sed-ml-discuss — Migrating to google groups: https://groups.google.com/d/forum/sed-ml-discuss

[SED-ML-discuss] Status of the SED-ML tools

[Nicolas R. <nik...@gm...>]

Hello,

I would be nice to get an update of which tools have been updated to 
support SED-ML L1V2.
And this info would be useful in the showcase part of the sedml.org web 
site.

Even more, is there already some tools or libraries that have been 
updated to support the L1V3 draft specification or
intend to do it in the near future? In particular, it might be useful 
for the whole-cell modeling summer school.

Thanks,
Nico

Re: [SED-ML-discuss] SED-ED tool

[Nicolas R. <nik...@gm...>]

> Dear All,
>
> I have just started to use SED-ED SED-ML Editor. I was wondering if there
> is anyone using SED-ED to generate simulation pipelines?
>
> I worked out how to use SED-ED / SBCIVisual to simulate a model and
> plot/report the results. Now my next task is to use output of one
> simulation as an input to next simulation (for example via changing the
> initial values of the second model based on output of the first), then I
> want to test more complicated tasks such as introducing data processing
> between simulations.
>
> So my question is: Do you think that such simulation pipelines can be built
> in SED-ED?

Just to let people know, the answer to Pnar question seems to be that 
SED-ED has
not been updated to support SED-ML L1V2 and there does no seem to be any 
plan
to update it for now.

Nico

[SED-ML-discuss] SED-ED tool

[Pnar P. <pn...@gm...>]

Dear All,

I have just started to use SED-ED SED-ML Editor. I was wondering if there
is anyone using SED-ED to generate simulation pipelines?

I worked out how to use SED-ED / SBCIVisual to simulate a model and
plot/report the results. Now my next task is to use output of one
simulation as an input to next simulation (for example via changing the
initial values of the second model based on output of the first), then I
want to test more complicated tasks such as introducing data processing
between simulations.

So my question is: Do you think that such simulation pipelines can be built
in SED-ED? Are there any sample pipelines that I can practice with?

Many thanks!

-- 
Pnar Pir

[SED-ML-discuss] Voting Results ...

[Frank B. <fbe...@ca...>]

Dear SED-ML Community … 

a happy New Year to you all!

The voting results are in. It is my pleasure to Announce that David Nickerson (16 votes) and Brett Olivier(15 votes) have been elected as new SED-ML editors, replacing both me (Frank Bergmann) and Dagmar Waltemath. Let us also thank Felix Winter (7 votes) again for standing for the election. 

Thank you again for a very successful four years. 

All the best, 
Frank 

Re: [SED-ML-discuss] Election of SED-ML editors 2014

[Frank B. <fbe...@ca...>]

Hello, 

this is a reminder, that the election for the next SED-ML editors is still open. You have until midnight December 28th to vote: 

http://goo.gl/ZvyQbc

Happy holidays, 

Frank 


> On Dec 3, 2014, at 9:38 AM, Frank Bergmann <fbe...@ca...> wrote:
> 
> This is a call for votes for electing two new SED-ML Editors to replace Frank Bergmann and Dagmar Waltemath, whose current 3-year terms end at the end of this year. Every individual member of the SED-ML Forum (as determined by membership on the sed...@li... mailing list) is entitled to vote. Please vote for 2 candidates using the voting form at: 
> 
> 
> 
> http://goo.gl/ZvyQbc
> 
> 
> 
> Voting will end at midnight on December 28, 2014.
> 
> The previously issued call for nominations resulted in 5 unique nominees, 3 of whom have accepted their nominations. Each confirmed candidate is listed below in alphabetical order. Please vote for two candidates, the two candidates who receive the most votes (and who accept) will be considered elected as new SBML Editors for 3-year terms beginning in January 2015 and ending December 31, 2017.  
> 
> Thank you in advance for your participation in this important process!
> 
> 
> 
> Frank,
> 
> on behalf of the SED-ML editors
> ------------------------------------------------------------------------------
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Re: [SED-ML-discuss] Election of SED-ML editors 2014

[Frank B. <fbe...@ca...>]

Ok … habe die Änderung gemacht. generell denke ich aber dass die Anzahl der abgegebenen  Votes übersichtlich bleibt, und dementsprechend werden wir so etwas einfach herausfinden. Und sicherstellen, dass in dem Fall der gleiche Kandidat nur als eine Stimme gezählt wird. 

Frank


> On Dec 4, 2014, at 10:45 AM, Felix Winter <wi...@ka...> wrote:
> 
> Hallo Frank,
> 
> ist es möglich die Abstimmung so einzurichten dass man auch nur eine Stimme
> abgeben kann? Es scheint zwar möglich zu sein beide Felder mit dem gleichen
> Kandidaten auszufüllen (das habe ich gerade gemacht) aber wird dass dann auch
> nur als eine Stimme gezählt? Lieber wäre mir wenn nur das erste Feld
> verpflichtend wäre.
> 
> Gruß, Felix
> 
> 
>> On December 3, 2014 at 9:38 AM Frank Bergmann <fbe...@ca...> wrote:
>> 
>> 
>> This is a call for votes for electing two new SED-ML Editors to replace Frank
>> Bergmann and Dagmar Waltemath, whose current 3-year terms end at the end of
>> this year. Every individual member of the SED-ML Forum (as determined by
>> membership on the sed...@li... mailing list) is entitled to
>> vote. Please vote for 2 candidates using the voting form at: 
>> 
>> 
>> 
>> http://goo.gl/ZvyQbc
>> 
>> 
>> 
>> Voting will end at midnight on December 28, 2014.
>> 
>> The previously issued call for nominations resulted in 5 unique nominees, 3 of
>> whom have accepted their nominations. Each confirmed candidate is listed below
>> in alphabetical order. Please vote for two candidates, the two candidates who
>> receive the most votes (and who accept) will be considered elected as new SBML
>> Editors for 3-year terms beginning in January 2015 and ending December 31,
>> 2017.  
>> 
>> Thank you in advance for your participation in this important process!
>> 
>> 
>> 
>> Frank,
>> 
>> on behalf of the SED-ML editors
>> ------------------------------------------------------------------------------
>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
>> with Interactivity, Sharing, Native Excel Exports, App Integration & more
>> Get technology previously reserved for billion-dollar corporations, FREE
>> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> Felix Winter
> Thomas-Müntzer-Platz 63
> 18057 Rostock
> 
> IM: fw...@ja...
> 
> ------------------------------------------------------------------------------
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Re: [SED-ML-discuss] Election of SED-ML editors 2014

[Felix W. <wi...@ka...>]

Hallo Frank,

ist es möglich die Abstimmung so einzurichten dass man auch nur eine Stimme
abgeben kann? Es scheint zwar möglich zu sein beide Felder mit dem gleichen
Kandidaten auszufüllen (das habe ich gerade gemacht) aber wird dass dann auch
nur als eine Stimme gezählt? Lieber wäre mir wenn nur das erste Feld
verpflichtend wäre.

Gruß, Felix


> On December 3, 2014 at 9:38 AM Frank Bergmann <fbe...@ca...> wrote:
> 
> 
> This is a call for votes for electing two new SED-ML Editors to replace Frank
> Bergmann and Dagmar Waltemath, whose current 3-year terms end at the end of
> this year. Every individual member of the SED-ML Forum (as determined by
> membership on the sed...@li... mailing list) is entitled to
> vote. Please vote for 2 candidates using the voting form at: 
> 
> 
> 
> http://goo.gl/ZvyQbc
> 
> 
> 
> Voting will end at midnight on December 28, 2014.
> 
> The previously issued call for nominations resulted in 5 unique nominees, 3 of
> whom have accepted their nominations. Each confirmed candidate is listed below
> in alphabetical order. Please vote for two candidates, the two candidates who
> receive the most votes (and who accept) will be considered elected as new SBML
> Editors for 3-year terms beginning in January 2015 and ending December 31,
> 2017.  
> 
> Thank you in advance for your participation in this important process!
> 
>  
> 
> Frank,
> 
> on behalf of the SED-ML editors
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
> http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
Felix Winter
Thomas-Müntzer-Platz 63
18057 Rostock

IM: fw...@ja...

[SED-ML-discuss] Election of SED-ML editors 2014

[Frank B. <fbe...@ca...>]

This is a call for votes for electing two new SED-ML Editors to replace Frank Bergmann and Dagmar Waltemath, whose current 3-year terms end at the end of this year. Every individual member of the SED-ML Forum (as determined by membership on the sed...@li... mailing list) is entitled to vote. Please vote for 2 candidates using the voting form at: 



http://goo.gl/ZvyQbc



Voting will end at midnight on December 28, 2014.

The previously issued call for nominations resulted in 5 unique nominees, 3 of whom have accepted their nominations. Each confirmed candidate is listed below in alphabetical order. Please vote for two candidates, the two candidates who receive the most votes (and who accept) will be considered elected as new SBML Editors for 3-year terms beginning in January 2015 and ending December 31, 2017.  

Thank you in advance for your participation in this important process!

 

Frank,

on behalf of the SED-ML editors

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

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

Hi Felix,

That is a great showcase of SED-ML actually! Thanks for sharing.

On 02/12/14 09:50, Felix Winter wrote:
> Hi again.
>
> Thanks for all this valuable feedback. As I guess someone may wonder why I care
> about this topic at all, I decided to share a little bit of the background story
> which brought up the question. Maybe someone can use it as a use case for
> SED-ML.
>
> The company I currently work for is using a quality management system (DIN ISO
> 9001 certified). As part of this there are regulary audits. In one of the last
> audits, the question arose how I check the validity of my modelling results,
> especially with respect to the correct implementation and calling of the
> underlying ode solver. One idea I currently try to test for its feasibility is
> to automatically verify the model simulation in a software different to the one
> which was used to build the model (which is mainly COPASI and some handwritten
> C++ code). As I already follow the development of SED-ML for some time, I
> assumed it would be the ideal language to implement a system that does what I
> need: A precise description of the simulation experiment which can be supplied
> to different software packages to run the same simulation. As I consider it very
> unlikely that two implentations share the same error, I would consider the
> simulation correct if the output of the independent simulations is equal.
>
> To make sure that I really have the same output using the same SED-ML file
> (assuming the ode solvers are correct) I need to guarantee that the SED-ML file
> is always interpreted in the same way. While checking the current spec for
> possible challenges I came across the use of Xpath. And that's how my inital
> question arose.
>
> With best thanks,
>
> Felix
>
> ------------------------------------------------------------------------------
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> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>


-- 
Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
Tel: +441223496433 Fax: +441223496034 Mob:+447833147074 twitter:@lenovere
Skype:n.lenovere, n.l...@gm..., ORCID: 0000-0002-6309-7327
http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

[Felix W. <wi...@ka...>]

Hi again.

Thanks for all this valuable feedback. As I guess someone may wonder why I care
about this topic at all, I decided to share a little bit of the background story
which brought up the question. Maybe someone can use it as a use case for
SED-ML.

The company I currently work for is using a quality management system (DIN ISO
9001 certified). As part of this there are regulary audits. In one of the last
audits, the question arose how I check the validity of my modelling results,
especially with respect to the correct implementation and calling of the
underlying ode solver. One idea I currently try to test for its feasibility is
to automatically verify the model simulation in a software different to the one
which was used to build the model (which is mainly COPASI and some handwritten
C++ code). As I already follow the development of SED-ML for some time, I
assumed it would be the ideal language to implement a system that does what I
need: A precise description of the simulation experiment which can be supplied
to different software packages to run the same simulation. As I consider it very
unlikely that two implentations share the same error, I would consider the
simulation correct if the output of the independent simulations is equal.

To make sure that I really have the same output using the same SED-ML file
(assuming the ode solvers are correct) I need to guarantee that the SED-ML file
is always interpreted in the same way. While checking the current spec for
possible challenges I came across the use of Xpath. And that's how my inital
question arose. 

With best thanks,

Felix

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

[Felix W. <wi...@ka...>]

Hi Frank,


> - addXML: I actually think ‘adding’ already contains a position for the
> element to be added, and that is after all existing child nodes of that
> element. This is also what will happen in the xpath apis i looked at (for
> example the appendchild method on xpathnavigators in .net). But i would not
> mind adding a clarification, that the newElement, is indeed added at the end
> of the list of child nodes. In that case all index based addressing of the dom
> elements will continue to work. 

I would encourage such a clarification because there is a difference between an
"add" operation and an "add at the end" (= "append") operation for unordered
lists. This would indeed allow index based addressing if ( and only if) the
ordering of the elements in the model does not change. As this cannot be
guaranteed at least for CellML and SBML, I would still consider index based
addressing unsafe. 

Cheers, Felix

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

[Frank B. <fbe...@ca...>]

Coming late to the party, i just want to add my opinion on a couple of points: 

- xpath expressions: We definitely don’t want to roll our own here, and stick with the standard, as there are libraries for xpath around that do short work of most of the work. 

- best practices: it really is a best practice to use specifically crafted xpath expressions, as some software don’t implement full xpath processing. 

- addXML: I actually think ‘adding’ already contains a position for the element to be added, and that is after all existing child nodes of that element. This is also what will happen in the xpath apis i looked at (for example the appendchild method on xpathnavigators in .net). But i would not mind adding a clarification, that the newElement, is indeed added at the end of the list of child nodes. In that case all index based addressing of the dom elements will continue to work. 

Cheers
Frank


> On Nov 30, 2014, at 10:06 PM, Felix Winter <wi...@ka...> wrote:
> 
>> I think it is better to assume that authors (or more specifically,
>> authoring tools) will follow the relevant "best practice" guidelines
>> for the type of data they are addressing. I suspect that such
>> guidelines are probably not always that obvious currently and it might
>> be worth writing them up somewhere and seeing if we all agree on them.
> This is a very good idea. In this special case I suspect such guidelines would
> have helped me to understand the situation a little bit earlier. 
> 
>> There is at least one proposal, from Jonathan Cooper, to use an
>> alternate to xpath to address items in models using ontological terms.
> 
> I will try to find it. Thanks a lot for the tip.
> 
> Thanks again for your help. I learned a lot!
> 
> Best regards, Felix.
> 
> ------------------------------------------------------------------------------
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> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
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> _______________________________________________
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> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

[Felix W. <wi...@ka...>]

> I think it is better to assume that authors (or more specifically,
> authoring tools) will follow the relevant "best practice" guidelines
> for the type of data they are addressing. I suspect that such
> guidelines are probably not always that obvious currently and it might
> be worth writing them up somewhere and seeing if we all agree on them.
This is a very good idea. In this special case I suspect such guidelines would
have helped me to understand the situation a little bit earlier. 

> There is at least one proposal, from Jonathan Cooper, to use an
> alternate to xpath to address items in models using ontological terms.

I will try to find it. Thanks a lot for the tip.

Thanks again for your help. I learned a lot!

Best regards, Felix.

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

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

As David alludes to, there is a big difference between saying 'order
doesn't matter in SBML/CellML', which means that several different
documents may all encode exactly the same model, and saying 'find this
element of this particular document by relying on its order', which is a
perfectly reasonable thing to do, even if the first statement is also true
of that same document.  It does mean that if you manipulate that document,
you might lose the ability to find the element you originally wanted to
get, but avoiding that is relatively simple:  just don't change the target
document, and if you do, change the corresponding SEDML files, too.

Now, order is not the *only* way that XPath can find XML elements, it just
happens to be the most straightforward.  So if you planned to manipulate a
target file after creating your SEDML file, it might be a good idea to use
XPath in an order-agnostic way ('the element with the metaid "tk-421"'),
but I would tend to put that into a 'best practices' category, and not try
to dictate in the spec things like 'only use the order-agnostic subset of
XPath', which seems a little draconican, not to mention unnecessary.

-Lucian

On Sat, Nov 29, 2014 at 6:41 PM, David Nickerson <dav...@gm...>
wrote:

> > Doesn't the statement look right or is it the situation which worries
> you? I
> > just looked again into the Xpath definition and it in fact imposes a
> document
> > order including ordered lists of child nodes. If Xpath is used to access
> a child
> > using its subscript (which is a valid use of Xpath ) the result cannot be
> > predicted, if the underlying document format(e.g. CellML) does not
> require
> > ordered child nodes. I assume for SED-ML this could be a problem as I
> see no way
> > to guarantee that the different children will always be in the same
> order. If I
> > understood your earlier email correctly, exchanging two children in a
> single
> > node would not change the model itself and therefore the reference in an
> SED-ML
> > file would be valid for both XML versions which encode the same model.
>
> ahhh...ok, I see what you are saying - and you are correct. That is
> why, for models in CellML and SBML and other formats that don't use
> document order to imply any significance, authors and/or authoring
> tools are much better off using xpath expressions based on other
> information. Such as @name="bob" or cmeta:id="r39405" (in CellML a
> component name and a variable name is sufficient to ensure a
> document-unique target variable). Xpath expressions relying on
> specific document order are still valid, but as you say they may
> return a different result after the source model is read into and
> written out of a given tool.
>
> > One way to prevent this situation would be to define a subset of Xpath,
>
> I don't think we want to do that.
>
> > excluding the subscript access, which can be used with SED-ML. The other
> way
> > would be to just trust the authors of SED-ML files that they know what
> they are
> > doing and only use Xpath expressions which are failsafe for the model
> format
> > they are referencing. Basically, the subset of valid Xpath expressions
> depends
> > on the model format. The question is just who is responsible for
> checking that
> > this subset is not left.
>
> I think it is better to assume that authors (or more specifically,
> authoring tools) will follow the relevant "best practice" guidelines
> for the type of data they are addressing. I suspect that such
> guidelines are probably not always that obvious currently and it might
> be worth writing them up somewhere and seeing if we all agree on them.
>
> There is at least one proposal, from Jonathan Cooper, to use an
> alternate to xpath to address items in models using ontological terms.
>
>
>
> Cheers,
> David.
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
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> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
>
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> _______________________________________________
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> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

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

> Doesn't the statement look right or is it the situation which worries you? I
> just looked again into the Xpath definition and it in fact imposes a document
> order including ordered lists of child nodes. If Xpath is used to access a child
> using its subscript (which is a valid use of Xpath ) the result cannot be
> predicted, if the underlying document format(e.g. CellML) does not require
> ordered child nodes. I assume for SED-ML this could be a problem as I see no way
> to guarantee that the different children will always be in the same order. If I
> understood your earlier email correctly, exchanging two children in a single
> node would not change the model itself and therefore the reference in an SED-ML
> file would be valid for both XML versions which encode the same model.

ahhh...ok, I see what you are saying - and you are correct. That is
why, for models in CellML and SBML and other formats that don't use
document order to imply any significance, authors and/or authoring
tools are much better off using xpath expressions based on other
information. Such as @name="bob" or cmeta:id="r39405" (in CellML a
component name and a variable name is sufficient to ensure a
document-unique target variable). Xpath expressions relying on
specific document order are still valid, but as you say they may
return a different result after the source model is read into and
written out of a given tool.

> One way to prevent this situation would be to define a subset of Xpath,

I don't think we want to do that.

> excluding the subscript access, which can be used with SED-ML. The other way
> would be to just trust the authors of SED-ML files that they know what they are
> doing and only use Xpath expressions which are failsafe for the model format
> they are referencing. Basically, the subset of valid Xpath expressions depends
> on the model format. The question is just who is responsible for checking that
> this subset is not left.

I think it is better to assume that authors (or more specifically,
authoring tools) will follow the relevant "best practice" guidelines
for the type of data they are addressing. I suspect that such
guidelines are probably not always that obvious currently and it might
be worth writing them up somewhere and seeing if we all agree on them.

There is at least one proposal, from Jonathan Cooper, to use an
alternate to xpath to address items in models using ontological terms.



Cheers,
David.

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

[Felix W. <wi...@ka...>]

> > Having such a statement would immediately make it clear that using
> > an Xpath reference which addresses a list element via its subscript would
> > give
> > an undefined result.
> 
> hmmmm...that doesn't sound right.

Doesn't the statement look right or is it the situation which worries you? I
just looked again into the Xpath definition and it in fact imposes a document
order including ordered lists of child nodes. If Xpath is used to access a child
using its subscript (which is a valid use of Xpath ) the result cannot be
predicted, if the underlying document format(e.g. CellML) does not require
ordered child nodes. I assume for SED-ML this could be a problem as I see no way
to guarantee that the different children will always be in the same order. If I
understood your earlier email correctly, exchanging two children in a single
node would not change the model itself and therefore the reference in an SED-ML
file would be valid for both XML versions which encode the same model.

One way to prevent this situation would be to define a subset of Xpath,
excluding the subscript access, which can be used with SED-ML. The other way
would be to just trust the authors of SED-ML files that they know what they are
doing and only use Xpath expressions which are failsafe for the model format
they are referencing. Basically, the subset of valid Xpath expressions depends
on the model format. The question is just who is responsible for checking that
this subset is not left.


> > In summary, I would now assume that the ordering of elements is required to
> > be
> > conserved if an XML format specification does not explicitly say that it is
> > irrelevant.
> 
> I think the key point is that as far as a tool is concerned, it is
> simply modifying/accessing the source DOM, for example, according to
> the set of provided XPath expressions. If the xpath expression defines
> an axis that implies a sequence, then that should be followed
> regardless of the specific XML format. Its just that knowing the
> actual format of the XML document allows us to take shortcuts when
> creating the xpath expressions, e.g., ignoring order when it is not
> required.
I agree with you.

Best regards, Felix.

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

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

> Having such a statement would immediately make it clear that using
> an Xpath reference which addresses a list element via its subscript would give
> an undefined result.

hmmmm...that doesn't sound right.

> In summary, I would now assume that the ordering of elements is required to be
> conserved if an XML format specification does not explicitly say that it is
> irrelevant.

I think the key point is that as far as a tool is concerned, it is
simply modifying/accessing the source DOM, for example, according to
the set of provided XPath expressions. If the xpath expression defines
an axis that implies a sequence, then that should be followed
regardless of the specific XML format. Its just that knowing the
actual format of the XML document allows us to take shortcuts when
creating the xpath expressions, e.g., ignoring order when it is not
required.


Cheers,
David.

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

[Felix W. <wi...@ka...>]

Hi David,

Thanks! Your answer helps a lot. As I have not worked with CellML before, I
wasn't aware of the fact that in CellML the ordering of the elements does not
carry any meaning. I will try to find the corresponding information in the
specification and see whether something along the lines can be found in the
latest SBML and SED-ML specs. If it is indeed in the SED-ML spec I have missed
it until now. Having such a statement would immediately make it clear that using
an Xpath reference which addresses a list element via its subscript would give
an undefined result.

In summary, I would now assume that the ordering of elements is required to be
conserved if an XML format specification does not explicitly say that it is
irrelevant. 


Best regards, 

Felix.


> On November 29, 2014 at 10:14 AM David Nickerson <dav...@gm...>
> wrote:
> 
> 
> Hi Felix,
> 
> I think it is generally the responsibility of an XML format to
> determine when and where element ordering makes a difference. MathML
> is another one where the ordering of elements can make a huge
> difference. Unlike Nicolas, I would expect all XML DOM parsers to
> return the elements in the same order :)
> 
> I know that the CellML specification explicitly states that the
> ordering of CellML elements is irrelevant. And I'm pretty sure the
> SBML specifications have similar rules. SED-ML itself also does, I
> think.
> 
> Going back to your original example, I believe that since the "author"
> of the SED-ML knows they are dealing with an SBML model where element
> ordering is not important they can leave it up the to processing tool
> to determine where the element is inserted into the list. If you were
> working with a format where order is important (like a MathML
> expression), you'd probably use an XPath expression like the one you
> suggest.
> 
> Not sure if that helps clarify your question?
> 
> 
> Cheers,
> David.
> 
> 
> On Sat, Nov 29, 2014 at 9:31 PM, Felix Winter <wi...@ka...> wrote:
> > Hi Nicolas,
> >
> > thanks for the fast reply. I always assumed that only the order of
> > attributes
> > was not to be considered consistent. With respect to the elements of lists,
> > I
> > tried to find the answer on my own before consulting the mailing list but it
> > seems there is contradicting information on this topic available. One
> > noticeable
> > example includes an email by Michael Kay, where he says that while
> > conserving
> > the element order is not specifically demanded by the specification, it is
> > something that is assumed to be obvious:
> >
> > http://lists.xml.org/archives/xml-dev/201003/msg00045.html
> >
> > And when it comes to XHTML, the order of elements in lists may very well be
> > important. For example in tables, not preserving the <td> elements would mix
> > the
> > content of the table.
> >
> > Again, the question would be: Is there a general (possibly written down)
> > rule
> > which states when the order of elements is important? And assuming that your
> > answer is authoritative, would that answer also extend to the other COMBINE
> > standards which can be expressed in XML, such as CellML and SBML?
> >
> > Best regards, Felix.
> >
> >
> >> On November 28, 2014 at 11:41 PM Nicolas Le Novere <n.l...@gm...>
> >> wrote:
> >>
> >>
> >>
> >> Hi Felix,
> >>
> >> The content of a SED-ML list is not ordered. In general, the content of an
> >> XML
> >> element is not ordered. Different parsers might return the elements in
> >> different order.
> >>
> >> Cheers
> >>
> >> On 28/11/14 22:07, Felix Winter wrote:
> >> > Hi everyone.
> >> >
> >> > (This question may be a little bit too general for the SED-ML mailing
> >> > list
> >> > but
> >> > as it came to my mind as I read the specification I thought it might be
> >> > admissible.)
> >> >
> >> > In the SED-ML L1V2 specification there is a listing explaining the use of
> >> > an
> >> > xpath expression inside the addXML element (Listing 2.36) The xpath
> >> > relates
> >> > to
> >> > the listOfParameters and as explained below the listing, is intended to
> >> > specify
> >> > that a new parameter is added to the list of parameters:
> >> >
> >> > --> from the spec
> >> > [...]
> >> > <addXML target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> >> > [...]
> >> > "The code of the model is changed so that a parameter with ID VmT is
> >> > added
> >> > to
> >> > its list of parameters. The newXML element adds an  additional XML
> >> > element
> >> > to
> >> > the original model. The element's name is parameter and it is added to
> >> > the
> >> > existing parent element
> >> > listOfParameters that is addressed by the XPath expression in the target
> >> > attribute"
> >> > <---
> >> >
> >> > I wonder whether it is necessary to specify where exactly in the
> >> > listOfParameters the new element should be added. I am no expert here but
> >> > isn't
> >> > the ordering of elements inside the list something which is not supposed
> >> > to
> >> > change? While all the other examples of xpath in the spec use something
> >> > like
> >> >
> >> > /sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id=`X'] to
> >> > identify a
> >> > specific element in a list, wouldn't it be in principle possible to use
> >> > /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[1] to get the
> >> > first
> >> > parameter? If so, it should be specified that new elements are only to be
> >> > put at
> >> > the end of listOf* . Or is there already a general rule for this kind of
> >> > operations which I has escaped my attention?
> >> >
> >> > With kind regards,
> >> >
> >> > Felix
> >> >
> >> >
> >> >
> >> >
> >> > Felix Winter
> >> > Thomas-Müntzer-Platz 63
> >> > 18057 Rostock
> >> >
> >> > IM: fw...@ja...
> >> >
> >> > ------------------------------------------------------------------------------
> >> > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> >> > from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> >> > with Interactivity, Sharing, Native Excel Exports, App Integration & more
> >> > Get technology previously reserved for billion-dollar corporations, FREE
> >> > http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
> >> > _______________________________________________
> >> > SED-ML-discuss mailing list
> >> > SED...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >> >
> >>
> >>
> >> --
> >> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
> >> Tel: +441223496433 Fax: +441223496034 Mob:+447833147074 twitter:@lenovere
> >> Skype:n.lenovere, n.l...@gm..., ORCID: 0000-0002-6309-7327
> >> http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/
> >>
> >> ------------------------------------------------------------------------------
> >> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> >> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> >> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> >> Get technology previously reserved for billion-dollar corporations, FREE
> >> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
> >> _______________________________________________
> >> SED-ML-discuss mailing list
> >> SED...@li...
> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> > Felix Winter
> > Thomas-Müntzer-Platz 63
> > 18057 Rostock
> >
> > IM: fw...@ja...
> >
> > ------------------------------------------------------------------------------
> > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> > from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> > with Interactivity, Sharing, Native Excel Exports, App Integration & more
> > Get technology previously reserved for billion-dollar corporations, FREE
> > http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> 
> 
> -- 
> 
> 
> David Nickerson
> about.me/david.nickerson
Felix Winter
Thomas-Müntzer-Platz 63
18057 Rostock

IM: fw...@ja...

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

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

Hi Felix,

I think it is generally the responsibility of an XML format to
determine when and where element ordering makes a difference. MathML
is another one where the ordering of elements can make a huge
difference. Unlike Nicolas, I would expect all XML DOM parsers to
return the elements in the same order :)

I know that the CellML specification explicitly states that the
ordering of CellML elements is irrelevant. And I'm pretty sure the
SBML specifications have similar rules. SED-ML itself also does, I
think.

Going back to your original example, I believe that since the "author"
of the SED-ML knows they are dealing with an SBML model where element
ordering is not important they can leave it up the to processing tool
to determine where the element is inserted into the list. If you were
working with a format where order is important (like a MathML
expression), you'd probably use an XPath expression like the one you
suggest.

Not sure if that helps clarify your question?


Cheers,
David.


On Sat, Nov 29, 2014 at 9:31 PM, Felix Winter <wi...@ka...> wrote:
> Hi Nicolas,
>
> thanks for the fast reply. I always assumed that only the order of attributes
> was not to be considered consistent. With respect to the elements of lists, I
> tried to find the answer on my own before consulting the mailing list but it
> seems there is contradicting information on this topic available. One noticeable
> example includes an email by Michael Kay, where he says that while conserving
> the element order is not specifically demanded by the specification, it is
> something that is assumed to be obvious:
>
> http://lists.xml.org/archives/xml-dev/201003/msg00045.html
>
> And when it comes to XHTML, the order of elements in lists may very well be
> important. For example in tables, not preserving the <td> elements would mix the
> content of the table.
>
> Again, the question would be: Is there a general (possibly written down) rule
> which states when the order of elements is important? And assuming that your
> answer is authoritative, would that answer also extend to the other COMBINE
> standards which can be expressed in XML, such as CellML and SBML?
>
> Best regards, Felix.
>
>
>> On November 28, 2014 at 11:41 PM Nicolas Le Novere <n.l...@gm...>
>> wrote:
>>
>>
>>
>> Hi Felix,
>>
>> The content of a SED-ML list is not ordered. In general, the content of an XML
>> element is not ordered. Different parsers might return the elements in
>> different order.
>>
>> Cheers
>>
>> On 28/11/14 22:07, Felix Winter wrote:
>> > Hi everyone.
>> >
>> > (This question may be a little bit too general for the SED-ML mailing list
>> > but
>> > as it came to my mind as I read the specification I thought it might be
>> > admissible.)
>> >
>> > In the SED-ML L1V2 specification there is a listing explaining the use of an
>> > xpath expression inside the addXML element (Listing 2.36) The xpath relates
>> > to
>> > the listOfParameters and as explained below the listing, is intended to
>> > specify
>> > that a new parameter is added to the list of parameters:
>> >
>> > --> from the spec
>> > [...]
>> > <addXML target="/sbml:sbml/sbml:model/sbml:listOfParameters">
>> > [...]
>> > "The code of the model is changed so that a parameter with ID VmT is added
>> > to
>> > its list of parameters. The newXML element adds an  additional XML element
>> > to
>> > the original model. The element's name is parameter and it is added to the
>> > existing parent element
>> > listOfParameters that is addressed by the XPath expression in the target
>> > attribute"
>> > <---
>> >
>> > I wonder whether it is necessary to specify where exactly in the
>> > listOfParameters the new element should be added. I am no expert here but
>> > isn't
>> > the ordering of elements inside the list something which is not supposed to
>> > change? While all the other examples of xpath in the spec use something like
>> >
>> > /sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id=`X'] to identify a
>> > specific element in a list, wouldn't it be in principle possible to use
>> > /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[1] to get the
>> > first
>> > parameter? If so, it should be specified that new elements are only to be
>> > put at
>> > the end of listOf* . Or is there already a general rule for this kind of
>> > operations which I has escaped my attention?
>> >
>> > With kind regards,
>> >
>> > Felix
>> >
>> >
>> >
>> >
>> > Felix Winter
>> > Thomas-Müntzer-Platz 63
>> > 18057 Rostock
>> >
>> > IM: fw...@ja...
>> >
>> > ------------------------------------------------------------------------------
>> > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
>> > from Actuate! Instantly Supercharge Your Business Reports and Dashboards
>> > with Interactivity, Sharing, Native Excel Exports, App Integration & more
>> > Get technology previously reserved for billion-dollar corporations, FREE
>> > http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
>> > _______________________________________________
>> > SED-ML-discuss mailing list
>> > SED...@li...
>> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> >
>>
>>
>> --
>> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
>> Tel: +441223496433 Fax: +441223496034 Mob:+447833147074 twitter:@lenovere
>> Skype:n.lenovere, n.l...@gm..., ORCID: 0000-0002-6309-7327
>> http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/
>>
>> ------------------------------------------------------------------------------
>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
>> with Interactivity, Sharing, Native Excel Exports, App Integration & more
>> Get technology previously reserved for billion-dollar corporations, FREE
>> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> Felix Winter
> Thomas-Müntzer-Platz 63
> 18057 Rostock
>
> IM: fw...@ja...
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss



-- 


David Nickerson
about.me/david.nickerson

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

[Felix W. <wi...@ka...>]

Hi Nicolas,

thanks for the fast reply. I always assumed that only the order of attributes
was not to be considered consistent. With respect to the elements of lists, I
tried to find the answer on my own before consulting the mailing list but it
seems there is contradicting information on this topic available. One noticeable
example includes an email by Michael Kay, where he says that while conserving
the element order is not specifically demanded by the specification, it is
something that is assumed to be obvious:

http://lists.xml.org/archives/xml-dev/201003/msg00045.html

And when it comes to XHTML, the order of elements in lists may very well be
important. For example in tables, not preserving the <td> elements would mix the
content of the table.

Again, the question would be: Is there a general (possibly written down) rule
which states when the order of elements is important? And assuming that your
answer is authoritative, would that answer also extend to the other COMBINE
standards which can be expressed in XML, such as CellML and SBML?

Best regards, Felix.


> On November 28, 2014 at 11:41 PM Nicolas Le Novere <n.l...@gm...>
> wrote:
> 
> 
> 
> Hi Felix,
> 
> The content of a SED-ML list is not ordered. In general, the content of an XML
> element is not ordered. Different parsers might return the elements in
> different order.
> 
> Cheers
> 
> On 28/11/14 22:07, Felix Winter wrote:
> > Hi everyone.
> >
> > (This question may be a little bit too general for the SED-ML mailing list
> > but
> > as it came to my mind as I read the specification I thought it might be
> > admissible.)
> >
> > In the SED-ML L1V2 specification there is a listing explaining the use of an
> > xpath expression inside the addXML element (Listing 2.36) The xpath relates
> > to
> > the listOfParameters and as explained below the listing, is intended to
> > specify
> > that a new parameter is added to the list of parameters:
> >
> > --> from the spec
> > [...]
> > <addXML target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> > [...]
> > "The code of the model is changed so that a parameter with ID VmT is added
> > to
> > its list of parameters. The newXML element adds an  additional XML element
> > to
> > the original model. The element's name is parameter and it is added to the
> > existing parent element
> > listOfParameters that is addressed by the XPath expression in the target
> > attribute"
> > <---
> >
> > I wonder whether it is necessary to specify where exactly in the
> > listOfParameters the new element should be added. I am no expert here but
> > isn't
> > the ordering of elements inside the list something which is not supposed to
> > change? While all the other examples of xpath in the spec use something like
> >
> > /sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id=`X'] to identify a
> > specific element in a list, wouldn't it be in principle possible to use
> > /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[1] to get the
> > first
> > parameter? If so, it should be specified that new elements are only to be
> > put at
> > the end of listOf* . Or is there already a general rule for this kind of
> > operations which I has escaped my attention?
> >
> > With kind regards,
> >
> > Felix
> >
> >
> >
> >
> > Felix Winter
> > Thomas-Müntzer-Platz 63
> > 18057 Rostock
> >
> > IM: fw...@ja...
> >
> > ------------------------------------------------------------------------------
> > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> > from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> > with Interactivity, Sharing, Native Excel Exports, App Integration & more
> > Get technology previously reserved for billion-dollar corporations, FREE
> > http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> 
> 
> -- 
> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
> Tel: +441223496433 Fax: +441223496034 Mob:+447833147074 twitter:@lenovere
> Skype:n.lenovere, n.l...@gm..., ORCID: 0000-0002-6309-7327
> http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/
> 
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
Felix Winter
Thomas-Müntzer-Platz 63
18057 Rostock

IM: fw...@ja...

Re: [SED-ML-discuss] Xpath expression in SED-ML Spec

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

Hi Felix,

The content of a SED-ML list is not ordered. In general, the content of an XML element is not ordered. Different parsers might return the elements in different order.

Cheers

On 28/11/14 22:07, Felix Winter wrote:
> Hi everyone.
>
> (This question may be a little bit too general for the SED-ML mailing list but
> as it came to my mind as I read the specification I thought it might be
> admissible.)
>
> In the SED-ML L1V2 specification there is a listing explaining the use of an
> xpath expression inside the addXML element (Listing 2.36) The xpath relates to
> the listOfParameters and as explained below the listing, is intended to specify
> that a new parameter is added to the list of parameters:
>
> --> from the spec
> [...]
> <addXML target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> [...]
> "The code of the model is changed so that a parameter with ID VmT is added to
> its list of parameters. The newXML element adds an  additional XML element to
> the original model. The element's name is parameter and it is added to the
> existing parent element
> listOfParameters that is addressed by the XPath expression in the target
> attribute"
> <---
>
> I wonder whether it is necessary to specify where exactly in the
> listOfParameters the new element should be added. I am no expert here but isn't
> the ordering of elements inside the list something which is not supposed to
> change? While all the other examples of xpath in the spec use something like
>
> /sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id=`X'] to identify a
> specific element in a list, wouldn't it be in principle possible to use
> /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[1] to get the first
> parameter? If so, it should be specified that new elements are only to be put at
> the end of listOf* . Or is there already a general rule for this kind of
> operations which I has escaped my attention?
>
> With kind regards,
>
> Felix
>
>
>
>
> Felix Winter
> Thomas-Müntzer-Platz 63
> 18057 Rostock
>
> IM: fw...@ja...
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>


-- 
Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
Tel: +441223496433 Fax: +441223496034 Mob:+447833147074 twitter:@lenovere
Skype:n.lenovere, n.l...@gm..., ORCID: 0000-0002-6309-7327
http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/

[SED-ML-discuss] Xpath expression in SED-ML Spec

[Felix W. <wi...@ka...>]

Hi everyone.

(This question may be a little bit too general for the SED-ML mailing list but
as it came to my mind as I read the specification I thought it might be
admissible.)

In the SED-ML L1V2 specification there is a listing explaining the use of an
xpath expression inside the addXML element (Listing 2.36) The xpath relates to
the listOfParameters and as explained below the listing, is intended to specify
that a new parameter is added to the list of parameters:

--> from the spec
[...]
<addXML target="/sbml:sbml/sbml:model/sbml:listOfParameters">
[...]
"The code of the model is changed so that a parameter with ID VmT is added to
its list of parameters. The newXML element adds an  additional XML element to
the original model. The element's name is parameter and it is added to the
existing parent element
listOfParameters that is addressed by the XPath expression in the target
attribute"
<---

I wonder whether it is necessary to specify where exactly in the
listOfParameters the new element should be added. I am no expert here but isn't
the ordering of elements inside the list something which is not supposed to
change? While all the other examples of xpath in the spec use something like

/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id=`X'] to identify a
specific element in a list, wouldn't it be in principle possible to use
/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[1] to get the first
parameter? If so, it should be specified that new elements are only to be put at
the end of listOf* . Or is there already a general rule for this kind of
operations which I has escaped my attention?

With kind regards, 

Felix




Felix Winter
Thomas-Müntzer-Platz 63
18057 Rostock

IM: fw...@ja...

[SED-ML-discuss] HARMONY 2015 - Registration

[Falk S. <fal...@mo...>]

Dear COMBINE community!

The registration for HARMONY 2015 is now open.

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. 

HARMONY 2015 will take place 

Mon. 20- Fri. 24 April 2015 in at the Leucorea in Wittenberg, Germany

More information can be found here: http://www.co.mbine.org/events/HARMONY_2015

Please note that up to 35 rooms can be provided at a special rate of 30 euros per night without breakfast at the meeting place (Leucorea) at a first come first served basis.

We hope to see you in Wittenberg!

Dagmar Waltemath, Tobias Czauderna & Falk Schreiber

[SED-ML-discuss] [just 4 more days] call for nominations for two SED-ML editors

[Frank B. <fbe...@ca...>]

Dear colleagues, 

only 4 days left to nominate your candidates for SED-ML editors. The form is at: 

> http://goo.gl/V8tp8M

All the best
Frank Bergmann

Begin forwarded message:

> From: Frank Bergmann <fbe...@ca...>
> Subject: [SED-ML-discuss] call for nominations for two SED-ML editors
> Date: November 7, 2014 at 2:09:48 PM GMT+1
> To: sed...@li...
> Reply-To: sed...@li...
> 
> Dear colleagues,
> 
> this is a call for nominations for two SED-ML editors to replace Frank Bergmann and Dagmar Waltemath, whose terms end on the 31st of December 2014.
> 
> The length of a SED-ML Editor's term is 3 years, starting from the 1st of January 2015.
> 
> The current editors are Frank Bergmann (to be replaced), Jonathan Cooper (until 2015), Ion Moraru (until 2016), Sven Sahle (until 2016) and Dagmar Waltemath (to be replaced).
> 
> 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 nomination page is at: http://goo.gl/V8tp8M
> 
> The call for nomination is open from now until the 25th of November 2014.  After nomination phase, we will issue a call for voting.
> 
> Frank Bergmann,
> on behalf of the SED-ML Editors.
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[SED-ML-discuss] call for nominations for two SED-ML editors

[Frank B. <fbe...@ca...>]

Dear colleagues,

this is a call for nominations for two SED-ML editors to replace Frank Bergmann and Dagmar Waltemath, whose terms end on the 31st of December 2014.

The length of a SED-ML Editor's term is 3 years, starting from the 1st of January 2015.

The current editors are Frank Bergmann (to be replaced), Jonathan Cooper (until 2015), Ion Moraru (until 2016), Sven Sahle (until 2016) and Dagmar Waltemath (to be replaced).

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 nomination page is at: http://goo.gl/V8tp8M

The call for nomination is open from now until the 25th of November 2014.  After nomination phase, we will issue a call for voting.

Frank Bergmann,
on behalf of the SED-ML Editors.