledgements?

[Brett G. O. <b.g...@vu...>]

You could consider the Yeast Consensus Reconstruction as it supports 
groups as well (yeast 7.6 at least)  http://yeast.sourceforge.net

Brett


On 29/02/2016 20:41, Lucian Smith wrote:
> Thus far, in the acknowledgements, I mention Brett and Anna as people 
> that have implemented 'groups' support.  I now know Andreas also has 
> Groups support in BiGG--is there anyone else?
>
> -Lucian

-- 
Brett G. Olivier PhD

Systems Bioinformatics
VU University Amsterdam
Amsterdam, The Netherlands

Email: b.g.olivier[AT]vu[dot]nl
Tel (office) +31 20 5987248

[sbml-groups] Anyone else implement 'Groups' support that we can mention in the acknowledgements?

[Lucian S. <luc...@gm...>]

Thus far, in the acknowledgements, I mention Brett and Anna as people that
have implemented 'groups' support.  I now know Andreas also has Groups
support in BiGG--is there anyone else?

-Lucian

[sbml-groups] Release Candidate 3

[Lucian S. <luc...@gm...>]

OK, there were a few more suggestions for changes to the Groups spec--the
latest is up at

https://sourceforge.net/p/sbml/code/HEAD/tree/trunk/specifications/sbml-level-3/version-1/groups/specification/groups-rc3.pdf

The changes are:
* Typos fixed
* Clarified wording here and there
* Update description of 'membership' to include nested groups
* Validation rule added to match main text:  no circular groups.

Assuming nobody has any issues with the above changes (or has a new issue
with something) I'll send this to the editors tomorrow.

-Lucian

Re: [sbml-groups] New version of Groups, RC2

[Lucian S. <luc...@gm...>]

Thanks for the fixes!

Also, with your objection to 'copyNestingInformation' (since we're not
copying information about nesting, which is fair), I'm trying
'copyInformationToNestedLists', which is more accurate, if more wordy.
Will that work for people?

Assuming people like that change, libsbml-experimental in SVN is ready for
testing.  Brett (or anyone else), if you want a precompiled version for
your system, let us know, and we can build you one.

Otherwise, I'm sending this version off to the SBML Editors!  Thanks for
your comments, everyone, and it's still not too late to get in more, if you
find them.

-Lucian

On Fri, Feb 5, 2016 at 3:21 AM, Sarah Keating <sar...@te...>
wrote:

> FYI
>
> Theses are in svn :-)
>
> Sarah
>
>
>
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Re: [sbml-groups] New version of Groups, RC2

[Sarah K. <ske...@ca...>]

> Looking forward to it! When you have the new stuff in libsbml ready, let me know and I'll work on implementing it.

The code for id/name on a listOfMembers is in libsbml-experimental svn 
along with most of the validation of groups.

Sarah

Re: [sbml-groups] New version of Groups, RC2

[Sarah K. <sar...@te...>]

FYI

Theses are in svn :-)

Sarah

Re: [sbml-groups] New version of Groups, RC2

[Sarah K. <ske...@ca...>]

Typo in Rule 20312

'same SBML object' -> should be the 'same SBase object'

to avoid confusion with the <sbml> element :-)

Sarah

Re: [sbml-groups] New version of Groups, RC2

[Sarah K. <ske...@ca...>]

Typo in Section 3.2.2

ID is an XML type !!!!

Needs to be 'id' or 'identifier'

:-)

Sarah