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

Re: [SED-ML-discuss] setValue and listOfVariables

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

Hello Andrew, 

Thank you for the comment (and of course to Dan who let us know about it
last week). Looking at the section in the spec I believe we can be much more
descriptive about the setValue element and I plan to do so. The description
will be updated to say that the 'SetValue' element inherits from
'ComputeChange' and extends it with the attributes 'modelReference' and
'range'. That will give it all features that were intended and will leave
all examples stand as they are. 

Thanks again 

All the best
Frank

> -----Original Message-----
> From: Andrew Miller [mailto:ak....@au...]
> Sent: Monday, May 27, 2013 7:03 AM
> To: sed...@li...
> Subject: [SED-ML-discuss] setValue and listOfVariables
> 
> Hi all,
> 
> When trying to implement the latest SED-ML L1V2 draft (which I checked out
> from Subversion and built myself since I believe the PDF file is not up to
date)
> I noticed that setValue, as defined in the text, can't contain a
listOfVariables
> (it inherits from variable, and 2.4.8.4 says that range and math are the
only
> additions).
> 
> I presume the intention is to include a listOfVariables child - the
examples do
> so, and otherwise, it is not possible to make setValue depend on the
values
> from the previous timestep.
> 
> Best wishes,
> Andrew
> 
> 
>
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[SED-ML-discuss] setValue and listOfVariables

[Andrew M. <ak....@au...>]

Hi all,

When trying to implement the latest SED-ML L1V2 draft (which I checked 
out from Subversion and built myself since I believe the PDF file is not 
up to date) I noticed that setValue, as defined in the text, can't 
contain a listOfVariables (it inherits from variable, and 2.4.8.4 says 
that range and math are the only additions).

I presume the intention is to include a listOfVariables child - the 
examples do so, and otherwise, it is not possible to make setValue 
depend on the values from the previous timestep.

Best wishes,
Andrew

[SED-ML-discuss] [Combine-announce] Update on COMBINE 2013

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

Dear Colleagues,

Now that HARMONY has ended, and the developers have been fed, it is time to 
turn to the other side of our activity and talk about standard development. 
The plans for COMBINE forum 2013 are shaping up nicely, thanks to the local 
organisers - the bioinformatics unit of Institut Curie - and in particular 
Eric Bonnet.

The meeting will start on Monday 16th September, with a scientific 
conference. The theme will be the different modelling approaches used in 
biology. There will be invited talks, short talks selected from abstracts 
and poster sessions. So far, we have confirmation of lectures by:

Vincent Danos (CNRS, Paris-Diderot, Univ Edinburgh, rule-based modelling)
Marc Lavielle (INRIA, Paris-sud, pharmacometrics)
Benjamin Ribba (INRIA, multi-scale modelling of tumours)
Denis Thieffry (ENS, logical modelling)
Andrei Zinovyev (Curie, network analysis)

We are waiting for a couple more confirmations.

This meeting should give us an overview of what we cover or not, and fuel 
the dicussions of the subsequent days.  The traditional COMBINE forum will 
then take place from Tuesday 17 to Friday 20.

The first day will be open and free for all. It is anticipated that 
participation to the remaining workshop will be subjected to the usual 
minimal fees.

The registration system is not yet in place, but please book your week, and 
spread the word.

Best regards

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



_______________________________________________
Combine-announce mailing list
Com...@eb...
http://listserver.ebi.ac.uk/mailman/listinfo/combine-announce

[SED-ML-discuss] New release of jlibsedml

[Vasilescu,Dan <vas...@uc...>]

Hello all in SED-ML-discuss,

A couple of days ago I uploaded to the jlibsedml SourceForge repository a first version of an Java SED-ML L1V2 implementation based on the Dec 15 2012 draft.
There are a few assumptions I made which may prove to be wrong and the specifications may change in time. Hopefuly most issues will be clarified during Harmony 2013.

Regards,
Dan Vasilescu
CCAM / UCONN

Re: [SED-ML-discuss] FunctionalRange - terminating conditions

[Pedro M. <ped...@ma...>]

On 05/20/2013 04:09 AM, Andrew Miller wrote:
> For example, you could describe a fitting which stops when a tolerance
> is reached using a FunctionalRange with a termination condition.
> However, that type of application raises the question of whether we
> really want to make SED-ML task descriptions Turing complete, and
> whether we might be better off adding new tasks / simulations that more
> cleanly describe that type of procedure.

Hi Andrew,

I think we should have different tasks. In particular fitting (parameter 
estimation) should definitely be a task on its own. It requires quite a 
bit more specification than other tasks because it involves an external 
data set. This data set needs to be matched with the elements of the 
model before the fitting problem can even be described. Then there are 
many different methods by which the fitting procedure can be executed. 
All this makes parameter estimation be better on its own right as a 
task. We're having a session on this topic this week at HARMONY 2013.

best wishes
Pedro


-- 
Pedro Mendes
Professor of Computational Systems Biology
School of Computer Science
Manchester Centre for Integrative Systems Biology
University of Manchester

Manchester Institute of Biotechnology
131 Princess Street
Manchester, M1 7DN, U.K.

Re: [SED-ML-discuss] FunctionalRange - terminating conditions

[Andrew M. <ak....@au...>]

On 20/05/13 14:51, Frank T. Bergmann wrote:
> What I have been doing, and how I intended it to be used, was that the functionalRange needed to be parameterized by another range. When I was using it I was usually having this other range be a uniformRange, though of course other ones would work to. In that case it was quite easy to figure out when it would be terminating.
>
> Do you have an example when this would not be feasible?
I think if you have at least one vector or uniform range, that means 
that the number of steps in the simulation experiment are fixed, which 
covers a lot of the experiments people are going to want to do, but it 
is very easy to come up with potential experiments that you could only 
do with non-fixed numbers of steps.

For example, you could describe a fitting which stops when a tolerance 
is reached using a FunctionalRange with a termination condition. 
However, that type of application raises the question of whether we 
really want to make SED-ML task descriptions Turing complete, and 
whether we might be better off adding new tasks / simulations that more 
cleanly describe that type of procedure.

In either case, there really needs to be a bit of text in the 
specification explaining what the restrictions are (e.g. that there must 
be at least one VectorRange or UniformRange) and precisely how SED-ML 
simulators are supposed to process tasks; otherwise, every 
implementation is going to end up handling corner cases differently, and 
we will be back to having non-reproducible simulation experiments.

Best wishes,
Andrew

Re: [SED-ML-discuss] FunctionalRange - terminating conditions

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

What I have been doing, and how I intended it to be used, was that the functionalRange needed to be parameterized by another range. When I was using it I was usually having this other range be a uniformRange, though of course other ones would work to. In that case it was quite easy to figure out when it would be terminating. 

Do you have an example when this would not be feasible? 

thanks
Frank

On May 19, 2013, at 5:53 PM, Andrew Miller <ak....@au...> wrote:

> Hi all,
> 
> Another L1V2 minor issue:
> 
> There doesn't seem to be any explicit advice in the specification on how 
> to determine when a RepeatedTask using FunctionalRange terminates.
> 
> One option could be to add a new element giving content MathML for a 
> boolean expression to determine if the current step should be the last. 
> Another option could be to have a rule that if the function produces the 
> exact same value twice, to terminate (however, this means that two 
> implementations might give different results if they use slightly 
> different rounding, which is not good for reproducibility; it also has 
> the downside that functions that depend on the index might produce the 
> same value twice but then go on to produce different values).
> 
> Best wishes,
> Andrew
> 
> 
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[SED-ML-discuss] FunctionalRange - terminating conditions

[Andrew M. <ak....@au...>]

Hi all,

Another L1V2 minor issue:

There doesn't seem to be any explicit advice in the specification on how 
to determine when a RepeatedTask using FunctionalRange terminates.

One option could be to add a new element giving content MathML for a 
boolean expression to determine if the current step should be the last. 
Another option could be to have a rule that if the function produces the 
exact same value twice, to terminate (however, this means that two 
implementations might give different results if they use slightly 
different rounding, which is not good for reproducibility; it also has 
the downside that functions that depend on the index might produce the 
same value twice but then go on to produce different values).

Best wishes,
Andrew

Re: [SED-ML-discuss] Tracker for minor issues in L1V2 draft? listOfTasks needs to contain AbstractTask not Task

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

> There doesn't seem to be an issue tracker for the L1V2 draft document, 
> aside from the proposals tracker; I'm not sure if the proposals tracker 
> is the right place for issues that don't change the intent of the 
> specification but instead ask for details to be corrected, so I'm 
> sending this here. I suggest that a L1V2 Draft tracker be created.
> 

we can do that. thanks! But please feel also free to let us know about all issue here (or at the editors list), and we will address them as fast as possible.  

> I'm working on implementing the Nested Tasks proposal in the SED-ML 
> Processing Service (for those who haven't come across it before, that is 
> the C++ implementation of SED-ML that currently ships with the CellML 
> API), and am taking a close look for any issues with the specification 
> as I do this.
> 

Great, thank you!

> I've found one issue with the L1V2 draft on the website already: 
> previously, in L1V1, there was just Task, and listOfTasks was a list of 
> Task. The specification introduces a new class of task, RepeatedTask, 
> and a new abstract base class, AbstractTask, which RepeatedTask 
> specialises. Presumably, the intention is that listOfTasks now becomes a 
> list of AbstractTasks rather than Tasks. However, the specification 
> still says it is a list of Tasks (page 69, line 241; UML diagram, page 
> 35, section 2.3.8.7).
> 

Sorry, as I tried to indicate in the last mail. The UML diagrams in the draft have not yet been updated. 

> The other issue that I can see is that subTasks need to reference a task 
> defined in listOfTasks, which means that people will put things under 
> listOfTasks that don't make sense as a task on their own, solely so they 
> can refer to them from a subTask.

I actually think these tasks could also make sense standing by themselves. But I'd be happy to discuss things. 

> Some software (e.g. non-graphical 
> software) is just going to want to run all the tasks, and so it is 
> unhelpful if there are tasks that are not useful simulation experiments 
> in their own right that are not distinguished from the useful simulation 
> experiments.

What I do, is to analyze what output is requested, and only run those tasks that are needed to produce output. But of course that is a tool decision. 

Frank

[SED-ML-discuss] Tracker for minor issues in L1V2 draft? listOfTasks needs to contain AbstractTask not Task

[Andrew M. <ak....@au...>]

Hi,

There doesn't seem to be an issue tracker for the L1V2 draft document, 
aside from the proposals tracker; I'm not sure if the proposals tracker 
is the right place for issues that don't change the intent of the 
specification but instead ask for details to be corrected, so I'm 
sending this here. I suggest that a L1V2 Draft tracker be created.

I'm working on implementing the Nested Tasks proposal in the SED-ML 
Processing Service (for those who haven't come across it before, that is 
the C++ implementation of SED-ML that currently ships with the CellML 
API), and am taking a close look for any issues with the specification 
as I do this.

I've found one issue with the L1V2 draft on the website already: 
previously, in L1V1, there was just Task, and listOfTasks was a list of 
Task. The specification introduces a new class of task, RepeatedTask, 
and a new abstract base class, AbstractTask, which RepeatedTask 
specialises. Presumably, the intention is that listOfTasks now becomes a 
list of AbstractTasks rather than Tasks. However, the specification 
still says it is a list of Tasks (page 69, line 241; UML diagram, page 
35, section 2.3.8.7).

The other issue that I can see is that subTasks need to reference a task 
defined in listOfTasks, which means that people will put things under 
listOfTasks that don't make sense as a task on their own, solely so they 
can refer to them from a subTask. Some software (e.g. non-graphical 
software) is just going to want to run all the tasks, and so it is 
unhelpful if there are tasks that are not useful simulation experiments 
in their own right that are not distinguished from the useful simulation 
experiments. It would be possible to detect such tasks by looking 
through all the repeatedTasks and flagging those which are referenced as 
subTasks, but in some cases something might be both a useful simulation 
experiment and a subtask (this especially applies if people start 
recursively defining repeatedTasks, in which case there might not be any 
tasks that aren't referenced as subtasks). An attribute on AbstractTask 
to flag a task as a task that doesn't exist solely for other tasks to 
reference would address this.

Best wishes,
Andrew

Re: [SED-ML-discuss] questions about SetValue

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

Hello Dan, 

sorry that we did not finish the new version before HARMONY. Three editors are currently traveling there. But to answer your question: 

- The listOfChanges contains setValue objects. 
- setValue inherits from variable, that is currently not included in the 'temporary' UML diagram 2.34, dagmar is working hard on getting the UML diagrams updated in the meantime. This is the reason you don't see the listOfVariables
- In the discussions at COMBINE and since then, it was decided to allow setValue to refer to range ids as target. And to use that in favor of other xpath queries on the SED-ML document (so far all xpath queries went into the model). 

In fact Jonathan was proposing to extend this sort of referencing scheme for other entities as well, but we are not there yet. 

Please let me know if you have further questions. 

All the best
Frank


Current draft: 
http://sourceforge.net/p/sed-ml/code/HEAD/tree/sed-ml/specification/trunk/level-1/version-2/sed-ml-L1V2.pdf

On May 17, 2013, at 2:45 PM, "Vasilescu,Dan" <vas...@uc...> wrote:

> Hello all in SED-ML-discuss,
> 
> I am working on a Java SED-ML L1V2 implementation based on the Dec 15 2012 draft. I am not sure which way to go about setValue, I would greatly appreciate some clarifications.
> 
> One of the examples provided (Listing 2.48) shows setValue as containing a listOfVariables field while the formal description in Fig. 2.34 does not show such field. Which one is right?
> 
> Also, related to the variable entity in the example provided in Listing 2.48: <variable id="val" name="current range value" target="#current" />  The target field seems to act as a reference to a range rather than an XPath... is this consistent with the meaning of "target" within a Variable?
> 
> Finally, if SetValue is a "Variable", is this not overloading the listOfChanges (which should contain "Change" types)?
> 
> Thank you,
> Dan Vasilescu
> CCAM / UCONN
> 
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> security visibility with the essential security capabilities. Easily and
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[SED-ML-discuss] questions about SetValue

[Vasilescu,Dan <vas...@uc...>]

Hello all in SED-ML-discuss,

I am working on a Java SED-ML L1V2 implementation based on the Dec 15 2012 draft. I am not sure which way to go about setValue, I would greatly appreciate some clarifications.

One of the examples provided (Listing 2.48) shows setValue as containing a listOfVariables field while the formal description in Fig. 2.34 does not show such field. Which one is right?

Also, related to the variable entity in the example provided in Listing 2.48: <variable id="val" name="current range value" target="#current" />  The target field seems to act as a reference to a range rather than an XPath... is this consistent with the meaning of "target" within a Variable?

Finally, if SetValue is a "Variable", is this not overloading the listOfChanges (which should contain "Change" types)?

Thank you,
Dan Vasilescu
CCAM / UCONN

[SED-ML-discuss] pre-HARMONY survey

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

Hi all,

In order to maximise SED-ML productivity at the upcoming HARMONY
meeting (http://co.mbine.org/events/HARMONY_2013), the SED-ML editors
are interested to know what topics would be of most interest to the
attendees. This will help us arrange suitable locations and times for
focused sessions that will best address the needs of the community.

We have put up a brief survey to collect your suggestions: http://goo.gl/XpNHW

And remember, if you plan to attend HARMONY, please make sure to book
your hotel and, if needed, apply for financial support as soon as
possible. See travel info and details at
http://www.co.mbine.org/events/HARMONY_2013.


Cheers,
David.

Re: [SED-ML-discuss] Hello and updates from COPASI

[Brett G. O. <bre...@gm...>]

Interesting, I've built and installed libSBML on Windows,  Mac and Linux
and never considered it's size to be an issue.

Nevertheless, if Frank can pull in the required source automatically, a
solution which sounds both neat and won't require a lot of disk space, then
this dependency is a non-issue.

Regards
Brett
On 26 Apr 2013 13:58, "Frank T. Bergmann" <fbe...@ca...> wrote:

> > Brett, I personally have two issues with the libSBML dependency. The
> first
> > one is that it's not 'neat' (but I appreciate that various constraints
> may
> mean
> > that there are (currently, at least) no other alternatives). The second
> one is
> > that libSBML is not that small. I have just unpacked the Ubuntu binaries
> and
> > we are talking about ~50MB. As for Windows 64-bit, and after having
> > removed the 'unnecessary' bits, I ended up with ~315MB (!!).
> > (libsbml.lib alone is ~305MB!)
> >
>
> Just to speak about the size issue: just the fact that libSBML installers
> contain installers for different versions of python, matlab and the like
> should not be held against it :). There is 20MB of source code + tests. The
> rest of the source archive is documentation + examples  + build files.
> People ask the SBML team for installers that contains *everything*. Which
> is
> why we produce them. Though we probably should not distribute a static
> library, that will only work with one version of Visual Studio.
>
> However, if this dependency happens to be an issue for people. I would not
> mind altering the files to implicitly reference the project and pull the
> sources automatically. That way users of libSEDML would not have to locate
> /
> install / deal with libSBML themselves.
>
> Cheers
> Frank
>
>
>
> ------------------------------------------------------------------------------
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>

Re: [SED-ML-discuss] Hello and updates from COPASI

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

> Brett, I personally have two issues with the libSBML dependency. The first
> one is that it's not 'neat' (but I appreciate that various constraints may
mean
> that there are (currently, at least) no other alternatives). The second
one is
> that libSBML is not that small. I have just unpacked the Ubuntu binaries
and
> we are talking about ~50MB. As for Windows 64-bit, and after having
> removed the 'unnecessary' bits, I ended up with ~315MB (!!).
> (libsbml.lib alone is ~305MB!)
> 

Just to speak about the size issue: just the fact that libSBML installers
contain installers for different versions of python, matlab and the like
should not be held against it :). There is 20MB of source code + tests. The
rest of the source archive is documentation + examples  + build files.
People ask the SBML team for installers that contains *everything*. Which is
why we produce them. Though we probably should not distribute a static
library, that will only work with one version of Visual Studio. 

However, if this dependency happens to be an issue for people. I would not
mind altering the files to implicitly reference the project and pull the
sources automatically. That way users of libSEDML would not have to locate /
install / deal with libSBML themselves. 

Cheers
Frank

Re: [SED-ML-discuss] Hello and updates from COPASI

[Alan G. <ala...@in...>]

Agreed with Jonathan. This is indeed what I had in mind as an ultimate
software solution, though I appreciate that resources are limited, so it may
not happen any time soon (if at all).

Brett, I personally have two issues with the libSBML dependency. The first
one is that it's not 'neat' (but I appreciate that various constraints may
mean that there are (currently, at least) no other alternatives). The second
one is that libSBML is not that small. I have just unpacked the Ubuntu
binaries and we are talking about ~50MB. As for Windows 64-bit, and after
having removed the 'unnecessary' bits, I ended up with ~315MB (!!).
(libsbml.lib alone is ~305MB!)

This being all said, it might be a way to 'force' me to use SBML...

Alan

> -----Original Message-----
> From: Jonathan Cooper [mailto:jon...@cs...]
> Sent: 26 April 2013 08:40
> To: sed...@li...
> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> 
> Hi all,
> 
> I'm also very happy that Frank is working on this!  Regarding the libSBML
> dependency, it seems to me that there's an argument here for splitting
> libSBML up, and extracting the XML parsing to AST into a separate library,
> which multiple ML standards could use. I'm not too familiar with the
> internals of libSBML, but does that sound sensible?
> 
> Best wishes,
> Jonathan
> 
> On 26/04/2013 06:52, Frank T. Bergmann wrote:
> > Hello Alan,
> >
> > There is two parts of libSBML that are required, the XML parsing
> > layer, and the AST nodes. While theoretically possible to extract all
> > that, it will make interaction with libSBML for those that do want to
> > support SBML a lot harder (as after the extraction there will be
> > different *incompatible* AST / XML classes). I don't think at this point
this
> would be worth the effort.
> > But even though libSBML is being used, at present there are no
> > functions specific to a particular modeling language.
> >
> > Cheers
> > Frank
> >
> > P.S: I'm sure we will work all this out. Like I said I'm flexible with
> > respect of the naming of the library. For the time being I would use
> > libSEDML, mainly because of linux being picky to clone the repository
> > otherwise.
> >
> >> -----Original Message-----
> >> From: Alan Garny [mailto:ala...@in...]
> >> Sent: Thursday, April 25, 2013 10:47 PM
> >> To: sed...@li...
> >> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> >>
> >> Hi Frank,
> >>
> >> +1 from me too.
> >>
> >> However, I couldn't help but notice (from
> >> http://fbergmann.github.io/libSEDML/) that libSEDML has a (big)
> >> dependency on libSBML. Is there really no way to remove that
> >> dependency so that those of us who don't (currently, at least) use
> >> SBML could still
> > take
> >> advantage of libSEDML? Maybe the libSBML's XML parsing layer could,
> >> somehow, be 'extracted' and taken advantage of?
> >>
> >> Cheers, Alan.
> >>
> >> PS: what is the correct casing for it? libSEDML, LibSEDML, Libsedml,
...?
> >>
> >>> -----Original Message-----
> >>> From: Frank T. Bergmann [mailto:fbe...@ca...]
> >>> Sent: 25 April 2013 15:15
> >>> To: sed...@li...
> >>> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> >>>
> >>> To provide just a little bit more detail on this. I've started to
> >>> create
> >> a library
> >>> based on classes adapted from libSBML (such as SBase -> SedBase and
> >>> the like). From there I modified a prototype from Sarah Keating that
> >>> would
> >> allow
> >>> to generate basic C++ classes. After rounds of refinement, I am now
> >>> at a point where the core of SEDML L1V1 with the exception of the
> >>> raw XML manipulation classes AddXML and ChangeXML are
> implemented.
> >>> Via SWIG
> >> I
> >>> then created rudimentary language bindings for C#, Java, Python,
> >>> Ruby,
> >> Perl
> >>> and R.
> >>>
> >>> The project is currently hosted at github:
> >>> http://fbergmann.github.io/libSEDML/
> >>>
> >>> For examples on how the library can be used in the individual
> >>> languages
> >> see:
> >>> https://github.com/fbergmann/libSEDML/tree/master/examples
> >>>
> >>> In order to compile you need only to have CMake and libSBML. This
> >>> library
> >> is
> >>> written for the raw manipulation of the SEDML classes. It presently
> >>> does
> >> not
> >>> perform any of the utility functions as provided by my C# library
> >>> (http://libsedml.sf.net) where models are resolved no matter where
> >>> they are, stylesheet transformations for changes are applied, or the
> >>> simulation experiments can be scheduled and run.
> >>>
> >>> Any feedback would be appreciated. And bugs can be filed under:
> >>>
> >>> https://github.com/fbergmann/libSEDML/issues
> >>>
> >>> Cheers
> >>> Frank
> >>>
> >>>
> >>> On Apr 25, 2013, at 1:15 PM, Pedro Mendes
> >>> <ped...@ma...> wrote:
> >>>
> >>>> Hello all in SED-ML-discuss
> >>>>
> >>>> Just joined the list and a few colleagues of mine will join too. As
> >>>> you may know, currently COPASI does not support SED-ML. This will
> >>>> change and we are committed to add SED-ML support. We will also
> >>>> bring in some ideas to develop further SED-ML, since currently our
> >>>> CopasiML has the functionality of what SED-ML aspires (ie it stores
> >>>> both the model and all the tasks to be carried out, so it is like
> >>>> SBML+SED-ML
> >>> together).
> >>>> Many of the tasks that you can do in COPASI currently cannot be
> >>>> specified in SED-ML, so we would like to help development too.
> >>>>
> >>>> The first step for us will be to create a library, in C++ (since
> >>>> that is what we use), to read/write SED-ML. Other colleagues from a
> >>>> FP7 project (Eric Boix and Bertrand Moreau at CoSMo) also want to
> >>>> use SED-ML and would like such a library. I suspect others here may
> >>>> also be
> >>> interested?
> >>>> Right now, it would be great to hear from anyone already writing
> >>>> such a a library (in C/C++) to avoid duplication of efforts. Our
> >>>> plan is to create a libSEDML following the same steps as libSBML --
> >>>> written in C/C++ and then create bindings for other languages.
> >>>> Frank Bergmann has also expressed interest and that he'd help.
> >>>>
> >>>> best
> >>>> Pedro
> >>>>
> >>>> --
> >>>> Pedro Mendes
> >>>> Professor of Computational Systems Biology School of Computer
> >>>> Science Manchester Centre for Integrative Systems Biology
> >>>> University of Manchester
> >>>>
> >>>> Manchester Institute of Biotechnology
> >>>> 131 Princess Street
> >>>> Manchester, M1 7DN, U.K.
> >>>>
> >>>> -------------------------------------------------------------------
> >>>> -
> >>>> --
> >>>> -------- Try New Relic Now & We'll Send You this Cool Shirt New
> >>>> Relic is the only SaaS-based application performance monitoring
> >>>> service that delivers powerful full stack analytics. Optimize and
> >>>> monitor your browser, app, & servers with just a few lines of code.
> >>>> Try New Relic and get this awesome Nerd Life shirt!
> >>>> http://p.sf.net/sfu/newrelic_d2d_apr
> >>>> _______________________________________________
> >>>> SED-ML-discuss mailing list
> >>>> SED...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >>>
> >>>
> > ----------------------------------------------------------------------
> > ------
> >> --
> >>> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the
> >>> only SaaS-based application performance monitoring service that
> >>> delivers powerful full stack analytics. Optimize and monitor your
> >>> browser, app, & servers with just a few lines of code. Try New Relic
> >>> and get this awesome Nerd Life shirt!
> >>> http://p.sf.net/sfu/newrelic_d2d_apr
> >>> _______________________________________________
> >>> SED-ML-discuss mailing list
> >>> SED...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >>
> >>
> > ----------------------------------------------------------------------
> > ------
> > --
> >> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the
> >> only
> > SaaS-
> >> based application performance monitoring service that delivers
> >> powerful
> > full
> >> stack analytics. Optimize and monitor your browser, app, & servers
> >> with
> > just
> >> a few lines of code. Try New Relic and get this awesome Nerd Life
shirt!
> >> http://p.sf.net/sfu/newrelic_d2d_apr
> >> _______________________________________________
> >> SED-ML-discuss mailing list
> >> SED...@li...
> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> > ----------------------------------------------------------------------
> > -------- Try New Relic Now & We'll Send You this Cool Shirt New Relic
> > is the only SaaS-based application performance monitoring service that
> > delivers powerful full stack analytics. Optimize and monitor your
> > browser, app, & servers with just a few lines of code. Try New Relic
> > and get this awesome Nerd Life shirt!
> > http://p.sf.net/sfu/newrelic_d2d_apr
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> 
>
----------------------------------------------------------------------------
--
> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only
> SaaS-based application performance monitoring service that delivers
> powerful full stack analytics. Optimize and monitor your browser, app, &
> servers with just a few lines of code. Try New Relic and get this awesome
> Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Hello and updates from COPASI

[Joseph O. D. <jos...@ma...>]

Dear All,

We are also currently reusing/adapting LIbSBML code expectially the XML 
parsing layer in the development of the LIBNUML 
(http://code.google.com/p/numl/). So, I will be in support of the separation 
of XML parsing layer into separate library for use in other ML standards.

Thanks, Joseph

> 
> Hi all,
> 
> I'm also very happy that Frank is working on this!  Regarding the
> libSBML dependency, it seems to me that there's an argument here for
> splitting libSBML up, and extracting the XML parsing to AST into a
> separate library, which multiple ML standards could use. I'm not too
> familiar with the internals of libSBML, but does that sound sensible?
> 
> Best wishes,
> Jonathan
> 
> On 26/04/2013 06:52, Frank T. Bergmann wrote:
> > Hello Alan,
> > 
> > There is two parts of libSBML that are required, the XML parsing layer,
> > and the AST nodes. While theoretically possible to extract all that, it
> > will make interaction with libSBML for those that do want to support
> > SBML a lot harder (as after the extraction there will be different
> > *incompatible* AST / XML classes). I don't think at this point this
> > would be worth the effort. But even though libSBML is being used, at
> > present there are no functions specific to a particular modeling
> > language.
> > 
> > Cheers
> > Frank
> > 
> > P.S: I'm sure we will work all this out. Like I said I'm flexible with
> > respect of the naming of the library. For the time being I would use
> > libSEDML, mainly because of linux being picky to clone the repository
> > otherwise.
> > 
> >> -----Original Message-----
> >> From: Alan Garny [mailto:ala...@in...]
> >> Sent: Thursday, April 25, 2013 10:47 PM
> >> To: sed...@li...
> >> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> >> 
> >> Hi Frank,
> >> 
> >> +1 from me too.
> >> 
> >> However, I couldn't help but notice (from
> >> http://fbergmann.github.io/libSEDML/) that libSEDML has a (big)
> >> dependency on libSBML. Is there really no way to remove that dependency
> >> so that those of us who don't (currently, at least) use SBML could still
> > 
> > take
> > 
> >> advantage of libSEDML? Maybe the libSBML's XML parsing layer could,
> >> somehow, be 'extracted' and taken advantage of?
> >> 
> >> Cheers, Alan.
> >> 
> >> PS: what is the correct casing for it? libSEDML, LibSEDML, Libsedml,
> >> ...?
> >> 
> >>> -----Original Message-----
> >>> From: Frank T. Bergmann [mailto:fbe...@ca...]
> >>> Sent: 25 April 2013 15:15
> >>> To: sed...@li...
> >>> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> >>> 
> >>> To provide just a little bit more detail on this. I've started to
> >>> create
> >> 
> >> a library
> >> 
> >>> based on classes adapted from libSBML (such as SBase -> SedBase and
> >>> the like). From there I modified a prototype from Sarah Keating that
> >>> would
> >> 
> >> allow
> >> 
> >>> to generate basic C++ classes. After rounds of refinement, I am now at
> >>> a point where the core of SEDML L1V1 with the exception of the raw XML
> >>> manipulation classes AddXML and ChangeXML are implemented. Via 
SWIG
> >> 
> >> I
> >> 
> >>> then created rudimentary language bindings for C#, Java, Python, Ruby,
> >> 
> >> Perl
> >> 
> >>> and R.
> >>> 
> >>> The project is currently hosted at github:
> >>> http://fbergmann.github.io/libSEDML/
> >>> 
> >>> For examples on how the library can be used in the individual
> >>> languages
> >> 
> >> see:
> >>> https://github.com/fbergmann/libSEDML/tree/master/examples
> >>> 
> >>> In order to compile you need only to have CMake and libSBML. This
> >>> library
> >> 
> >> is
> >> 
> >>> written for the raw manipulation of the SEDML classes. It presently
> >>> does
> >> 
> >> not
> >> 
> >>> perform any of the utility functions as provided by my C# library
> >>> (http://libsedml.sf.net) where models are resolved no matter where
> >>> they are, stylesheet transformations for changes are applied, or the
> >>> simulation experiments can be scheduled and run.
> >>> 
> >>> Any feedback would be appreciated. And bugs can be filed under:
> >>> 
> >>> https://github.com/fbergmann/libSEDML/issues
> >>> 
> >>> Cheers
> >>> Frank
> >>> 
> >>> 
> >>> On Apr 25, 2013, at 1:15 PM, Pedro Mendes
> >>> 
> >>> <ped...@ma...> wrote:
> >>>> Hello all in SED-ML-discuss
> >>>> 
> >>>> Just joined the list and a few colleagues of mine will join too. As
> >>>> you may know, currently COPASI does not support SED-ML. This will
> >>>> change and we are committed to add SED-ML support. We will also
> >>>> bring in some ideas to develop further SED-ML, since currently our
> >>>> CopasiML has the functionality of what SED-ML aspires (ie it stores
> >>>> both the model and all the tasks to be carried out, so it is like
> >>>> SBML+SED-ML
> >>> 
> >>> together).
> >>> 
> >>>> Many of the tasks that you can do in COPASI currently cannot be
> >>>> specified in SED-ML, so we would like to help development too.
> >>>> 
> >>>> The first step for us will be to create a library, in C++ (since
> >>>> that is what we use), to read/write SED-ML. Other colleagues from a
> >>>> FP7 project (Eric Boix and Bertrand Moreau at CoSMo) also want to
> >>>> use SED-ML and would like such a library. I suspect others here may
> >>>> also be
> >>> 
> >>> interested?
> >>> 
> >>>> Right now, it would be great to hear from anyone already writing
> >>>> such a a library (in C/C++) to avoid duplication of efforts. Our
> >>>> plan is to create a libSEDML following the same steps as libSBML --
> >>>> written in C/C++ and then create bindings for other languages. Frank
> >>>> Bergmann has also expressed interest and that he'd help.
> >>>> 
> >>>> best
> >>>> Pedro
> >>>> 
> >>>> --
> >>>> Pedro Mendes
> >>>> Professor of Computational Systems Biology School of Computer
> >>>> Science Manchester Centre for Integrative Systems Biology University
> >>>> of Manchester
> >>>> 
> >>>> Manchester Institute of Biotechnology
> >>>> 131 Princess Street
> >>>> Manchester, M1 7DN, U.K.
> >>>> 
> >>>> --------------------------------------------------------------------
> >>>> --
> >>>> -------- Try New Relic Now & We'll Send You this Cool Shirt New
> >>>> Relic is the only SaaS-based application performance monitoring
> >>>> service that delivers powerful full stack analytics. Optimize and
> >>>> monitor your browser, app, & servers with just a few lines of code.
> >>>> Try New Relic and get this awesome Nerd Life shirt!
> >>>> http://p.sf.net/sfu/newrelic_d2d_apr
> >>>> _______________________________________________
> >>>> SED-ML-discuss mailing list
> >>>> SED...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> > 
> > -------------------------------------------------------------------------
> > ---
> > 
> >> --
> >> 
> >>> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the
> >>> only SaaS-based application performance monitoring service that
> >>> delivers powerful full stack analytics. Optimize and monitor your
> >>> browser, app, & servers with just a few lines of code. Try New Relic
> >>> and get this awesome Nerd Life shirt!
> >>> http://p.sf.net/sfu/newrelic_d2d_apr
> >>> _______________________________________________
> >>> SED-ML-discuss mailing list
> >>> SED...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> > 
> > -------------------------------------------------------------------------
> > --- --
> > 
> >> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only
> > 
> > SaaS-
> > 
> >> based application performance monitoring service that delivers powerful
> > 
> > full
> > 
> >> stack analytics. Optimize and monitor your browser, app, & servers with
> > 
> > just
> > 
> >> a few lines of code. Try New Relic and get this awesome Nerd Life shirt!
> >> http://p.sf.net/sfu/newrelic_d2d_apr
> >> _______________________________________________
> >> SED-ML-discuss mailing list
> >> SED...@li...
> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> > 
> > -------------------------------------------------------------------------
> > ----- Try New Relic Now & We'll Send You this Cool Shirt
> > New Relic is the only SaaS-based application performance monitoring
> > service that delivers powerful full stack analytics. Optimize and
> > monitor your browser, app, & servers with just a few lines of code. Try
> > New Relic and get this awesome Nerd Life shirt!
> > http://p.sf.net/sfu/newrelic_d2d_apr
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> ------------------------------
> 
> Message: 2
> Date: Fri, 26 Apr 2013 11:40:27 +0200
> From: "Brett G. Olivier" <bre...@gm...>
> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> To: sed...@li...
> Message-ID:
> 	<CAGt-wg93RQckS2B3H6rgyYJTtxXg5ksK4iG-1YjhacpYsWVL-
A...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi
> 
> My feeling is that in the short to medium term, forking parts of libSBML is
> not the best way to utilize (what I assume are as always) limited developer
> resources. From a pragmatic perspective libSBML has an established
> cross-platform build system and itself has a low number of dependencies so
> I don't really see what the problem with having it as a dependency is?
> 
> Regards
> Brett
> 
> 
> On Fri, Apr 26, 2013 at 8:40 AM, Jonathan Cooper <
> 
> jon...@cs...> wrote:
> > Hi all,
> > 
> > I'm also very happy that Frank is working on this!  Regarding the
> > libSBML dependency, it seems to me that there's an argument here for
> > splitting libSBML up, and extracting the XML parsing to AST into a
> > separate library, which multiple ML standards could use. I'm not too
> > familiar with the internals of libSBML, but does that sound sensible?
> > 
> > Best wishes,
> > Jonathan
> > 
> > On 26/04/2013 06:52, Frank T. Bergmann wrote:
> > > Hello Alan,
> > > 
> > > There is two parts of libSBML that are required, the XML parsing layer,
> > 
> > and
> > 
> > > the AST nodes. While theoretically possible to extract all that, it
> > > will make interaction with libSBML for those that do want to support
> > > SBML a
> > 
> > lot
> > 
> > > harder (as after the extraction there will be different *incompatible*
> > 
> > AST /
> > 
> > > XML classes). I don't think at this point this would be worth the
> > > effort. But even though libSBML is being used, at present there are no
> > > functions specific to a particular modeling language.
> > > 
> > > Cheers
> > > Frank
> > > 
> > > P.S: I'm sure we will work all this out. Like I said I'm flexible with
> > > respect of the naming of the library. For the time being I would use
> > > libSEDML, mainly because of linux being picky to clone the repository
> > > otherwise.
> > > 
> > >> -----Original Message-----
> > >> From: Alan Garny [mailto:ala...@in...]
> > >> Sent: Thursday, April 25, 2013 10:47 PM
> > >> To: sed...@li...
> > >> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> > >> 
> > >> Hi Frank,
> > >> 
> > >> +1 from me too.
> > >> 
> > >> However, I couldn't help but notice (from
> > >> http://fbergmann.github.io/libSEDML/) that libSEDML has a (big)
> > >> dependency on libSBML. Is there really no way to remove that
> > >> dependency so that those of us who don't (currently, at least) use
> > >> SBML could still
> > > 
> > > take
> > > 
> > >> advantage of libSEDML? Maybe the libSBML's XML parsing layer could,
> > >> somehow, be 'extracted' and taken advantage of?
> > >> 
> > >> Cheers, Alan.
> > >> 
> > >> PS: what is the correct casing for it? libSEDML, LibSEDML, Libsedml,
> > 
> > ...?
> > 
> > >>> -----Original Message-----
> > >>> From: Frank T. Bergmann [mailto:fbe...@ca...]
> > >>> Sent: 25 April 2013 15:15
> > >>> To: sed...@li...
> > >>> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> > >>> 
> > >>> To provide just a little bit more detail on this. I've started to
> > >>> create
> > >> 
> > >> a library
> > >> 
> > >>> based on classes adapted from libSBML (such as SBase -> SedBase 
and
> > >>> the like). From there I modified a prototype from Sarah Keating that
> > >>> would
> > >> 
> > >> allow
> > >> 
> > >>> to generate basic C++ classes. After rounds of refinement, I am now
> > >>> at a point where the core of SEDML L1V1 with the exception of the
> > >>> raw XML manipulation classes AddXML and ChangeXML are 
implemented.
> > >>> Via SWIG
> > >> 
> > >> I
> > >> 
> > >>> then created rudimentary language bindings for C#, Java, Python,
> > >>> Ruby,
> > >> 
> > >> Perl
> > >> 
> > >>> and R.
> > >>> 
> > >>> The project is currently hosted at github:
> > >>> http://fbergmann.github.io/libSEDML/
> > >>> 
> > >>> For examples on how the library can be used in the individual
> > >>> languages
> > >> 
> > >> see:
> > >>> https://github.com/fbergmann/libSEDML/tree/master/examples
> > >>> 
> > >>> In order to compile you need only to have CMake and libSBML. This
> > >>> library
> > >> 
> > >> is
> > >> 
> > >>> written for the raw manipulation of the SEDML classes. It presently
> > >>> does
> > >> 
> > >> not
> > >> 
> > >>> perform any of the utility functions as provided by my C# library
> > >>> (http://libsedml.sf.net) where models are resolved no matter where
> > >>> they are, stylesheet transformations for changes are applied, or the
> > >>> simulation experiments can be scheduled and run.
> > >>> 
> > >>> Any feedback would be appreciated. And bugs can be filed under:
> > >>> 
> > >>> https://github.com/fbergmann/libSEDML/issues
> > >>> 
> > >>> Cheers
> > >>> Frank
> > >>> 
> > >>> 
> > >>> On Apr 25, 2013, at 1:15 PM, Pedro Mendes
> > >>> 
> > >>> <ped...@ma...> wrote:
> > >>>> Hello all in SED-ML-discuss
> > >>>> 
> > >>>> Just joined the list and a few colleagues of mine will join too. As
> > >>>> you may know, currently COPASI does not support SED-ML. This will
> > >>>> change and we are committed to add SED-ML support. We will also
> > >>>> bring in some ideas to develop further SED-ML, since currently our
> > >>>> CopasiML has the functionality of what SED-ML aspires (ie it stores
> > >>>> both the model and all the tasks to be carried out, so it is like
> > >>>> SBML+SED-ML
> > >>> 
> > >>> together).
> > >>> 
> > >>>> Many of the tasks that you can do in COPASI currently cannot be
> > >>>> specified in SED-ML, so we would like to help development too.
> > >>>> 
> > >>>> The first step for us will be to create a library, in C++ (since
> > >>>> that is what we use), to read/write SED-ML. Other colleagues from a
> > >>>> FP7 project (Eric Boix and Bertrand Moreau at CoSMo) also want to
> > >>>> use SED-ML and would like such a library. I suspect others here may
> > >>>> also be
> > >>> 
> > >>> interested?
> > >>> 
> > >>>> Right now, it would be great to hear from anyone already writing
> > >>>> such a a library (in C/C++) to avoid duplication of efforts. Our
> > >>>> plan is to create a libSEDML following the same steps as libSBML --
> > >>>> written in C/C++ and then create bindings for other languages. Frank
> > >>>> Bergmann has also expressed interest and that he'd help.
> > >>>> 
> > >>>> best
> > >>>> Pedro
> > >>>> 
> > >>>> --
> > >>>> Pedro Mendes
> > >>>> Professor of Computational Systems Biology School of Computer
> > >>>> Science Manchester Centre for Integrative Systems Biology University
> > >>>> of Manchester
> > >>>> 
> > >>>> Manchester Institute of Biotechnology
> > >>>> 131 Princess Street
> > >>>> Manchester, M1 7DN, U.K.
> > >>>> 
> > >>>> --------------------------------------------------------------------
> > >>>> --
> > >>>> -------- Try New Relic Now & We'll Send You this Cool Shirt New
> > >>>> Relic is the only SaaS-based application performance monitoring
> > >>>> service that delivers powerful full stack analytics. Optimize and
> > >>>> monitor your browser, app, & servers with just a few lines of code.
> > >>>> Try New Relic and get this awesome Nerd Life shirt!
> > >>>> http://p.sf.net/sfu/newrelic_d2d_apr
> > >>>> _______________________________________________
> > >>>> SED-ML-discuss mailing list
> > >>>> SED...@li...
> > >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> > 
> > -------------------------------------------------------------------------
> > ---
> > 
> > >> --
> > >> 
> > >>> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the
> > >>> only SaaS-based application performance monitoring service that
> > >>> delivers powerful full stack analytics. Optimize and monitor your
> > >>> browser, app, & servers with just a few lines of code. Try New Relic
> > >>> and get this awesome Nerd Life shirt!
> > >>> http://p.sf.net/sfu/newrelic_d2d_apr
> > >>> _______________________________________________
> > >>> SED-ML-discuss mailing list
> > >>> SED...@li...
> > >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> > 
> > -------------------------------------------------------------------------
> > ---
> > 
> > > --
> > > 
> > >> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the
> > >> only
> > > 
> > > SaaS-
> > > 
> > >> based application performance monitoring service that delivers
> > >> powerful
> > > 
> > > full
> > > 
> > >> stack analytics. Optimize and monitor your browser, app, & servers
> > >> with
> > > 
> > > just
> > > 
> > >> a few lines of code. Try New Relic and get this awesome Nerd Life
> > >> shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> > >> _______________________________________________
> > >> SED-ML-discuss mailing list
> > >> SED...@li...
> > >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> > 
> > -------------------------------------------------------------------------
> > -----
> > 
> > > Try New Relic Now & We'll Send You this Cool Shirt
> > > New Relic is the only SaaS-based application performance monitoring
> > 
> > service
> > 
> > > that delivers powerful full stack analytics. Optimize and monitor your
> > > browser, app, & servers with just a few lines of code. Try New Relic
> > > and get this awesome Nerd Life shirt!
> > 
> > http://p.sf.net/sfu/newrelic_d2d_apr
> > 
> > > _______________________________________________
> > > SED-ML-discuss mailing list
> > > SED...@li...
> > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> > 
> > -------------------------------------------------------------------------
> > ----- Try New Relic Now & We'll Send You this Cool Shirt
> > New Relic is the only SaaS-based application performance monitoring
> > service that delivers powerful full stack analytics. Optimize and
> > monitor your browser, app, & servers with just a few lines of code. Try
> > New Relic and get this awesome Nerd Life shirt!
> > http://p.sf.net/sfu/newrelic_d2d_apr
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Hello and updates from COPASI

[Brett G. O. <bre...@gm...>]

Hi

My feeling is that in the short to medium term, forking parts of libSBML is
not the best way to utilize (what I assume are as always) limited developer
resources. From a pragmatic perspective libSBML has an established
cross-platform build system and itself has a low number of dependencies so
I don't really see what the problem with having it as a dependency is?

Regards
Brett


On Fri, Apr 26, 2013 at 8:40 AM, Jonathan Cooper <
jon...@cs...> wrote:

> Hi all,
>
> I'm also very happy that Frank is working on this!  Regarding the
> libSBML dependency, it seems to me that there's an argument here for
> splitting libSBML up, and extracting the XML parsing to AST into a
> separate library, which multiple ML standards could use. I'm not too
> familiar with the internals of libSBML, but does that sound sensible?
>
> Best wishes,
> Jonathan
>
> On 26/04/2013 06:52, Frank T. Bergmann wrote:
> > Hello Alan,
> >
> > There is two parts of libSBML that are required, the XML parsing layer,
> and
> > the AST nodes. While theoretically possible to extract all that, it will
> > make interaction with libSBML for those that do want to support SBML a
> lot
> > harder (as after the extraction there will be different *incompatible*
> AST /
> > XML classes). I don't think at this point this would be worth the effort.
> > But even though libSBML is being used, at present there are no functions
> > specific to a particular modeling language.
> >
> > Cheers
> > Frank
> >
> > P.S: I'm sure we will work all this out. Like I said I'm flexible with
> > respect of the naming of the library. For the time being I would use
> > libSEDML, mainly because of linux being picky to clone the repository
> > otherwise.
> >
> >> -----Original Message-----
> >> From: Alan Garny [mailto:ala...@in...]
> >> Sent: Thursday, April 25, 2013 10:47 PM
> >> To: sed...@li...
> >> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> >>
> >> Hi Frank,
> >>
> >> +1 from me too.
> >>
> >> However, I couldn't help but notice (from
> >> http://fbergmann.github.io/libSEDML/) that libSEDML has a (big)
> >> dependency on libSBML. Is there really no way to remove that dependency
> >> so that those of us who don't (currently, at least) use SBML could still
> > take
> >> advantage of libSEDML? Maybe the libSBML's XML parsing layer could,
> >> somehow, be 'extracted' and taken advantage of?
> >>
> >> Cheers, Alan.
> >>
> >> PS: what is the correct casing for it? libSEDML, LibSEDML, Libsedml,
> ...?
> >>
> >>> -----Original Message-----
> >>> From: Frank T. Bergmann [mailto:fbe...@ca...]
> >>> Sent: 25 April 2013 15:15
> >>> To: sed...@li...
> >>> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> >>>
> >>> To provide just a little bit more detail on this. I've started to
> >>> create
> >> a library
> >>> based on classes adapted from libSBML (such as SBase -> SedBase and
> >>> the like). From there I modified a prototype from Sarah Keating that
> >>> would
> >> allow
> >>> to generate basic C++ classes. After rounds of refinement, I am now at
> >>> a point where the core of SEDML L1V1 with the exception of the raw XML
> >>> manipulation classes AddXML and ChangeXML are implemented. Via SWIG
> >> I
> >>> then created rudimentary language bindings for C#, Java, Python, Ruby,
> >> Perl
> >>> and R.
> >>>
> >>> The project is currently hosted at github:
> >>> http://fbergmann.github.io/libSEDML/
> >>>
> >>> For examples on how the library can be used in the individual
> >>> languages
> >> see:
> >>> https://github.com/fbergmann/libSEDML/tree/master/examples
> >>>
> >>> In order to compile you need only to have CMake and libSBML. This
> >>> library
> >> is
> >>> written for the raw manipulation of the SEDML classes. It presently
> >>> does
> >> not
> >>> perform any of the utility functions as provided by my C# library
> >>> (http://libsedml.sf.net) where models are resolved no matter where
> >>> they are, stylesheet transformations for changes are applied, or the
> >>> simulation experiments can be scheduled and run.
> >>>
> >>> Any feedback would be appreciated. And bugs can be filed under:
> >>>
> >>> https://github.com/fbergmann/libSEDML/issues
> >>>
> >>> Cheers
> >>> Frank
> >>>
> >>>
> >>> On Apr 25, 2013, at 1:15 PM, Pedro Mendes
> >>> <ped...@ma...> wrote:
> >>>
> >>>> Hello all in SED-ML-discuss
> >>>>
> >>>> Just joined the list and a few colleagues of mine will join too. As
> >>>> you may know, currently COPASI does not support SED-ML. This will
> >>>> change and we are committed to add SED-ML support. We will also
> >>>> bring in some ideas to develop further SED-ML, since currently our
> >>>> CopasiML has the functionality of what SED-ML aspires (ie it stores
> >>>> both the model and all the tasks to be carried out, so it is like
> >>>> SBML+SED-ML
> >>> together).
> >>>> Many of the tasks that you can do in COPASI currently cannot be
> >>>> specified in SED-ML, so we would like to help development too.
> >>>>
> >>>> The first step for us will be to create a library, in C++ (since
> >>>> that is what we use), to read/write SED-ML. Other colleagues from a
> >>>> FP7 project (Eric Boix and Bertrand Moreau at CoSMo) also want to
> >>>> use SED-ML and would like such a library. I suspect others here may
> >>>> also be
> >>> interested?
> >>>> Right now, it would be great to hear from anyone already writing
> >>>> such a a library (in C/C++) to avoid duplication of efforts. Our
> >>>> plan is to create a libSEDML following the same steps as libSBML --
> >>>> written in C/C++ and then create bindings for other languages. Frank
> >>>> Bergmann has also expressed interest and that he'd help.
> >>>>
> >>>> best
> >>>> Pedro
> >>>>
> >>>> --
> >>>> Pedro Mendes
> >>>> Professor of Computational Systems Biology School of Computer
> >>>> Science Manchester Centre for Integrative Systems Biology University
> >>>> of Manchester
> >>>>
> >>>> Manchester Institute of Biotechnology
> >>>> 131 Princess Street
> >>>> Manchester, M1 7DN, U.K.
> >>>>
> >>>> --------------------------------------------------------------------
> >>>> --
> >>>> -------- Try New Relic Now & We'll Send You this Cool Shirt New
> >>>> Relic is the only SaaS-based application performance monitoring
> >>>> service that delivers powerful full stack analytics. Optimize and
> >>>> monitor your browser, app, & servers with just a few lines of code.
> >>>> Try New Relic and get this awesome Nerd Life shirt!
> >>>> http://p.sf.net/sfu/newrelic_d2d_apr
> >>>> _______________________________________________
> >>>> SED-ML-discuss mailing list
> >>>> SED...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >>>
> >>>
> >
> ----------------------------------------------------------------------------
> >> --
> >>> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the
> >>> only SaaS-based application performance monitoring service that
> >>> delivers powerful full stack analytics. Optimize and monitor your
> >>> browser, app, & servers with just a few lines of code. Try New Relic
> >>> and get this awesome Nerd Life shirt!
> >>> http://p.sf.net/sfu/newrelic_d2d_apr
> >>> _______________________________________________
> >>> SED-ML-discuss mailing list
> >>> SED...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >>
> >>
> >
> ----------------------------------------------------------------------------
> > --
> >> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only
> > SaaS-
> >> based application performance monitoring service that delivers powerful
> > full
> >> stack analytics. Optimize and monitor your browser, app, & servers with
> > just
> >> a few lines of code. Try New Relic and get this awesome Nerd Life shirt!
> >> http://p.sf.net/sfu/newrelic_d2d_apr
> >> _______________________________________________
> >> SED-ML-discuss mailing list
> >> SED...@li...
> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> >
> ------------------------------------------------------------------------------
> > Try New Relic Now & We'll Send You this Cool Shirt
> > New Relic is the only SaaS-based application performance monitoring
> service
> > that delivers powerful full stack analytics. Optimize and monitor your
> > browser, app, & servers with just a few lines of code. Try New Relic
> > and get this awesome Nerd Life shirt!
> http://p.sf.net/sfu/newrelic_d2d_apr
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>



-- 
Brett G. Olivier PhD

Re: [SED-ML-discuss] Hello and updates from COPASI

[Jonathan C. <jon...@cs...>]

Hi all,

I'm also very happy that Frank is working on this!  Regarding the 
libSBML dependency, it seems to me that there's an argument here for 
splitting libSBML up, and extracting the XML parsing to AST into a 
separate library, which multiple ML standards could use. I'm not too 
familiar with the internals of libSBML, but does that sound sensible?

Best wishes,
Jonathan

On 26/04/2013 06:52, Frank T. Bergmann wrote:
> Hello Alan,
>
> There is two parts of libSBML that are required, the XML parsing layer, and
> the AST nodes. While theoretically possible to extract all that, it will
> make interaction with libSBML for those that do want to support SBML a lot
> harder (as after the extraction there will be different *incompatible* AST /
> XML classes). I don't think at this point this would be worth the effort.
> But even though libSBML is being used, at present there are no functions
> specific to a particular modeling language.
>
> Cheers
> Frank
>
> P.S: I'm sure we will work all this out. Like I said I'm flexible with
> respect of the naming of the library. For the time being I would use
> libSEDML, mainly because of linux being picky to clone the repository
> otherwise.
>
>> -----Original Message-----
>> From: Alan Garny [mailto:ala...@in...]
>> Sent: Thursday, April 25, 2013 10:47 PM
>> To: sed...@li...
>> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
>>
>> Hi Frank,
>>
>> +1 from me too.
>>
>> However, I couldn't help but notice (from
>> http://fbergmann.github.io/libSEDML/) that libSEDML has a (big)
>> dependency on libSBML. Is there really no way to remove that dependency
>> so that those of us who don't (currently, at least) use SBML could still
> take
>> advantage of libSEDML? Maybe the libSBML's XML parsing layer could,
>> somehow, be 'extracted' and taken advantage of?
>>
>> Cheers, Alan.
>>
>> PS: what is the correct casing for it? libSEDML, LibSEDML, Libsedml, ...?
>>
>>> -----Original Message-----
>>> From: Frank T. Bergmann [mailto:fbe...@ca...]
>>> Sent: 25 April 2013 15:15
>>> To: sed...@li...
>>> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
>>>
>>> To provide just a little bit more detail on this. I've started to
>>> create
>> a library
>>> based on classes adapted from libSBML (such as SBase -> SedBase and
>>> the like). From there I modified a prototype from Sarah Keating that
>>> would
>> allow
>>> to generate basic C++ classes. After rounds of refinement, I am now at
>>> a point where the core of SEDML L1V1 with the exception of the raw XML
>>> manipulation classes AddXML and ChangeXML are implemented. Via SWIG
>> I
>>> then created rudimentary language bindings for C#, Java, Python, Ruby,
>> Perl
>>> and R.
>>>
>>> The project is currently hosted at github:
>>> http://fbergmann.github.io/libSEDML/
>>>
>>> For examples on how the library can be used in the individual
>>> languages
>> see:
>>> https://github.com/fbergmann/libSEDML/tree/master/examples
>>>
>>> In order to compile you need only to have CMake and libSBML. This
>>> library
>> is
>>> written for the raw manipulation of the SEDML classes. It presently
>>> does
>> not
>>> perform any of the utility functions as provided by my C# library
>>> (http://libsedml.sf.net) where models are resolved no matter where
>>> they are, stylesheet transformations for changes are applied, or the
>>> simulation experiments can be scheduled and run.
>>>
>>> Any feedback would be appreciated. And bugs can be filed under:
>>>
>>> https://github.com/fbergmann/libSEDML/issues
>>>
>>> Cheers
>>> Frank
>>>
>>>
>>> On Apr 25, 2013, at 1:15 PM, Pedro Mendes
>>> <ped...@ma...> wrote:
>>>
>>>> Hello all in SED-ML-discuss
>>>>
>>>> Just joined the list and a few colleagues of mine will join too. As
>>>> you may know, currently COPASI does not support SED-ML. This will
>>>> change and we are committed to add SED-ML support. We will also
>>>> bring in some ideas to develop further SED-ML, since currently our
>>>> CopasiML has the functionality of what SED-ML aspires (ie it stores
>>>> both the model and all the tasks to be carried out, so it is like
>>>> SBML+SED-ML
>>> together).
>>>> Many of the tasks that you can do in COPASI currently cannot be
>>>> specified in SED-ML, so we would like to help development too.
>>>>
>>>> The first step for us will be to create a library, in C++ (since
>>>> that is what we use), to read/write SED-ML. Other colleagues from a
>>>> FP7 project (Eric Boix and Bertrand Moreau at CoSMo) also want to
>>>> use SED-ML and would like such a library. I suspect others here may
>>>> also be
>>> interested?
>>>> Right now, it would be great to hear from anyone already writing
>>>> such a a library (in C/C++) to avoid duplication of efforts. Our
>>>> plan is to create a libSEDML following the same steps as libSBML --
>>>> written in C/C++ and then create bindings for other languages. Frank
>>>> Bergmann has also expressed interest and that he'd help.
>>>>
>>>> best
>>>> Pedro
>>>>
>>>> --
>>>> Pedro Mendes
>>>> Professor of Computational Systems Biology School of Computer
>>>> Science Manchester Centre for Integrative Systems Biology University
>>>> of Manchester
>>>>
>>>> Manchester Institute of Biotechnology
>>>> 131 Princess Street
>>>> Manchester, M1 7DN, U.K.
>>>>
>>>> --------------------------------------------------------------------
>>>> --
>>>> -------- Try New Relic Now & We'll Send You this Cool Shirt New
>>>> Relic is the only SaaS-based application performance monitoring
>>>> service that delivers powerful full stack analytics. Optimize and
>>>> monitor your browser, app, & servers with just a few lines of code.
>>>> Try New Relic and get this awesome Nerd Life shirt!
>>>> http://p.sf.net/sfu/newrelic_d2d_apr
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
> ----------------------------------------------------------------------------
>> --
>>> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the
>>> only SaaS-based application performance monitoring service that
>>> delivers powerful full stack analytics. Optimize and monitor your
>>> browser, app, & servers with just a few lines of code. Try New Relic
>>> and get this awesome Nerd Life shirt!
>>> http://p.sf.net/sfu/newrelic_d2d_apr
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
> ----------------------------------------------------------------------------
> --
>> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only
> SaaS-
>> based application performance monitoring service that delivers powerful
> full
>> stack analytics. Optimize and monitor your browser, app, & servers with
> just
>> a few lines of code. Try New Relic and get this awesome Nerd Life shirt!
>> http://p.sf.net/sfu/newrelic_d2d_apr
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Hello and updates from COPASI

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

Hello Alan, 

There is two parts of libSBML that are required, the XML parsing layer, and
the AST nodes. While theoretically possible to extract all that, it will
make interaction with libSBML for those that do want to support SBML a lot
harder (as after the extraction there will be different *incompatible* AST /
XML classes). I don't think at this point this would be worth the effort.
But even though libSBML is being used, at present there are no functions
specific to a particular modeling language. 

Cheers
Frank

P.S: I'm sure we will work all this out. Like I said I'm flexible with
respect of the naming of the library. For the time being I would use
libSEDML, mainly because of linux being picky to clone the repository
otherwise. 

> -----Original Message-----
> From: Alan Garny [mailto:ala...@in...]
> Sent: Thursday, April 25, 2013 10:47 PM
> To: sed...@li...
> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> 
> Hi Frank,
> 
> +1 from me too.
> 
> However, I couldn't help but notice (from
> http://fbergmann.github.io/libSEDML/) that libSEDML has a (big)
> dependency on libSBML. Is there really no way to remove that dependency
> so that those of us who don't (currently, at least) use SBML could still
take
> advantage of libSEDML? Maybe the libSBML's XML parsing layer could,
> somehow, be 'extracted' and taken advantage of?
> 
> Cheers, Alan.
> 
> PS: what is the correct casing for it? libSEDML, LibSEDML, Libsedml, ...?
> 
> > -----Original Message-----
> > From: Frank T. Bergmann [mailto:fbe...@ca...]
> > Sent: 25 April 2013 15:15
> > To: sed...@li...
> > Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> >
> > To provide just a little bit more detail on this. I've started to
> > create
> a library
> > based on classes adapted from libSBML (such as SBase -> SedBase and
> > the like). From there I modified a prototype from Sarah Keating that
> > would
> allow
> > to generate basic C++ classes. After rounds of refinement, I am now at
> > a point where the core of SEDML L1V1 with the exception of the raw XML
> > manipulation classes AddXML and ChangeXML are implemented. Via SWIG
> I
> > then created rudimentary language bindings for C#, Java, Python, Ruby,
> Perl
> > and R.
> >
> > The project is currently hosted at github:
> > http://fbergmann.github.io/libSEDML/
> >
> > For examples on how the library can be used in the individual
> > languages
> see:
> >
> > https://github.com/fbergmann/libSEDML/tree/master/examples
> >
> > In order to compile you need only to have CMake and libSBML. This
> > library
> is
> > written for the raw manipulation of the SEDML classes. It presently
> > does
> not
> > perform any of the utility functions as provided by my C# library
> > (http://libsedml.sf.net) where models are resolved no matter where
> > they are, stylesheet transformations for changes are applied, or the
> > simulation experiments can be scheduled and run.
> >
> > Any feedback would be appreciated. And bugs can be filed under:
> >
> > https://github.com/fbergmann/libSEDML/issues
> >
> > Cheers
> > Frank
> >
> >
> > On Apr 25, 2013, at 1:15 PM, Pedro Mendes
> > <ped...@ma...> wrote:
> >
> > > Hello all in SED-ML-discuss
> > >
> > > Just joined the list and a few colleagues of mine will join too. As
> > > you may know, currently COPASI does not support SED-ML. This will
> > > change and we are committed to add SED-ML support. We will also
> > > bring in some ideas to develop further SED-ML, since currently our
> > > CopasiML has the functionality of what SED-ML aspires (ie it stores
> > > both the model and all the tasks to be carried out, so it is like
> > > SBML+SED-ML
> > together).
> > > Many of the tasks that you can do in COPASI currently cannot be
> > > specified in SED-ML, so we would like to help development too.
> > >
> > > The first step for us will be to create a library, in C++ (since
> > > that is what we use), to read/write SED-ML. Other colleagues from a
> > > FP7 project (Eric Boix and Bertrand Moreau at CoSMo) also want to
> > > use SED-ML and would like such a library. I suspect others here may
> > > also be
> > interested?
> > >
> > > Right now, it would be great to hear from anyone already writing
> > > such a a library (in C/C++) to avoid duplication of efforts. Our
> > > plan is to create a libSEDML following the same steps as libSBML --
> > > written in C/C++ and then create bindings for other languages. Frank
> > > Bergmann has also expressed interest and that he'd help.
> > >
> > > best
> > > Pedro
> > >
> > > --
> > > Pedro Mendes
> > > Professor of Computational Systems Biology School of Computer
> > > Science Manchester Centre for Integrative Systems Biology University
> > > of Manchester
> > >
> > > Manchester Institute of Biotechnology
> > > 131 Princess Street
> > > Manchester, M1 7DN, U.K.
> > >
> > > --------------------------------------------------------------------
> > > --
> > > -------- Try New Relic Now & We'll Send You this Cool Shirt New
> > > Relic is the only SaaS-based application performance monitoring
> > > service that delivers powerful full stack analytics. Optimize and
> > > monitor your browser, app, & servers with just a few lines of code.
> > > Try New Relic and get this awesome Nerd Life shirt!
> > > http://p.sf.net/sfu/newrelic_d2d_apr
> > > _______________________________________________
> > > SED-ML-discuss mailing list
> > > SED...@li...
> > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> >
> >
>
----------------------------------------------------------------------------
> --
> > Try New Relic Now & We'll Send You this Cool Shirt New Relic is the
> > only SaaS-based application performance monitoring service that
> > delivers powerful full stack analytics. Optimize and monitor your
> > browser, app, & servers with just a few lines of code. Try New Relic
> > and get this awesome Nerd Life shirt!
> > http://p.sf.net/sfu/newrelic_d2d_apr
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> 
>
----------------------------------------------------------------------------
--
> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only
SaaS-
> based application performance monitoring service that delivers powerful
full
> stack analytics. Optimize and monitor your browser, app, & servers with
just
> a few lines of code. Try New Relic and get this awesome Nerd Life shirt!
> http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Hello and updates from COPASI

[Alan G. <ala...@in...>]

Hi Frank,

+1 from me too.

However, I couldn't help but notice (from
http://fbergmann.github.io/libSEDML/) that libSEDML has a (big) dependency
on libSBML. Is there really no way to remove that dependency so that those
of us who don't (currently, at least) use SBML could still take advantage of
libSEDML? Maybe the libSBML's XML parsing layer could, somehow, be
'extracted' and taken advantage of? 

Cheers, Alan.

PS: what is the correct casing for it? libSEDML, LibSEDML, Libsedml, ...?

> -----Original Message-----
> From: Frank T. Bergmann [mailto:fbe...@ca...]
> Sent: 25 April 2013 15:15
> To: sed...@li...
> Subject: Re: [SED-ML-discuss] Hello and updates from COPASI
> 
> To provide just a little bit more detail on this. I've started to create
a library
> based on classes adapted from libSBML (such as SBase -> SedBase and the
> like). From there I modified a prototype from Sarah Keating that would
allow
> to generate basic C++ classes. After rounds of refinement, I am now at a
> point where the core of SEDML L1V1 with the exception of the raw XML
> manipulation classes AddXML and ChangeXML are implemented. Via SWIG I
> then created rudimentary language bindings for C#, Java, Python, Ruby,
Perl
> and R.
> 
> The project is currently hosted at github:
> http://fbergmann.github.io/libSEDML/
> 
> For examples on how the library can be used in the individual languages
see:
> 
> https://github.com/fbergmann/libSEDML/tree/master/examples
> 
> In order to compile you need only to have CMake and libSBML. This library
is
> written for the raw manipulation of the SEDML classes. It presently does
not
> perform any of the utility functions as provided by my C# library
> (http://libsedml.sf.net) where models are resolved no matter where they
> are, stylesheet transformations for changes are applied, or the simulation
> experiments can be scheduled and run.
> 
> Any feedback would be appreciated. And bugs can be filed under:
> 
> https://github.com/fbergmann/libSEDML/issues
> 
> Cheers
> Frank
> 
> 
> On Apr 25, 2013, at 1:15 PM, Pedro Mendes
> <ped...@ma...> wrote:
> 
> > Hello all in SED-ML-discuss
> >
> > Just joined the list and a few colleagues of mine will join too. As
> > you may know, currently COPASI does not support SED-ML. This will
> > change and we are committed to add SED-ML support. We will also bring
> > in some ideas to develop further SED-ML, since currently our CopasiML
> > has the functionality of what SED-ML aspires (ie it stores both the
> > model and all the tasks to be carried out, so it is like SBML+SED-ML
> together).
> > Many of the tasks that you can do in COPASI currently cannot be
> > specified in SED-ML, so we would like to help development too.
> >
> > The first step for us will be to create a library, in C++ (since that
> > is what we use), to read/write SED-ML. Other colleagues from a FP7
> > project (Eric Boix and Bertrand Moreau at CoSMo) also want to use
> > SED-ML and would like such a library. I suspect others here may also be
> interested?
> >
> > Right now, it would be great to hear from anyone already writing such
> > a a library (in C/C++) to avoid duplication of efforts. Our plan is to
> > create a libSEDML following the same steps as libSBML -- written in
> > C/C++ and then create bindings for other languages. Frank Bergmann has
> > also expressed interest and that he'd help.
> >
> > best
> > Pedro
> >
> > --
> > Pedro Mendes
> > Professor of Computational Systems Biology School of Computer Science
> > Manchester Centre for Integrative Systems Biology University of
> > Manchester
> >
> > Manchester Institute of Biotechnology
> > 131 Princess Street
> > Manchester, M1 7DN, U.K.
> >
> > ----------------------------------------------------------------------
> > -------- Try New Relic Now & We'll Send You this Cool Shirt New Relic
> > is the only SaaS-based application performance monitoring service that
> > delivers powerful full stack analytics. Optimize and monitor your
> > browser, app, & servers with just a few lines of code. Try New Relic
> > and get this awesome Nerd Life shirt!
> > http://p.sf.net/sfu/newrelic_d2d_apr
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> 
>
----------------------------------------------------------------------------
--
> Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only
> SaaS-based application performance monitoring service that delivers
> powerful full stack analytics. Optimize and monitor your browser, app, &
> servers with just a few lines of code. Try New Relic and get this awesome
> Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Hello and updates from COPASI

[Brett G. O. <bre...@gm...>]

Great news and cool initiative

+1 for anything with bindings

I agree with Frank, as a developer the nice thing having two solutions
(mature/new) is that you can use the mature one (perhaps via a roundabout
route) right now even as the other is developing ... to my mind a serious
win-win situation.

Best regards
Brett


On Thu, Apr 25, 2013 at 5:36 PM, Frank T. Bergmann <fbe...@ca...>wrote:

> > Just a quick comment on naming. Its a bit confusing the have two
> > libsedml's in different languages and with different features. Whats
> > the plan to deal with that? Will we be seeing the current C# libsedml
> > phased out and replaced by the C# bindings to the C++ libsedml?
>
> It will be years before the c++ library can do what the current C# one
> does. And even then there is something to be said for a fully native
> solution. As long as SED-ML is developing rapidly, there is need for a
> library that can adapt quickly and that makes it easy to prototype in. So
> the C# library will continue to be developed.
>
> the C++ library is there to make it easier to construct the raw SED-ML
> tree in languages other than C#  …
>
> as for names … i'm open to having the c++ one renamed to whatever suits, I
> don't think it matters much at this stage.
>
> Cheers
> Frank
>
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
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> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
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>



-- 
Brett G. Olivier PhD

Re: [SED-ML-discuss] Hello and updates from COPASI

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

> Just a quick comment on naming. Its a bit confusing the have two
> libsedml's in different languages and with different features. Whats
> the plan to deal with that? Will we be seeing the current C# libsedml
> phased out and replaced by the C# bindings to the C++ libsedml?

It will be years before the c++ library can do what the current C# one does. And even then there is something to be said for a fully native solution. As long as SED-ML is developing rapidly, there is need for a library that can adapt quickly and that makes it easy to prototype in. So the C# library will continue to be developed. 

the C++ library is there to make it easier to construct the raw SED-ML tree in languages other than C#  … 

as for names … i'm open to having the c++ one renamed to whatever suits, I don't think it matters much at this stage. 

Cheers
Frank

Re: [SED-ML-discuss] Hello and updates from COPASI

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

Hi Frank,

+1 to developing a C++ library :)

Just a quick comment on naming. Its a bit confusing the have two
libsedml's in different languages and with different features. Whats
the plan to deal with that? Will we be seeing the current C# libsedml
phased out and replaced by the C# bindings to the C++ libsedml?


Cheers,
David.

On Thu, Apr 25, 2013 at 9:14 AM, Frank T. Bergmann <fbe...@ca...> wrote:
> To provide just a little bit more detail on this. I've started to create  a library based on classes adapted from libSBML (such as SBase -> SedBase and the like). From there I modified a prototype from Sarah Keating that would allow to generate basic C++ classes. After rounds of refinement, I am now at a point where the core of SEDML L1V1 with the exception of the raw XML manipulation classes AddXML and ChangeXML are implemented. Via SWIG I then created rudimentary language bindings for C#, Java, Python, Ruby, Perl and R.
>
> The project is currently hosted at github: http://fbergmann.github.io/libSEDML/
>
> For examples on how the library can be used in the individual languages see:
>
> https://github.com/fbergmann/libSEDML/tree/master/examples
>
> In order to compile you need only to have CMake and libSBML. This library is written for the raw manipulation of the SEDML classes. It presently does not perform any of the utility functions as provided by my C# library (http://libsedml.sf.net) where models are resolved no matter where they are, stylesheet transformations for changes are applied, or the simulation experiments can be scheduled and run.
>
> Any feedback would be appreciated. And bugs can be filed under:
>
> https://github.com/fbergmann/libSEDML/issues
>
> Cheers
> Frank
>
>
> On Apr 25, 2013, at 1:15 PM, Pedro Mendes <ped...@ma...> wrote:
>
>> Hello all in SED-ML-discuss
>>
>> Just joined the list and a few colleagues of mine will join too. As you
>> may know, currently COPASI does not support SED-ML. This will change and
>> we are committed to add SED-ML support. We will also bring in some ideas
>> to develop further SED-ML, since currently our CopasiML has the
>> functionality of what SED-ML aspires (ie it stores both the model and
>> all the tasks to be carried out, so it is like SBML+SED-ML together).
>> Many of the tasks that you can do in COPASI currently cannot be
>> specified in SED-ML, so we would like to help development too.
>>
>> The first step for us will be to create a library, in C++ (since that is
>> what we use), to read/write SED-ML. Other colleagues from a FP7 project
>> (Eric Boix and Bertrand Moreau at CoSMo) also want to use SED-ML and
>> would like such a library. I suspect others here may also be interested?
>>
>> Right now, it would be great to hear from anyone already writing such a
>> a library (in C/C++) to avoid duplication of efforts. Our plan is to
>> create a libSEDML following the same steps as libSBML -- written in
>> C/C++ and then create bindings for other languages. Frank Bergmann has
>> also expressed interest and that he'd help.
>>
>> best
>> Pedro
>>
>> --
>> Pedro Mendes
>> Professor of Computational Systems Biology
>> School of Computer Science
>> Manchester Centre for Integrative Systems Biology
>> University of Manchester
>>
>> Manchester Institute of Biotechnology
>> 131 Princess Street
>> Manchester, M1 7DN, U.K.
>>
>> ------------------------------------------------------------------------------
>> Try New Relic Now & We'll Send You this Cool Shirt
>> New Relic is the only SaaS-based application performance monitoring service
>> that delivers powerful full stack analytics. Optimize and monitor your
>> browser, app, & servers with just a few lines of code. Try New Relic
>> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Hello and updates from COPASI

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

To provide just a little bit more detail on this. I've started to create  a library based on classes adapted from libSBML (such as SBase -> SedBase and the like). From there I modified a prototype from Sarah Keating that would allow to generate basic C++ classes. After rounds of refinement, I am now at a point where the core of SEDML L1V1 with the exception of the raw XML manipulation classes AddXML and ChangeXML are implemented. Via SWIG I then created rudimentary language bindings for C#, Java, Python, Ruby, Perl and R. 

The project is currently hosted at github: http://fbergmann.github.io/libSEDML/

For examples on how the library can be used in the individual languages see: 

https://github.com/fbergmann/libSEDML/tree/master/examples

In order to compile you need only to have CMake and libSBML. This library is written for the raw manipulation of the SEDML classes. It presently does not perform any of the utility functions as provided by my C# library (http://libsedml.sf.net) where models are resolved no matter where they are, stylesheet transformations for changes are applied, or the simulation experiments can be scheduled and run. 

Any feedback would be appreciated. And bugs can be filed under: 

https://github.com/fbergmann/libSEDML/issues

Cheers
Frank


On Apr 25, 2013, at 1:15 PM, Pedro Mendes <ped...@ma...> wrote:

> Hello all in SED-ML-discuss
> 
> Just joined the list and a few colleagues of mine will join too. As you 
> may know, currently COPASI does not support SED-ML. This will change and 
> we are committed to add SED-ML support. We will also bring in some ideas 
> to develop further SED-ML, since currently our CopasiML has the 
> functionality of what SED-ML aspires (ie it stores both the model and 
> all the tasks to be carried out, so it is like SBML+SED-ML together). 
> Many of the tasks that you can do in COPASI currently cannot be 
> specified in SED-ML, so we would like to help development too.
> 
> The first step for us will be to create a library, in C++ (since that is 
> what we use), to read/write SED-ML. Other colleagues from a FP7 project 
> (Eric Boix and Bertrand Moreau at CoSMo) also want to use SED-ML and 
> would like such a library. I suspect others here may also be interested?
> 
> Right now, it would be great to hear from anyone already writing such a 
> a library (in C/C++) to avoid duplication of efforts. Our plan is to 
> create a libSEDML following the same steps as libSBML -- written in 
> C/C++ and then create bindings for other languages. Frank Bergmann has 
> also expressed interest and that he'd help.
> 
> best
> Pedro
> 
> -- 
> Pedro Mendes
> Professor of Computational Systems Biology
> School of Computer Science
> Manchester Centre for Integrative Systems Biology
> University of Manchester
> 
> Manchester Institute of Biotechnology
> 131 Princess Street
> Manchester, M1 7DN, U.K.
> 
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service 
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss