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

[SED-ML-discuss] Voting results and runoff: SED-ML Editors

[Dagmar W. <dag...@un...>]

Dear members of the SED-ML community,

the first round of voting for two new SED-ML editors has closed. We received a total of 21 votes. Thank you very much!

One new SED-ML Editor will be [now borrowing the drums from the SBML crew]:  
Sven Sahle (University of Heidelberg). 
He received 16 votes. Congratulations and welcome to the SED-ML editorial board!

Three candidates tied for the second position (receiving 9 votes each), namely:
Brett Olivier, Ion Moraru, Felix Winter. Congratulations! 

Unfortunately, we can only appoint one more editor at this time. 
We thus invite all members of sed-ml-discuss to vote for your favorite candidate among the three for the remaining position: https://www.surveymonkey.com/s/3DNXJKF

The deadline for this election is Monday, 13 January 2014, 23:59:59 (GMT).

Thank you!
Dagmar, on behalf of the SED-ML Editors.


Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics,
University of Rostock, D-18051 Rostock, Germany
Web: http://www.sbi.uni-rostock.de/sems
Skype: dagmar.waltemath

[SED-ML-discuss] [Combine-announce] Harmony 2014

[Neil S. <Nei...@ma...>]

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

[SED-ML-discuss] Vote for new SED-ML Editors

[Dagmar W. <dag...@un...>]

Dear colleagues,

the vote for new SED-ML Editors is now open.

The previous call for nominations resulted in 6 unique nominees. 5 
nominees have accepted their nominations.
Please vote for your favorite candidates at:

https://www.surveymonkey.com/s/QVTBB7H

Voting will end on December 30, 2013. All members of sed-ml-discuss are 
entitled to vote.

Thank you very much for your participation.

Dagmar Waltemath,
on behalf of the (current) SED-ML Editors.

[SED-ML-discuss] Final release of SED-ML Level 1 Version 2

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

Dear Colleagues,

We are pleased to announce the release of the final specification for the
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version
2. It is available now from:

http://identifiers.org/combine.specifications/sed-ml.level-1.version-2

SED-ML is an XML-based format for encoding experiments involving the
numerical simulations of quantitative models. SED-ML describes the selection
and modifications of the models to be used in the experiment, the simulation
procedures that will be applied, the simulation experiments themselves, and
the post-processing and output of numerical results.

This second version of SED-ML enhances the time course simulation
experiments of Version 1 with repeated simulation tasks, where the variables
and parameters used can vary depending on other simulation runs. 

We would like to thank all of the members of the SED-ML community for their
continued support and use of SED-ML. 


The SED-ML editors
Frank Bergmann, Jonathan Cooper, Nicolas Le Novère, David Nickerson and
Dagmar Waltemath

[SED-ML-discuss] Call for SED-ML Editor nominations

[Dagmar W. <dag...@un...>]

Dear colleagues,

this is a call for nominations for two SED-ML editors to replace Nicolas 
Le Novère and David Nickerson, whose terms end on the 31st of December 
2013.
The length of a SED-ML Editor's term is 3 years, starting from the 1st 
of January 2014.
The current editors are Frank Bergmann (until 2014), Jonathan Cooper 
(until 2015), Nicolas Le Novère (to be replaced), David Nickerson (to be 
replaced), Dagmar Waltemath (until 2014).

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.
Please note that Nicolas Le Novère and David Nickerson cannot be elected 
at this time, due to the required stand down period of one year.
The nomination page is at: https://www.surveymonkey.com/s/V5QJ2DR

The call for nomination is open until the 11th of December 2013. After 
nomination phase, we will issue a call for voting.

Dagmar Waltemath,
on behalf of the SED-ML Editors.
http://sed-ml.org

[SED-ML-discuss] Call for papers: Workshop on Cell Based and Individual Based Modelling (CBIBM)

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

We are pleased to announce the first Workshop on Cell Based and 
Individual Based Modelling (CBIBM) which will be held as part of the 
2014 International Conference on Computational Science in Cairns, 
Australia, on the 10th -12th June 2014.

Individual and cell based models are increasingly being used to study 
the behaviour of natural systems, from modelling individual cells to 
study tissue development through to representations of whole organisms 
to study population dynamics. The aim of this workshop is to bring 
together scientists who are developing and using individual based 
modelling tools and software. The workshop will cover all aspects of 
model and tool development but will focus on the following.
- Computational or mathematical methods for the simulation (or analysis) 
of multicellular or multiagent systems.
- The development of simulation tools for multicellular or multiagent 
systems.
- The development of novel cell based or individual based models.
- Standards for specification of multicellular systems.
- Connecting individual based and continuum based modelling approaches.
- Novel applications of cell based and individual based modelling.
- Connecting individual based models to experimental data.

This call is for 10 page original research papers to be part of the 
workshop. The deadline for submission is the 6th of January 2014.

For more details see: http://www.cs.ox.ac.uk/conferences/CBIBM/ or email 
CB...@cs... <mailto:CB...@cs...>

Many thanks

The CBIBM workshop organisers.

Re: [SED-ML-discuss] Fwd: Re: [sbml-multi] Representing molecular fragments

[Robert P. <rp...@in...>]

I think it was Lily who asked:

"Should each fragment be its own molecule?"

I've always favored the notion that products of a protease reaction should
be represented as separate molecules. You never know when one of those
fragments will turn out to be a transcription factor or perform some other
function of its own that is NOT performed by the full length protein.

If there are contrasting views on this question, I'd really like to hear
them.

Bob

Robert D Phair PhD  |  Chief Science Officer  |  Integrative Bioinformatics
Inc
Mountain View, CA
www.integrativebioinformatics.com

ProcessDB: Modeling for Biological Discovery


On Thu, Nov 14, 2013 at 12:48 AM, Nicolas Le Novere <n.l...@gm...>wrote:

> Dear SED-MLers,
>
> Forwarding a discussion from the sbml-multi list, where SED-ML was
> mentioned. It indeed looks like such a distribution sampling would
> sometimes be in the realm of SED-ML. It does look similar to generating
> initial positions for a particle-based spatial model for instance. What
> do-you think?
>
>
> -------- Original Message --------
> Subject: Re: [sbml-multi] Representing molecular fragments
> Date: Wed, 13 Nov 2013 15:34:37 -0800
> From: Lucian Smith <luc...@gm...>
> Reply-To: Discussions of the SBML Level 3 'multi' package <
> sbm...@li...>
> To: Discussions of the SBML Level 3 'multi' package <
> sbm...@li...>
>
> There are a couple ways of dealing with this, the simplest of which would
> be to have the 'occur' attribute be an SIdRef to a Parameter instead of
> being a double (you could even require that the Parameter be constant and
> that it resolve to a positive integer, to make things simpler).  Not only
> would this open up the possibility of setting the value as a distribution,
> but it would open up the possibility of setting it via some other
> calculation--for example, if you knew that for two elements, the sum of
> their 'occur' values was 10, you could set one to x, one to y, and then set
> y via an InitialAssignment to '10-x'.  Then you only would need to set x
> once per 'simulation experiment'.
>
> The other possibility wouldn't really work until SBML L3v2, but in that,
> you could make the SpeciesFeatureType have mathematical meaning itself, set
> by the 'occur' attribute in the same way that the 'value' attribute sets
> the value on a Parameter.  But it's probably simpler to just have the
> attribute be an SIdRef.
>
> Finally, if the only thing you ever wanted to do was to relate the
> SpeciesFeatureType to a distribution, you could do that by giving it a
> child 'Uncertainty' element from the Distributions package.  Actually
> working with it would be the realm of SED-ML or the like, but at least the
> information would be there and be exchangeable.
>
> -Lucian
>
>
> On Wed, Nov 13, 2013 at 2:47 PM, Zhang, Fengkai (NIH/NIAID) [E] <
> zha...@ni...> wrote:
>
> >
> >
> > On 11/13/2013 02:47 PM, Lucian Smith wrote:
> > > I can answer the second question--the ability to choose numbers from a
> > > distribution is the scope of the 'Distributions' package (
> > > http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/distrib
> )
> > and
> > > should, at least in theory, work seamlessly with the 'multi' package,
> > > allowing you to define what you want.
> >
> >
> > There is one potential difficulty at the current version of multi for
> > this issue. A speciesType may have multiple speciesTypeInstances (for
> > example binding sites) at "occur" in a positiveInteger, which is not a
> > variable and may not be possible to define distribution without changing
> > the multi spec. A possible solution is to change the definition of the
> > occur attribute or add a new attribute to the SpeciesTypeInstance class,
> > say, occurVar, to reference the id of a parameter. Then constraints such
> > as a range and distributions could be added to the parameter. We will
> > work on this and try to integrate it at the next multi release.
> >
> > I have a comment for the use of distribution for copy number of a site.
> > I am thinking it should not be part of a model. Rather, it could be part
> > of a protocol or simulation description which perhaps can be defined in
> > SED-ML somehow.
> >
> > >
> > > -Lucian
> > >
> > >
> > > On Wed, Nov 13, 2013 at 11:18 AM, Lily Chylek <la...@co...>
> > wrote:
> > >
> > >> Hi Fengkai,
> > >>
> > >> Thanks for the reply. I have two more questions/comments about the
> multi
> > >> spec:
> > >>
> > >> 1) There seems to be a mistake in the list of references. The 2006 Sci
> > STKE
> > >> article about rule-based modeling (currently cited as Faeder et al.
> > 2006)
> > >> is actually the following:
> > >> Hlavacek, W.S., Faeder, J.R., Blinov, M.L., Posner, R.G., Hucka, M.,
> > >> and Fontana, W. (2006) Rules for modeling signal-transduction systems.
> > >> Sci. STKE, 2006:re6.
> >
> >
> > Thanks for pointing this out. The correction has been made for the next
> > multi release.
> >
> >
> > Fengkai
> >
> >
> >
> >
> > >>
> > >> 2) Is there a way of using multi to assign a molecule N copies of a
> > >> site, with N drawn from some distribution (e.g., a binomial
> > >> distribution)? An example of where this would be useful is if one
> > >> wanted to model the interactions of an antigen tagged with C3
> > >> molecules. The molecule type definition would be Antigen(C3,C3,C3...).
> > >> Not every antigen would carry the same number of C3's, so it would be
> > >> helpful to be able to define a distribution.
> > >>
> > >> Thanks,
> > >>
> > >> Lily
> > >>
> > >>
> > >> On Tue, Nov 12, 2013 at 11:49 PM, Zhang, Fengkai (NIH/NIAID) [E] <
> > >> zha...@ni...> wrote:
> > >>
> > >>> Dear Lily,
> > >>>
> > >>> I put my comments inline.I use "..." the same way as that in the
> multi
> > >>> documentation for the code fragments not important for the purpose of
> > >>> illustration.
> > >>>
> > >>> Regards,
> > >>>
> > >>> Fengkai
> > >>>
> > >>> On 11/12/13, 7:42 PM, Lily Chylek wrote:
> > >>>> Hi,
> > >>>>
> > >>>> I'm working on visualization tools for rule-based models. I'm
> > >> interested
> > >>> in
> > >>>> how SBML multi can be used to capture various biochemical processes
> > >> that
> > >>>> I've encoded in BNGL and visualized. The attached paper about model
> > >>>> visualization contains several examples.
> > >>>>
> > >>>> My question relates to the example shown in Fig S4 of the paper, the
> > >>> complement
> > >>>> cascade, which involved repeated protein cleavage at specific sites.
> > In
> > >>>> this example, the C3 molecule is cleaved to yield C3a and C3b. C3b
> is
> > >>>> cleaved to yield iC3b, which is further cleaved to C3dg. C3dg is
> > >> finally
> > >>>> cleaved into C3d and C3g. My question is: How can SBML multi can be
> > >> used
> > >>> to
> > >>>> represent molecular fragments, meaning the products of cleavage
> > >>> reactions?
> > >>> I generated the multi xml code corresponding to your sample model 1
> > >>> which should demonstrate how multi can represent molecule fragments.
> It
> > >>> is actually one of important features covered by multi.
> > >>>> It seems that there are at least two ways that this could be
> > >> represented
> > >>> in
> > >>>> a rule-based modeling language, and I'm attaching two BNGL files as
> > >>>> illustration. In the first model, terminal fragments (C3d and C3g)
> are
> > >>>> represented as molecules, and the larger precursor (C3dg) is
> > >> represented
> > >>> as
> > >>>> a complex of these fragments. The bond is a covalent bond between
> two
> > >>> amino
> > >>>> acid residues.
> > >>> Here is the multi code corresponding to the first model.
> > >>>
> > >>> <?xml version="1.0" encoding="UTF-8"?>
> > >>> <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
> level="3"
> > >>> version="1"
> > >>>
> > >>> xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1
> "
> > >>> multi:required="true">
> > >>>      <model name="complement simple 1">
> > >>>         ...
> > >>>         <multi:listOfSpeciesTypes>
> > >>>            <multi:speciesType multi:id="st_K1001"
> > >>> multi:isBindingSite="true" />
> > >>>            <multi:speciesType multi:id="st_C3g"
> > >> multi:isBindingSite="false">
> > >>>               <multi:listOfSpeciesTypeInstances>
> > >>>                  <multi:component multi:id="K1001"
> > >>> multi:speciesType="st_K1001" multi:occur="1" />
> > >>>               </multi:listOfSpeciesTypeInstances>
> > >>>            </multi:speciesType>
> > >>>            <multi:speciesType multi:id="st_H1002"
> > >>> multi:isBindingSite="true" />
> > >>>            <multi:speciesType multi:id="st_C3d"
> > >> multi:isBindingSite="false">
> > >>>               <multi:listOfSpeciesTypeInstances>
> > >>>                  <multi:component multi:id="H1002"
> > >>> multi:speciesType="st_H1002" multi:occur="1" />
> > >>>               </multi:listOfSpeciesTypeInstances>
> > >>>            </multi:speciesType>
> > >>>            <multi:speciesType multi:id="st_C3dg"
> > >>> multi:isBindingSite="false">
> > >>>               <multi:listOfSpeciesTypeInstances>
> > >>>                  <multi:component multi:id="C3g"
> > >>> multi:speciesType="st_C3g" multi:occur="1" />
> > >>>                  <multi:component multi:id="C3d"
> > >>> multi:speciesType="st_C3d" multi:occur="1" />
> > >>>               </multi:listOfSpeciesTypeInstances>
> > >>>               <multi:listOfInSpeciesTypeBonds>
> > >>>                  <multi:inSpeciesTypeBond multi:bindingSite1="K1001"
> > >>>                     multi:bindingSite2="H1002" />
> > >>>               </multi:listOfInSpeciesTypeBonds>
> > >>>            </multi:speciesType>
> > >>>         </multi:listOfSpeciesTypes>
> > >>>         <listOfSpecies>
> > >>>            <species id="C3g_free" name="C3g"
> multi:speciesType="st_C3g"
> > >> ...>
> > >>>               <multi:listOfOutwardBindingSites>
> > >>>                  <multi:outwardBindingSite multi:component="K1001"
> > >>> multi:bindingStatus="unbound" />
> > >>>               </multi:listOfOutwardBindingSites>
> > >>>            </species>
> > >>>            <species id="C3d_free" multi:speciesType="st_C3d" ...>
> > >>>               <multi:listOfOutwardBindingSites>
> > >>>                  <multi:outwardBindingSite multi:component="H1002"
> > >>> multi:bindingStatus="unbound" />
> > >>>               </multi:listOfOutwardBindingSites>
> > >>>            </species>
> > >>>            <species id="C3dg" multi:speciesType="st_C3dg"
> > >>> initialAmount="100" ... />
> > >>>         </listOfSpecies>
> > >>>         <listOfParameters>
> > >>>            <parameter id="k" value="1" constant="true" />
> > >>>         </listOfParameters>
> > >>>         <listOfReactions>
> > >>>            <reaction id="C3dg_cleavage" ...>
> > >>>               <listOfReactants>
> > >>>                  <speciesReference species="C3dg" ... />
> > >>>               </listOfReactants>
> > >>>               <listOfProducts>
> > >>>                  <speciesReference species="C3g_free" ... />
> > >>>                  <speciesReference species="C3d_free" ... />
> > >>>               </listOfProducts>
> > >>>               <kineticLaw>
> > >>>                  <math xmlns="http://www.w3.org/1998/Math/MathML">
> > >>>                     ...
> > >>>                  </math>
> > >>>               </kineticLaw>
> > >>>            </reaction>
> > >>>            ...
> > >>>          </listOfReactions>
> > >>>      </model>
> > >>> </sbml>
> > >>>
> > >>>> In the second model, each molecule (C3dg, C3d, and C3g) is
> > >>>> represented individually, and the cleavage reaction is represented
> as
> > >>>> degradation of the precursor (C3dg) and synthesis of terminal
> > fragments
> > >>>> (C3d and C3g).
> > >>> The SBML core should be able to cover the second model.
> > >>>
> > >>> <?xml version="1.0" encoding="UTF-8"?>
> > >>> <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core"
> level="3"
> > >>> version="1">
> > >>>      <model name="complement simple 2">
> > >>>         ...
> > >>>         <listOfSpecies>
> > >>>            <species id="C3g" ... />
> > >>>            <species id="C3d" ... />
> > >>>            <species id="C3dg" initialAmount="100" ... />
> > >>>         </listOfSpecies>
> > >>>         <listOfParameters>
> > >>>            <parameter id="k" value="1" constant="true" />
> > >>>         </listOfParameters>
> > >>>         <listOfReactions>
> > >>>            <reaction id="C3dg_cleavage" ...>
> > >>>               <listOfReactants>
> > >>>                  <speciesReference species="C3dg" ... />
> > >>>               </listOfReactants>
> > >>>               <listOfProducts>
> > >>>                  <speciesReference species="C3g" ... />
> > >>>                  <speciesReference species="C3d" ... />
> > >>>               </listOfProducts>
> > >>>               <kineticLaw>
> > >>>                  <math xmlns="http://www.w3.org/1998/Math/MathML">
> > >>>                     ...
> > >>>                  </math>
> > >>>               </kineticLaw>
> > >>>            </reaction>
> > >>>            ...
> > >>>          </listOfReactions>
> > >>>      </model>
> > >>> </sbml>
> > >>>> This is a simple example, but the full cascade (and other
> > >>>> similar ones, like the caspase cascade) would include many instances
> > >>>> fragments being generated and cleaved to yield additional fragments.
> > >>>>
> > >>>> It seems that the current SBML-multi documentation doesn't contain
> an
> > >>> example
> > >>>> like this. So is there currently a standardized way of representing
> > >>>> fragments? Should each fragment be its own molecule? Is there a way
> of
> > >>>> preserving information about the mechanism by which one fragment is
> > >>> cleaved
> > >>>> to yield another? Or, should only terminal fragments be represented
> as
> > >>>> molecules, with precursor fragments represented as complexes?
> > >>> Perhaps I did not completely get your question. The bionetgen and
> > carbon
> > >>> mapping examplesin the documentation should be sufficient to
> > demonstrate
> > >>> the features required by your sample models.
> > >>>
> > >>>> Thanks,
> > >>>>
> > >>>> Lily
> > >>>>
> > >>>>
> > >>>>
> > >>>
> > >>
> >
> ------------------------------------------------------------------------------
> > >>>> DreamFactory - Open Source REST & JSON Services for HTML5 & Native
> > Apps
> > >>>> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API
> Access
> > >>>> Free app hosting. Or install the open source package on any LAMP
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> > >>>>
> > >>>
> > >>
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
> > >>>>
> > >>>>
> > >>>> _______________________________________________
> > >>>> Sbml-multi mailing list
> > >>>> Sbm...@li...
> > >>>> https://lists.sourceforge.net/lists/listinfo/sbml-multi
> > >>>
> > >>> --
> > >>> ===============================
> > >>> Fengkai Zhang, MD, MMath
> > >>> Staff Scientist
> > >>> Laboratory of Systems Biology, DIR, NIAID
> > >>> 9000 Rockville Pike
> > >>> Building 4, Room 137
> > >>> MSC 0421
> > >>> Bethesda MD 20892
> > >>> Phone: 301.496.0985
> > >>> Fax: 301.480.1660
> > >>> NIAID, National Institutes of Health, DHHS
> > >>>
> > >>>
> > >>>
> > >>> "Disclaimer:
> > >>>
> > >>> The information in this e-mail and any of its attachments is
> > confidential
> > >>> and may contain sensitive information. It should not be used by
> anyone
> > >> who
> > >>> is not the original intended recipient. If you have received this
> > e-mail
> > >> in
> > >>> error please inform the sender and delete it from your mailbox or any
> > >> other
> > >>> storage devices. National Institute of Allergy and Infectious
> Diseases
> > >>> shall not accept liability for any statements made that are sender's
> > own
> > >>> and not expressly made on behalf of the NIAID by one of its
> > >>> representatives. "
> > >>>
> > >>>
> > >>>
> > >>
> >
> ------------------------------------------------------------------------------
> > >>> DreamFactory - Open Source REST & JSON Services for HTML5 & Native
> Apps
> > >>> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
> > >>> Free app hosting. Or install the open source package on any LAMP
> > server.
> > >>> Sign up and see examples for AngularJS, jQuery, Sencha Touch and
> > Native!
> > >>>
> > >>
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
> > >>> _______________________________________________
> > >>> Sbml-multi mailing list
> > >>> Sbm...@li...
> > >>> https://lists.sourceforge.net/lists/listinfo/sbml-multi
> > >>>
> > >>>
> > >>>
> > >>
> > >>
> >
> ------------------------------------------------------------------------------
> > >> DreamFactory - Open Source REST & JSON Services for HTML5 & Native
> Apps
> > >> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
> > >> Free app hosting. Or install the open source package on any LAMP
> server.
> > >> Sign up and see examples for AngularJS, jQuery, Sencha Touch and
> Native!
> > >>
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
> > >> _______________________________________________
> > >> Sbml-multi mailing list
> > >> Sbm...@li...
> > >> https://lists.sourceforge.net/lists/listinfo/sbml-multi
> > >>
> > >
> >
> ------------------------------------------------------------------------------
> > > DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
> > > OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
> > > Free app hosting. Or install the open source package on any LAMP
> server.
> > > Sign up and see examples for AngularJS, jQuery, Sencha Touch and
> Native!
> > >
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
> > > _______________________________________________
> > > Sbml-multi mailing list
> > > Sbm...@li...
> > > https://lists.sourceforge.net/lists/listinfo/sbml-multi
> > >
> >
> > --
> >
> > =========================
> > Fengkai Zhang, MD, MMath
> > Staff Scientist
> > Laboratory of Systems Biology, DIR, NIAID
> > 9000 Rockville Pike
> > Building 4, Room 137
> > MSC 0421
> > Bethesda MD 20892
> > Phone: 301.496.0985
> > Fax: 301.480.1660
> > NIAID, National Institutes of Health, DHHS
> >
> >
> > "Disclaimer:
> >
> > The information in this e-mail and any of its attachments is
> > confidential and may contain sensitive information. It should not be
> > used by anyone who is not the original intended recipient. If you have
> > received this e-mail in error please inform the sender and delete it
> > from your mailbox or any other storage devices. National Institute of
> > Allergy and Infectious Diseases shall not accept liability for any
> > statements made that are sender's own and not expressly made on behalf
> > of the NIAID by one of its representatives. "
> >
> >
> >
> ------------------------------------------------------------------------------
> > DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
> > OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
> > Free app hosting. Or install the open source package on any LAMP server.
> > Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Sbml-multi mailing list
> > Sbm...@li...
> > https://lists.sourceforge.net/lists/listinfo/sbml-multi
> >
>
> ------------------------------------------------------------------------------
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> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
> Free app hosting. Or install the open source package on any LAMP server.
> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/sbml-multi
>
>
>
>
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Re: [SED-ML-discuss] Fwd: Re: [sbml-multi] Representing molecular fragments

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

Dear Nicolas,

This is really in the realm of SED-ML. What Lucian describes in that 
posting is the sampling of one parameter (eg initial concentration), 
that is a simulation task. He also mentions the setting of a dependency 
between two parameters, and that should be in the realm of SBML (initial 
assignment).

Needless to say, that COPASI does all these operations already and their 
use is probably widespread (so it is not a hypothetical use).

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.


On 11/14/2013 08:48 AM, Nicolas Le Novere wrote:
> Dear SED-MLers,
>
> Forwarding a discussion from the sbml-multi list, where SED-ML was mentioned. It indeed looks like such a distribution sampling would sometimes be in the realm of SED-ML. It does look similar to generating initial positions for a particle-based spatial model for instance. What do-you think?
>
>
> -------- Original Message --------
> Subject: Re: [sbml-multi] Representing molecular fragments
> Date: Wed, 13 Nov 2013 15:34:37 -0800
> From: Lucian Smith <luc...@gm...>
> Reply-To: Discussions of the SBML Level 3 'multi' package <sbm...@li...>
> To: Discussions of the SBML Level 3 'multi' package <sbm...@li...>
>
> There are a couple ways of dealing with this, the simplest of which would
> be to have the 'occur' attribute be an SIdRef to a Parameter instead of
> being a double (you could even require that the Parameter be constant and
> that it resolve to a positive integer, to make things simpler).  Not only
> would this open up the possibility of setting the value as a distribution,
> but it would open up the possibility of setting it via some other
> calculation--for example, if you knew that for two elements, the sum of
> their 'occur' values was 10, you could set one to x, one to y, and then set
> y via an InitialAssignment to '10-x'.  Then you only would need to set x
> once per 'simulation experiment'.
>
> The other possibility wouldn't really work until SBML L3v2, but in that,
> you could make the SpeciesFeatureType have mathematical meaning itself, set
> by the 'occur' attribute in the same way that the 'value' attribute sets
> the value on a Parameter.  But it's probably simpler to just have the
> attribute be an SIdRef.
>
> Finally, if the only thing you ever wanted to do was to relate the
> SpeciesFeatureType to a distribution, you could do that by giving it a
> child 'Uncertainty' element from the Distributions package.  Actually
> working with it would be the realm of SED-ML or the like, but at least the
> information would be there and be exchangeable.
>
> -Lucian
>
>
> On Wed, Nov 13, 2013 at 2:47 PM, Zhang, Fengkai (NIH/NIAID) [E] <
> zha...@ni...> wrote:
>
>>
>>
>> On 11/13/2013 02:47 PM, Lucian Smith wrote:
>>> I can answer the second question--the ability to choose numbers from a
>>> distribution is the scope of the 'Distributions' package (
>>> http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/distrib)
>> and
>>> should, at least in theory, work seamlessly with the 'multi' package,
>>> allowing you to define what you want.
>>
>>
>> There is one potential difficulty at the current version of multi for
>> this issue. A speciesType may have multiple speciesTypeInstances (for
>> example binding sites) at "occur" in a positiveInteger, which is not a
>> variable and may not be possible to define distribution without changing
>> the multi spec. A possible solution is to change the definition of the
>> occur attribute or add a new attribute to the SpeciesTypeInstance class,
>> say, occurVar, to reference the id of a parameter. Then constraints such
>> as a range and distributions could be added to the parameter. We will
>> work on this and try to integrate it at the next multi release.
>>
>> I have a comment for the use of distribution for copy number of a site.
>> I am thinking it should not be part of a model. Rather, it could be part
>> of a protocol or simulation description which perhaps can be defined in
>> SED-ML somehow.
>>
>>>
>>> -Lucian
>>>
>>>
>>> On Wed, Nov 13, 2013 at 11:18 AM, Lily Chylek <la...@co...>
>> wrote:
>>>
>>>> Hi Fengkai,
>>>>
>>>> Thanks for the reply. I have two more questions/comments about the multi
>>>> spec:
>>>>
>>>> 1) There seems to be a mistake in the list of references. The 2006 Sci
>> STKE
>>>> article about rule-based modeling (currently cited as Faeder et al.
>> 2006)
>>>> is actually the following:
>>>> Hlavacek, W.S., Faeder, J.R., Blinov, M.L., Posner, R.G., Hucka, M.,
>>>> and Fontana, W. (2006) Rules for modeling signal-transduction systems.
>>>> Sci. STKE, 2006:re6.
>>
>>
>> Thanks for pointing this out. The correction has been made for the next
>> multi release.
>>
>>
>> Fengkai
>>
>>
>>
>>
>>>>
>>>> 2) Is there a way of using multi to assign a molecule N copies of a
>>>> site, with N drawn from some distribution (e.g., a binomial
>>>> distribution)? An example of where this would be useful is if one
>>>> wanted to model the interactions of an antigen tagged with C3
>>>> molecules. The molecule type definition would be Antigen(C3,C3,C3...).
>>>> Not every antigen would carry the same number of C3's, so it would be
>>>> helpful to be able to define a distribution.
>>>>
>>>> Thanks,
>>>>
>>>> Lily
>>>>
>>>>
>>>> On Tue, Nov 12, 2013 at 11:49 PM, Zhang, Fengkai (NIH/NIAID) [E] <
>>>> zha...@ni...> wrote:
>>>>
>>>>> Dear Lily,
>>>>>
>>>>> I put my comments inline.I use "..." the same way as that in the multi
>>>>> documentation for the code fragments not important for the purpose of
>>>>> illustration.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Fengkai
>>>>>
>>>>> On 11/12/13, 7:42 PM, Lily Chylek wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I'm working on visualization tools for rule-based models. I'm
>>>> interested
>>>>> in
>>>>>> how SBML multi can be used to capture various biochemical processes
>>>> that
>>>>>> I've encoded in BNGL and visualized. The attached paper about model
>>>>>> visualization contains several examples.
>>>>>>
>>>>>> My question relates to the example shown in Fig S4 of the paper, the
>>>>> complement
>>>>>> cascade, which involved repeated protein cleavage at specific sites.
>> In
>>>>>> this example, the C3 molecule is cleaved to yield C3a and C3b. C3b is
>>>>>> cleaved to yield iC3b, which is further cleaved to C3dg. C3dg is
>>>> finally
>>>>>> cleaved into C3d and C3g. My question is: How can SBML multi can be
>>>> used
>>>>> to
>>>>>> represent molecular fragments, meaning the products of cleavage
>>>>> reactions?
>>>>> I generated the multi xml code corresponding to your sample model 1
>>>>> which should demonstrate how multi can represent molecule fragments. It
>>>>> is actually one of important features covered by multi.
>>>>>> It seems that there are at least two ways that this could be
>>>> represented
>>>>> in
>>>>>> a rule-based modeling language, and I'm attaching two BNGL files as
>>>>>> illustration. In the first model, terminal fragments (C3d and C3g) are
>>>>>> represented as molecules, and the larger precursor (C3dg) is
>>>> represented
>>>>> as
>>>>>> a complex of these fragments. The bond is a covalent bond between two
>>>>> amino
>>>>>> acid residues.
>>>>> Here is the multi code corresponding to the first model.
>>>>>
>>>>> <?xml version="1.0" encoding="UTF-8"?>
>>>>> <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3"
>>>>> version="1"
>>>>>
>>>>> xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
>>>>> multi:required="true">
>>>>>       <model name="complement simple 1">
>>>>>          ...
>>>>>          <multi:listOfSpeciesTypes>
>>>>>             <multi:speciesType multi:id="st_K1001"
>>>>> multi:isBindingSite="true" />
>>>>>             <multi:speciesType multi:id="st_C3g"
>>>> multi:isBindingSite="false">
>>>>>                <multi:listOfSpeciesTypeInstances>
>>>>>                   <multi:component multi:id="K1001"
>>>>> multi:speciesType="st_K1001" multi:occur="1" />
>>>>>                </multi:listOfSpeciesTypeInstances>
>>>>>             </multi:speciesType>
>>>>>             <multi:speciesType multi:id="st_H1002"
>>>>> multi:isBindingSite="true" />
>>>>>             <multi:speciesType multi:id="st_C3d"
>>>> multi:isBindingSite="false">
>>>>>                <multi:listOfSpeciesTypeInstances>
>>>>>                   <multi:component multi:id="H1002"
>>>>> multi:speciesType="st_H1002" multi:occur="1" />
>>>>>                </multi:listOfSpeciesTypeInstances>
>>>>>             </multi:speciesType>
>>>>>             <multi:speciesType multi:id="st_C3dg"
>>>>> multi:isBindingSite="false">
>>>>>                <multi:listOfSpeciesTypeInstances>
>>>>>                   <multi:component multi:id="C3g"
>>>>> multi:speciesType="st_C3g" multi:occur="1" />
>>>>>                   <multi:component multi:id="C3d"
>>>>> multi:speciesType="st_C3d" multi:occur="1" />
>>>>>                </multi:listOfSpeciesTypeInstances>
>>>>>                <multi:listOfInSpeciesTypeBonds>
>>>>>                   <multi:inSpeciesTypeBond multi:bindingSite1="K1001"
>>>>>                      multi:bindingSite2="H1002" />
>>>>>                </multi:listOfInSpeciesTypeBonds>
>>>>>             </multi:speciesType>
>>>>>          </multi:listOfSpeciesTypes>
>>>>>          <listOfSpecies>
>>>>>             <species id="C3g_free" name="C3g" multi:speciesType="st_C3g"
>>>> ...>
>>>>>                <multi:listOfOutwardBindingSites>
>>>>>                   <multi:outwardBindingSite multi:component="K1001"
>>>>> multi:bindingStatus="unbound" />
>>>>>                </multi:listOfOutwardBindingSites>
>>>>>             </species>
>>>>>             <species id="C3d_free" multi:speciesType="st_C3d" ...>
>>>>>                <multi:listOfOutwardBindingSites>
>>>>>                   <multi:outwardBindingSite multi:component="H1002"
>>>>> multi:bindingStatus="unbound" />
>>>>>                </multi:listOfOutwardBindingSites>
>>>>>             </species>
>>>>>             <species id="C3dg" multi:speciesType="st_C3dg"
>>>>> initialAmount="100" ... />
>>>>>          </listOfSpecies>
>>>>>          <listOfParameters>
>>>>>             <parameter id="k" value="1" constant="true" />
>>>>>          </listOfParameters>
>>>>>          <listOfReactions>
>>>>>             <reaction id="C3dg_cleavage" ...>
>>>>>                <listOfReactants>
>>>>>                   <speciesReference species="C3dg" ... />
>>>>>                </listOfReactants>
>>>>>                <listOfProducts>
>>>>>                   <speciesReference species="C3g_free" ... />
>>>>>                   <speciesReference species="C3d_free" ... />
>>>>>                </listOfProducts>
>>>>>                <kineticLaw>
>>>>>                   <math xmlns="http://www.w3.org/1998/Math/MathML">
>>>>>                      ...
>>>>>                   </math>
>>>>>                </kineticLaw>
>>>>>             </reaction>
>>>>>             ...
>>>>>           </listOfReactions>
>>>>>       </model>
>>>>> </sbml>
>>>>>
>>>>>> In the second model, each molecule (C3dg, C3d, and C3g) is
>>>>>> represented individually, and the cleavage reaction is represented as
>>>>>> degradation of the precursor (C3dg) and synthesis of terminal
>> fragments
>>>>>> (C3d and C3g).
>>>>> The SBML core should be able to cover the second model.
>>>>>
>>>>> <?xml version="1.0" encoding="UTF-8"?>
>>>>> <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3"
>>>>> version="1">
>>>>>       <model name="complement simple 2">
>>>>>          ...
>>>>>          <listOfSpecies>
>>>>>             <species id="C3g" ... />
>>>>>             <species id="C3d" ... />
>>>>>             <species id="C3dg" initialAmount="100" ... />
>>>>>          </listOfSpecies>
>>>>>          <listOfParameters>
>>>>>             <parameter id="k" value="1" constant="true" />
>>>>>          </listOfParameters>
>>>>>          <listOfReactions>
>>>>>             <reaction id="C3dg_cleavage" ...>
>>>>>                <listOfReactants>
>>>>>                   <speciesReference species="C3dg" ... />
>>>>>                </listOfReactants>
>>>>>                <listOfProducts>
>>>>>                   <speciesReference species="C3g" ... />
>>>>>                   <speciesReference species="C3d" ... />
>>>>>                </listOfProducts>
>>>>>                <kineticLaw>
>>>>>                   <math xmlns="http://www.w3.org/1998/Math/MathML">
>>>>>                      ...
>>>>>                   </math>
>>>>>                </kineticLaw>
>>>>>             </reaction>
>>>>>             ...
>>>>>           </listOfReactions>
>>>>>       </model>
>>>>> </sbml>
>>>>>> This is a simple example, but the full cascade (and other
>>>>>> similar ones, like the caspase cascade) would include many instances
>>>>>> fragments being generated and cleaved to yield additional fragments.
>>>>>>
>>>>>> It seems that the current SBML-multi documentation doesn't contain an
>>>>> example
>>>>>> like this. So is there currently a standardized way of representing
>>>>>> fragments? Should each fragment be its own molecule? Is there a way of
>>>>>> preserving information about the mechanism by which one fragment is
>>>>> cleaved
>>>>>> to yield another? Or, should only terminal fragments be represented as
>>>>>> molecules, with precursor fragments represented as complexes?
>>>>> Perhaps I did not completely get your question. The bionetgen and
>> carbon
>>>>> mapping examplesin the documentation should be sufficient to
>> demonstrate
>>>>> the features required by your sample models.
>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Lily
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>> ------------------------------------------------------------------------------
>>>>>> DreamFactory - Open Source REST & JSON Services for HTML5 & Native
>> Apps
>>>>>> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
>>>>>> Free app hosting. Or install the open source package on any LAMP
>>>> server.
>>>>>> Sign up and see examples for AngularJS, jQuery, Sencha Touch and
>>>> Native!
>>>>>>
>>>>>
>>>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Sbml-multi mailing list
>>>>>> Sbm...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/sbml-multi
>>>>>
>>>>> --
>>>>> ===============================
>>>>> Fengkai Zhang, MD, MMath
>>>>> Staff Scientist
>>>>> Laboratory of Systems Biology, DIR, NIAID
>>>>> 9000 Rockville Pike
>>>>> Building 4, Room 137
>>>>> MSC 0421
>>>>> Bethesda MD 20892
>>>>> Phone: 301.496.0985
>>>>> Fax: 301.480.1660
>>>>> NIAID, National Institutes of Health, DHHS
>>>>>
>>>>>
>>>>>
>>>>> "Disclaimer:
>>>>>
>>>>> The information in this e-mail and any of its attachments is
>> confidential
>>>>> and may contain sensitive information. It should not be used by anyone
>>>> who
>>>>> is not the original intended recipient. If you have received this
>> e-mail
>>>> in
>>>>> error please inform the sender and delete it from your mailbox or any
>>>> other
>>>>> storage devices. National Institute of Allergy and Infectious Diseases
>>>>> shall not accept liability for any statements made that are sender's
>> own
>>>>> and not expressly made on behalf of the NIAID by one of its
>>>>> representatives. "
>>>>>
>>>>>
>>>>>
>>>>
>> ------------------------------------------------------------------------------
>>>>> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
>>>>> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
>>>>> Free app hosting. Or install the open source package on any LAMP
>> server.
>>>>> Sign up and see examples for AngularJS, jQuery, Sencha Touch and
>> Native!
>>>>>
>>>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Sbml-multi mailing list
>>>>> Sbm...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/sbml-multi
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>> ------------------------------------------------------------------------------
>>>> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
>>>> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
>>>> Free app hosting. Or install the open source package on any LAMP server.
>>>> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
>>>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> Sbml-multi mailing list
>>>> Sbm...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sbml-multi
>>>>
>>>
>> ------------------------------------------------------------------------------
>>> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
>>> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
>>> Free app hosting. Or install the open source package on any LAMP server.
>>> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
>>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Sbml-multi mailing list
>>> Sbm...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sbml-multi
>>>
>>
>> --
>>
>> =========================
>> Fengkai Zhang, MD, MMath
>> Staff Scientist
>> Laboratory of Systems Biology, DIR, NIAID
>> 9000 Rockville Pike
>> Building 4, Room 137
>> MSC 0421
>> Bethesda MD 20892
>> Phone: 301.496.0985
>> Fax: 301.480.1660
>> NIAID, National Institutes of Health, DHHS
>>
>>
>> "Disclaimer:
>>
>> The information in this e-mail and any of its attachments is
>> confidential and may contain sensitive information. It should not be
>> used by anyone who is not the original intended recipient. If you have
>> received this e-mail in error please inform the sender and delete it
>> from your mailbox or any other storage devices. National Institute of
>> Allergy and Infectious Diseases shall not accept liability for any
>> statements made that are sender's own and not expressly made on behalf
>> of the NIAID by one of its representatives. "
>>
>>
>> ------------------------------------------------------------------------------
>> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
>> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
>> Free app hosting. Or install the open source package on any LAMP server.
>> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
>> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Sbml-multi mailing list
>> Sbm...@li...
>> https://lists.sourceforge.net/lists/listinfo/sbml-multi
>>
> ------------------------------------------------------------------------------
> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
> Free app hosting. Or install the open source package on any LAMP server.
> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
> http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/sbml-multi
>
>
>
> ------------------------------------------------------------------------------
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> Free app hosting. Or install the open source package on any LAMP server.
> Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native!
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>

[SED-ML-discuss] Fwd: Re: [sbml-multi] Representing molecular fragments

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

Dear SED-MLers,

Forwarding a discussion from the sbml-multi list, where SED-ML was mentioned. It indeed looks like such a distribution sampling would sometimes be in the realm of SED-ML. It does look similar to generating initial positions for a particle-based spatial model for instance. What do-you think?


-------- Original Message --------
Subject: Re: [sbml-multi] Representing molecular fragments
Date: Wed, 13 Nov 2013 15:34:37 -0800
From: Lucian Smith <luc...@gm...>
Reply-To: Discussions of the SBML Level 3 'multi' package <sbm...@li...>
To: Discussions of the SBML Level 3 'multi' package <sbm...@li...>

There are a couple ways of dealing with this, the simplest of which would
be to have the 'occur' attribute be an SIdRef to a Parameter instead of
being a double (you could even require that the Parameter be constant and
that it resolve to a positive integer, to make things simpler).  Not only
would this open up the possibility of setting the value as a distribution,
but it would open up the possibility of setting it via some other
calculation--for example, if you knew that for two elements, the sum of
their 'occur' values was 10, you could set one to x, one to y, and then set
y via an InitialAssignment to '10-x'.  Then you only would need to set x
once per 'simulation experiment'.

The other possibility wouldn't really work until SBML L3v2, but in that,
you could make the SpeciesFeatureType have mathematical meaning itself, set
by the 'occur' attribute in the same way that the 'value' attribute sets
the value on a Parameter.  But it's probably simpler to just have the
attribute be an SIdRef.

Finally, if the only thing you ever wanted to do was to relate the
SpeciesFeatureType to a distribution, you could do that by giving it a
child 'Uncertainty' element from the Distributions package.  Actually
working with it would be the realm of SED-ML or the like, but at least the
information would be there and be exchangeable.

-Lucian


On Wed, Nov 13, 2013 at 2:47 PM, Zhang, Fengkai (NIH/NIAID) [E] <
zha...@ni...> wrote:

>
>
> On 11/13/2013 02:47 PM, Lucian Smith wrote:
> > I can answer the second question--the ability to choose numbers from a
> > distribution is the scope of the 'Distributions' package (
> > http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/distrib)
> and
> > should, at least in theory, work seamlessly with the 'multi' package,
> > allowing you to define what you want.
>
>
> There is one potential difficulty at the current version of multi for
> this issue. A speciesType may have multiple speciesTypeInstances (for
> example binding sites) at "occur" in a positiveInteger, which is not a
> variable and may not be possible to define distribution without changing
> the multi spec. A possible solution is to change the definition of the
> occur attribute or add a new attribute to the SpeciesTypeInstance class,
> say, occurVar, to reference the id of a parameter. Then constraints such
> as a range and distributions could be added to the parameter. We will
> work on this and try to integrate it at the next multi release.
>
> I have a comment for the use of distribution for copy number of a site.
> I am thinking it should not be part of a model. Rather, it could be part
> of a protocol or simulation description which perhaps can be defined in
> SED-ML somehow.
>
> >
> > -Lucian
> >
> >
> > On Wed, Nov 13, 2013 at 11:18 AM, Lily Chylek <la...@co...>
> wrote:
> >
> >> Hi Fengkai,
> >>
> >> Thanks for the reply. I have two more questions/comments about the multi
> >> spec:
> >>
> >> 1) There seems to be a mistake in the list of references. The 2006 Sci
> STKE
> >> article about rule-based modeling (currently cited as Faeder et al.
> 2006)
> >> is actually the following:
> >> Hlavacek, W.S., Faeder, J.R., Blinov, M.L., Posner, R.G., Hucka, M.,
> >> and Fontana, W. (2006) Rules for modeling signal-transduction systems.
> >> Sci. STKE, 2006:re6.
>
>
> Thanks for pointing this out. The correction has been made for the next
> multi release.
>
>
> Fengkai
>
>
>
>
> >>
> >> 2) Is there a way of using multi to assign a molecule N copies of a
> >> site, with N drawn from some distribution (e.g., a binomial
> >> distribution)? An example of where this would be useful is if one
> >> wanted to model the interactions of an antigen tagged with C3
> >> molecules. The molecule type definition would be Antigen(C3,C3,C3...).
> >> Not every antigen would carry the same number of C3's, so it would be
> >> helpful to be able to define a distribution.
> >>
> >> Thanks,
> >>
> >> Lily
> >>
> >>
> >> On Tue, Nov 12, 2013 at 11:49 PM, Zhang, Fengkai (NIH/NIAID) [E] <
> >> zha...@ni...> wrote:
> >>
> >>> Dear Lily,
> >>>
> >>> I put my comments inline.I use "..." the same way as that in the multi
> >>> documentation for the code fragments not important for the purpose of
> >>> illustration.
> >>>
> >>> Regards,
> >>>
> >>> Fengkai
> >>>
> >>> On 11/12/13, 7:42 PM, Lily Chylek wrote:
> >>>> Hi,
> >>>>
> >>>> I'm working on visualization tools for rule-based models. I'm
> >> interested
> >>> in
> >>>> how SBML multi can be used to capture various biochemical processes
> >> that
> >>>> I've encoded in BNGL and visualized. The attached paper about model
> >>>> visualization contains several examples.
> >>>>
> >>>> My question relates to the example shown in Fig S4 of the paper, the
> >>> complement
> >>>> cascade, which involved repeated protein cleavage at specific sites.
> In
> >>>> this example, the C3 molecule is cleaved to yield C3a and C3b. C3b is
> >>>> cleaved to yield iC3b, which is further cleaved to C3dg. C3dg is
> >> finally
> >>>> cleaved into C3d and C3g. My question is: How can SBML multi can be
> >> used
> >>> to
> >>>> represent molecular fragments, meaning the products of cleavage
> >>> reactions?
> >>> I generated the multi xml code corresponding to your sample model 1
> >>> which should demonstrate how multi can represent molecule fragments. It
> >>> is actually one of important features covered by multi.
> >>>> It seems that there are at least two ways that this could be
> >> represented
> >>> in
> >>>> a rule-based modeling language, and I'm attaching two BNGL files as
> >>>> illustration. In the first model, terminal fragments (C3d and C3g) are
> >>>> represented as molecules, and the larger precursor (C3dg) is
> >> represented
> >>> as
> >>>> a complex of these fragments. The bond is a covalent bond between two
> >>> amino
> >>>> acid residues.
> >>> Here is the multi code corresponding to the first model.
> >>>
> >>> <?xml version="1.0" encoding="UTF-8"?>
> >>> <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3"
> >>> version="1"
> >>>
> >>> xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
> >>> multi:required="true">
> >>>      <model name="complement simple 1">
> >>>         ...
> >>>         <multi:listOfSpeciesTypes>
> >>>            <multi:speciesType multi:id="st_K1001"
> >>> multi:isBindingSite="true" />
> >>>            <multi:speciesType multi:id="st_C3g"
> >> multi:isBindingSite="false">
> >>>               <multi:listOfSpeciesTypeInstances>
> >>>                  <multi:component multi:id="K1001"
> >>> multi:speciesType="st_K1001" multi:occur="1" />
> >>>               </multi:listOfSpeciesTypeInstances>
> >>>            </multi:speciesType>
> >>>            <multi:speciesType multi:id="st_H1002"
> >>> multi:isBindingSite="true" />
> >>>            <multi:speciesType multi:id="st_C3d"
> >> multi:isBindingSite="false">
> >>>               <multi:listOfSpeciesTypeInstances>
> >>>                  <multi:component multi:id="H1002"
> >>> multi:speciesType="st_H1002" multi:occur="1" />
> >>>               </multi:listOfSpeciesTypeInstances>
> >>>            </multi:speciesType>
> >>>            <multi:speciesType multi:id="st_C3dg"
> >>> multi:isBindingSite="false">
> >>>               <multi:listOfSpeciesTypeInstances>
> >>>                  <multi:component multi:id="C3g"
> >>> multi:speciesType="st_C3g" multi:occur="1" />
> >>>                  <multi:component multi:id="C3d"
> >>> multi:speciesType="st_C3d" multi:occur="1" />
> >>>               </multi:listOfSpeciesTypeInstances>
> >>>               <multi:listOfInSpeciesTypeBonds>
> >>>                  <multi:inSpeciesTypeBond multi:bindingSite1="K1001"
> >>>                     multi:bindingSite2="H1002" />
> >>>               </multi:listOfInSpeciesTypeBonds>
> >>>            </multi:speciesType>
> >>>         </multi:listOfSpeciesTypes>
> >>>         <listOfSpecies>
> >>>            <species id="C3g_free" name="C3g" multi:speciesType="st_C3g"
> >> ...>
> >>>               <multi:listOfOutwardBindingSites>
> >>>                  <multi:outwardBindingSite multi:component="K1001"
> >>> multi:bindingStatus="unbound" />
> >>>               </multi:listOfOutwardBindingSites>
> >>>            </species>
> >>>            <species id="C3d_free" multi:speciesType="st_C3d" ...>
> >>>               <multi:listOfOutwardBindingSites>
> >>>                  <multi:outwardBindingSite multi:component="H1002"
> >>> multi:bindingStatus="unbound" />
> >>>               </multi:listOfOutwardBindingSites>
> >>>            </species>
> >>>            <species id="C3dg" multi:speciesType="st_C3dg"
> >>> initialAmount="100" ... />
> >>>         </listOfSpecies>
> >>>         <listOfParameters>
> >>>            <parameter id="k" value="1" constant="true" />
> >>>         </listOfParameters>
> >>>         <listOfReactions>
> >>>            <reaction id="C3dg_cleavage" ...>
> >>>               <listOfReactants>
> >>>                  <speciesReference species="C3dg" ... />
> >>>               </listOfReactants>
> >>>               <listOfProducts>
> >>>                  <speciesReference species="C3g_free" ... />
> >>>                  <speciesReference species="C3d_free" ... />
> >>>               </listOfProducts>
> >>>               <kineticLaw>
> >>>                  <math xmlns="http://www.w3.org/1998/Math/MathML">
> >>>                     ...
> >>>                  </math>
> >>>               </kineticLaw>
> >>>            </reaction>
> >>>            ...
> >>>          </listOfReactions>
> >>>      </model>
> >>> </sbml>
> >>>
> >>>> In the second model, each molecule (C3dg, C3d, and C3g) is
> >>>> represented individually, and the cleavage reaction is represented as
> >>>> degradation of the precursor (C3dg) and synthesis of terminal
> fragments
> >>>> (C3d and C3g).
> >>> The SBML core should be able to cover the second model.
> >>>
> >>> <?xml version="1.0" encoding="UTF-8"?>
> >>> <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3"
> >>> version="1">
> >>>      <model name="complement simple 2">
> >>>         ...
> >>>         <listOfSpecies>
> >>>            <species id="C3g" ... />
> >>>            <species id="C3d" ... />
> >>>            <species id="C3dg" initialAmount="100" ... />
> >>>         </listOfSpecies>
> >>>         <listOfParameters>
> >>>            <parameter id="k" value="1" constant="true" />
> >>>         </listOfParameters>
> >>>         <listOfReactions>
> >>>            <reaction id="C3dg_cleavage" ...>
> >>>               <listOfReactants>
> >>>                  <speciesReference species="C3dg" ... />
> >>>               </listOfReactants>
> >>>               <listOfProducts>
> >>>                  <speciesReference species="C3g" ... />
> >>>                  <speciesReference species="C3d" ... />
> >>>               </listOfProducts>
> >>>               <kineticLaw>
> >>>                  <math xmlns="http://www.w3.org/1998/Math/MathML">
> >>>                     ...
> >>>                  </math>
> >>>               </kineticLaw>
> >>>            </reaction>
> >>>            ...
> >>>          </listOfReactions>
> >>>      </model>
> >>> </sbml>
> >>>> This is a simple example, but the full cascade (and other
> >>>> similar ones, like the caspase cascade) would include many instances
> >>>> fragments being generated and cleaved to yield additional fragments.
> >>>>
> >>>> It seems that the current SBML-multi documentation doesn't contain an
> >>> example
> >>>> like this. So is there currently a standardized way of representing
> >>>> fragments? Should each fragment be its own molecule? Is there a way of
> >>>> preserving information about the mechanism by which one fragment is
> >>> cleaved
> >>>> to yield another? Or, should only terminal fragments be represented as
> >>>> molecules, with precursor fragments represented as complexes?
> >>> Perhaps I did not completely get your question. The bionetgen and
> carbon
> >>> mapping examplesin the documentation should be sufficient to
> demonstrate
> >>> the features required by your sample models.
> >>>
> >>>> Thanks,
> >>>>
> >>>> Lily
> >>>>
> >>>>
> >>>>
> >>>
> >>
> ------------------------------------------------------------------------------
> >>>> DreamFactory - Open Source REST & JSON Services for HTML5 & Native
> Apps
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> >>
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> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Sbml-multi mailing list
> >>>> Sbm...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/sbml-multi
> >>>
> >>> --
> >>> ===============================
> >>> Fengkai Zhang, MD, MMath
> >>> Staff Scientist
> >>> Laboratory of Systems Biology, DIR, NIAID
> >>> 9000 Rockville Pike
> >>> Building 4, Room 137
> >>> MSC 0421
> >>> Bethesda MD 20892
> >>> Phone: 301.496.0985
> >>> Fax: 301.480.1660
> >>> NIAID, National Institutes of Health, DHHS
> >>>
> >>>
> >>>
> >>> "Disclaimer:
> >>>
> >>> The information in this e-mail and any of its attachments is
> confidential
> >>> and may contain sensitive information. It should not be used by anyone
> >> who
> >>> is not the original intended recipient. If you have received this
> e-mail
> >> in
> >>> error please inform the sender and delete it from your mailbox or any
> >> other
> >>> storage devices. National Institute of Allergy and Infectious Diseases
> >>> shall not accept liability for any statements made that are sender's
> own
> >>> and not expressly made on behalf of the NIAID by one of its
> >>> representatives. "
> >>>
> >>>
> >>>
> >>
> ------------------------------------------------------------------------------
> >>> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
> >>> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
> >>> Free app hosting. Or install the open source package on any LAMP
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> >>
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> >>> _______________________________________________
> >>> Sbml-multi mailing list
> >>> Sbm...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/sbml-multi
> >>>
> >>>
> >>>
> >>
> >>
> ------------------------------------------------------------------------------
> >> DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps
> >> OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
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> >
> ------------------------------------------------------------------------------
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> > Sbml-multi mailing list
> > Sbm...@li...
> > https://lists.sourceforge.net/lists/listinfo/sbml-multi
> >
>
> --
>
> =========================
> Fengkai Zhang, MD, MMath
> Staff Scientist
> Laboratory of Systems Biology, DIR, NIAID
> 9000 Rockville Pike
> Building 4, Room 137
> MSC 0421
> Bethesda MD 20892
> Phone: 301.496.0985
> Fax: 301.480.1660
> NIAID, National Institutes of Health, DHHS
>
>
> "Disclaimer:
>
> The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be
> used by anyone who is not the original intended recipient. If you have
> received this e-mail in error please inform the sender and delete it
> from your mailbox or any other storage devices. National Institute of
> Allergy and Infectious Diseases shall not accept liability for any
> statements made that are sender's own and not expressly made on behalf
> of the NIAID by one of its representatives. "
>
>
> ------------------------------------------------------------------------------
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[SED-ML-discuss] SED-ML Level 1 Version 2 - Release Candidate 2

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

Dear SED-ML Community, 

We are pleased to announce the availability of Release Candidate 2 of the
SED-ML Level 1 Version 2 Specification. It is available online from: 

http://tinyurl.com/sed-ml-l1v2-rc2

As compared to the previous RC, this version contains a touch up of the UML
diagrams, fixed a number of typos, as well as a clarification of the KISAO
section. We consider this version ready for release. Barring any major
objections, we plan to release this version On Dec 2nd. 

Thank you, 

Frank T. Bergmann,
on behalf of the SED-ML Editors:  Dagmar Waltemath, Jonathan Cooper, David
Nickerson and Nicolas Le Novère

Re: [SED-ML-discuss] Discussion on SED-ML future from COMBINE 2013

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

The slides are now up:  http://co.mbine.org/events/COMBINE_2013/agenda
in the 'SED-ML future' section.

-Lucian

On Tue, Oct 1, 2013 at 9:00 PM, David Nickerson
<dav...@gm...> wrote:
> Hi all,
>
> At the recent COMBINE meeting in Paris we had a session where we
> discussed some potential future features and requirements that may be
> needed in SED-ML to make it more able to encode the requirements of
> various user communities. Slides and video from the session will
> (soon) be available at: http://co.mbine.org/events/COMBINE_2013/agenda
>
> The latter part of the session looked into some issues raised by Chris
> Meyers and his experiences in evaluating SED-ML for use with the
> iBioSim tool (http://www.async.ece.utah.edu/iBioSim/). As Chris was
> unable to attend the session at COMBINE, and because these issues are
> likely of wider interest to the SED-ML community, I provide here a
> summary of the discussion from that session (my recollection, at
> least, please correct me if I get anything wrong!). Everything is, of
> course, open for discussion :)
>
>> About a year ago, we implemented support for importing SED-ML files into iBioSim.  More specifically, the subset of SED-ML that is used in the SBML test suite.  This worked reasonably well, and we then considered potentially using SED-ML to describe internally the information that we store about our simulations, but we ran into several snags and have abandoned this for now.  Note that my comments are at least a year old, so some of these items may have been addressed, and others may have been our own ignorance of how to use SED-ML.  Also, this is likely not a complete list and some things are very specific to iBioSim.  However, you may find some of the limitations useful to know about.  Here are the items that we could not describe in SED-ML without using custom annotations:
>>
>> 1) Our SBML models are often converted to new models at various levels of abstraction.  Describing this process of conversion would not be easy to express.  We need to be able to say though which abstraction we are using.  This is likely a custom annotation.
>>
>
> agreed, this is a custom annotation. It would be nice to see these
> kinds of annotations and how they are used in SED-ML to see if anyone
> else uses this sort of information when performing simulation
> experiments. I wonder if this is somewhat similar to the idea of
> having a template simulation experiment which can be applied to many
> different models, as long as there is some systematic manner by which
> to identify the required data from the model... if so, there may be
> some overlap with Jonathan's functional curation work and some of the
> extensions he has been using with SED-ML might be worth investigating
> to see if there is any common ground that could be standardised and
> exchanged?
>
>> 2) It would be nice to know a general class of analysis algorithm being used (i.e., ODE, monte carlo, markovian, FBA, etc.)  as well as the more specific type of analyzer used.  Ideally, this can be handled by KISAO, but the support for KISAO did not make this very easy to do.  This may have been fixed by now.
>>
>
> This should now be handled by KiSAO and libKiSAO
> (http://biomodels.net/kisao/libkisao.html). If not, feature requests
> (or code!) should be submitted there.
>
>> 3) Since we develop new simulation methodologies, we are often creating new ones.  This would require a lot of back in forth with KISAO which is not very appealing especially since we abandon or consolidate methods as time goes by.  Perhaps, it is good to have custom analysis method term with a string for the custom method.  We also have methods like produce GraphViz file or xHTML file, etc.  Are these analysis methods for KISAO?  Not so sure that custom with string is not better for those as well.  Or in those, maybe term for display model and then a custom field for type of display.
>>
>
> Everyone agreed that being able to have a custom simulation algorithm
> would be a useful feature. I have added a feature request to the
> SED-ML tracker for this
> (https://sourceforge.net/p/sed-ml/feature-requests/5/). It would be
> good to get feedback from the community on this issue.
>
>> 4) We also have several options for an analysis that there is no field for, such as whether runs should be generated or just statistics, whether to use number of steps or a print interval (also have a minimal print interval for non-uniform stepping).  We need to be able to specify both minimum and maximum allowed time steps, absolute error, random seed, and number of runs.  Some of these may be supported but I pretty sure they are not all supported.
>>
>
> Some of these are possible in SED-ML L1V2 using the simulation
> algorithm parameters now available in KiSAO (http://goo.gl/Bg8Pm1).
> These can be specified in the new <algorithmParameter> construct
> introduced in SED-ML L1V2. Others can be implemented making use of the
> new nested tasks and simulation classes that will also be available in
> SED-ML L1V2. Others, such as random seed, might need extensions to
> KiSAO or SED-ML to be completely supported. Similar features may also
> be supported by the post-processing of simulation results in the
> SED-ML data generators.
>
> In any case, if there are specific use-cases not supported by any of
> the above we are very keen to hear about them and see them in action.
>
>> 5) I mentioned that we have various model abstraction techniques, things like applying steady state approximations, etc.  There is no way to specify these and their corresponding parameters.
>>
>
> SED-ML L1V2 introduces the steady-state simulation class which might
> address some of your requirements here. It would be great to see if
> you could encode your other abstraction techniques in SED-ML, perhaps
> using the custom simulation algorithm mentioned above along with some
> custom algorithm parameters.
>
>> 6) We have means to modify parameters and initial values for simulation, but I was not enamored with the method for this in SED-ML.  I feel like something like replacements and deletions in comp may work better.
>>
>
> People involved in the COMBINE discussion agreed that it would not be
> a good idea to make use of SBML's comp package directly and that the
> current methods available in SED-ML worked sufficiently well to meet
> peoples needs. If you have specific examples where something closer to
> the comp constructs might be better, then it would be great to discuss
> them here.
>
>> 7) We have a visualization tool that allows us to play back a simulation on a schematic, so we need a way to associate colors gradients to values from the simulation.
>>
>> 8) The graphing support in SED-ML is lacking things like colors to use, shapes to use, whether the points should be connected or not, or the shapes should be visible or filled.  Also, how to scale the plots, whether to have a log axis, should the legend be visible.  How about using an x-axis other than time?  We also support histograms for some types of data like the probability of each type of constraint being violated, and I don't think there is support for that.
>>
>
> SED-ML provides a method to encode the application of a simulation
> algorithm to a model to produce some data, along with pre- and
> post-processing steps. It doesn't have any concept for the graphical
> representation of the data, other than the possibly badly named plot*,
> curve, and surface elements. People at COMBINE feel that this is a
> good scope for SED-ML and that we don't want to start getting in to
> describing the graphical rendering of the resultant data. The output
> classes currently available in SED-ML are aimed at producing the
> required data, rather than what to actually do with that data - other
> than the hints provided by the element names such as plotting a curve
> on a set of axes. During the meeting, Nicolas pointed out the Charts
> Ontology (http://data.lirmm.fr/ontologies/chart), which might be
> useful if we want to extend the output classes in SED-ML in future
> versions if the community agrees that this is something we do need to
> address.
>
> Things like an x-axis other than time, scaling of data, and log axes
> are already a part of SED-ML.
>
> Issues like producing the data for a histogram or other more detailed
> post-processing are likely beyond the scope of the current data
> generators in SED-ML. One way to address this is by being able to link
> the results from one simulation as the inputs to another simulation,
> which would allow arbitrary complexity in the post-processing inasmuch
> as the modelling language you use to encode the model supports it.
> Feature requests and proposals for extensions to SED-ML are always
> welcome :)
>
>> I should probably look at SED-ML again and re-evaluate, but last time it seemed like our SED-ML file would be more custom annotation than SED-ML file which is why we abandoned it.  I'm not sure which items above are common across tools, but it would be interesting to see if there is at least some commonality that can be weaved into SED-ML.
>>
>
> It would be great if iBioSim were to be able to export SED-ML,
> especially given that you support (or will support) a large number of
> the SBML L3 packages and will therefore provide a great test-case for
> the usefulness of SED-ML with a wide range of types of SBML models. If
> you, or anyone out there, have any further questions or points for
> discussion, I'm sure there are people on this list happy to help out
> where possible.
>
> Stay tuned for the release of SED-ML L1V2 :)
>
>
> Cheers,
> David.
>
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[SED-ML-discuss] Discussion on SED-ML future from COMBINE 2013

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

Hi all,

At the recent COMBINE meeting in Paris we had a session where we
discussed some potential future features and requirements that may be
needed in SED-ML to make it more able to encode the requirements of
various user communities. Slides and video from the session will
(soon) be available at: http://co.mbine.org/events/COMBINE_2013/agenda

The latter part of the session looked into some issues raised by Chris
Meyers and his experiences in evaluating SED-ML for use with the
iBioSim tool (http://www.async.ece.utah.edu/iBioSim/). As Chris was
unable to attend the session at COMBINE, and because these issues are
likely of wider interest to the SED-ML community, I provide here a
summary of the discussion from that session (my recollection, at
least, please correct me if I get anything wrong!). Everything is, of
course, open for discussion :)

> About a year ago, we implemented support for importing SED-ML files into iBioSim.  More specifically, the subset of SED-ML that is used in the SBML test suite.  This worked reasonably well, and we then considered potentially using SED-ML to describe internally the information that we store about our simulations, but we ran into several snags and have abandoned this for now.  Note that my comments are at least a year old, so some of these items may have been addressed, and others may have been our own ignorance of how to use SED-ML.  Also, this is likely not a complete list and some things are very specific to iBioSim.  However, you may find some of the limitations useful to know about.  Here are the items that we could not describe in SED-ML without using custom annotations:
>
> 1) Our SBML models are often converted to new models at various levels of abstraction.  Describing this process of conversion would not be easy to express.  We need to be able to say though which abstraction we are using.  This is likely a custom annotation.
>

agreed, this is a custom annotation. It would be nice to see these
kinds of annotations and how they are used in SED-ML to see if anyone
else uses this sort of information when performing simulation
experiments. I wonder if this is somewhat similar to the idea of
having a template simulation experiment which can be applied to many
different models, as long as there is some systematic manner by which
to identify the required data from the model... if so, there may be
some overlap with Jonathan's functional curation work and some of the
extensions he has been using with SED-ML might be worth investigating
to see if there is any common ground that could be standardised and
exchanged?

> 2) It would be nice to know a general class of analysis algorithm being used (i.e., ODE, monte carlo, markovian, FBA, etc.)  as well as the more specific type of analyzer used.  Ideally, this can be handled by KISAO, but the support for KISAO did not make this very easy to do.  This may have been fixed by now.
>

This should now be handled by KiSAO and libKiSAO
(http://biomodels.net/kisao/libkisao.html). If not, feature requests
(or code!) should be submitted there.

> 3) Since we develop new simulation methodologies, we are often creating new ones.  This would require a lot of back in forth with KISAO which is not very appealing especially since we abandon or consolidate methods as time goes by.  Perhaps, it is good to have custom analysis method term with a string for the custom method.  We also have methods like produce GraphViz file or xHTML file, etc.  Are these analysis methods for KISAO?  Not so sure that custom with string is not better for those as well.  Or in those, maybe term for display model and then a custom field for type of display.
>

Everyone agreed that being able to have a custom simulation algorithm
would be a useful feature. I have added a feature request to the
SED-ML tracker for this
(https://sourceforge.net/p/sed-ml/feature-requests/5/). It would be
good to get feedback from the community on this issue.

> 4) We also have several options for an analysis that there is no field for, such as whether runs should be generated or just statistics, whether to use number of steps or a print interval (also have a minimal print interval for non-uniform stepping).  We need to be able to specify both minimum and maximum allowed time steps, absolute error, random seed, and number of runs.  Some of these may be supported but I pretty sure they are not all supported.
>

Some of these are possible in SED-ML L1V2 using the simulation
algorithm parameters now available in KiSAO (http://goo.gl/Bg8Pm1).
These can be specified in the new <algorithmParameter> construct
introduced in SED-ML L1V2. Others can be implemented making use of the
new nested tasks and simulation classes that will also be available in
SED-ML L1V2. Others, such as random seed, might need extensions to
KiSAO or SED-ML to be completely supported. Similar features may also
be supported by the post-processing of simulation results in the
SED-ML data generators.

In any case, if there are specific use-cases not supported by any of
the above we are very keen to hear about them and see them in action.

> 5) I mentioned that we have various model abstraction techniques, things like applying steady state approximations, etc.  There is no way to specify these and their corresponding parameters.
>

SED-ML L1V2 introduces the steady-state simulation class which might
address some of your requirements here. It would be great to see if
you could encode your other abstraction techniques in SED-ML, perhaps
using the custom simulation algorithm mentioned above along with some
custom algorithm parameters.

> 6) We have means to modify parameters and initial values for simulation, but I was not enamored with the method for this in SED-ML.  I feel like something like replacements and deletions in comp may work better.
>

People involved in the COMBINE discussion agreed that it would not be
a good idea to make use of SBML's comp package directly and that the
current methods available in SED-ML worked sufficiently well to meet
peoples needs. If you have specific examples where something closer to
the comp constructs might be better, then it would be great to discuss
them here.

> 7) We have a visualization tool that allows us to play back a simulation on a schematic, so we need a way to associate colors gradients to values from the simulation.
>
> 8) The graphing support in SED-ML is lacking things like colors to use, shapes to use, whether the points should be connected or not, or the shapes should be visible or filled.  Also, how to scale the plots, whether to have a log axis, should the legend be visible.  How about using an x-axis other than time?  We also support histograms for some types of data like the probability of each type of constraint being violated, and I don't think there is support for that.
>

SED-ML provides a method to encode the application of a simulation
algorithm to a model to produce some data, along with pre- and
post-processing steps. It doesn't have any concept for the graphical
representation of the data, other than the possibly badly named plot*,
curve, and surface elements. People at COMBINE feel that this is a
good scope for SED-ML and that we don't want to start getting in to
describing the graphical rendering of the resultant data. The output
classes currently available in SED-ML are aimed at producing the
required data, rather than what to actually do with that data - other
than the hints provided by the element names such as plotting a curve
on a set of axes. During the meeting, Nicolas pointed out the Charts
Ontology (http://data.lirmm.fr/ontologies/chart), which might be
useful if we want to extend the output classes in SED-ML in future
versions if the community agrees that this is something we do need to
address.

Things like an x-axis other than time, scaling of data, and log axes
are already a part of SED-ML.

Issues like producing the data for a histogram or other more detailed
post-processing are likely beyond the scope of the current data
generators in SED-ML. One way to address this is by being able to link
the results from one simulation as the inputs to another simulation,
which would allow arbitrary complexity in the post-processing inasmuch
as the modelling language you use to encode the model supports it.
Feature requests and proposals for extensions to SED-ML are always
welcome :)

> I should probably look at SED-ML again and re-evaluate, but last time it seemed like our SED-ML file would be more custom annotation than SED-ML file which is why we abandoned it.  I'm not sure which items above are common across tools, but it would be interesting to see if there is at least some commonality that can be weaved into SED-ML.
>

It would be great if iBioSim were to be able to export SED-ML,
especially given that you support (or will support) a large number of
the SBML L3 packages and will therefore provide a great test-case for
the usefulness of SED-ML with a wide range of types of SBML models. If
you, or anyone out there, have any further questions or points for
discussion, I'm sure there are people on this list happy to help out
where possible.

Stay tuned for the release of SED-ML L1V2 :)


Cheers,
David.

[SED-ML-discuss] SED-ML Level 1 Version 2 - Release Candidate

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

Dear SED-ML Community, 

it is my pleasure today to announce that the first release candidate of SED-ML Level 1 Version 2 is now available online: 

http://tinyurl.com/sed-ml-l1v2-rc

It includes the RepeatedTask concept as agreed and voted upon late last year, as well as the algorithm parameter proposal. We would welcome your feedback. 

To help you in your evaluation, the SED-ML Web Tools[1] have been updated, so you could look at these files. An XML Schema[2] is available as well. 

Thank you, 

Frank T. Bergmann, 
on behalf of the SED-ML Editors:  Dagmar Waltemath, Jonathan Cooper, David Nickerson and Nicolas Le Novere

[1] http://sysbioapps.dyndns.org/SED-ML_Web_Tools
[2] http://tinyurl.com/sed-ml-l1v2-rc-schema

Re: [SED-ML-discuss] [sed-ml-editors] Discussion on the future of SED-ML

[Chris J. M. <my...@ec...>]

> 
> "things like colors to use, shapes to use, whether the points should be connected or not, or the shapes should be visible or filled"
> 
> This was voluntarily omitted from the initial version of SED-ML. We did not aim to precise how to visually present the results, but which result to present (which variable versus which variables etc.) The results can be presented as a graph, but also as a movie etc. The words "plot", "curve", "surface" etc. are extremely misleading. For instance the timecourse of a variable X can perfectly be represented by an animated cylinder which height changes over time.
> 
Would be nice though to have as optional attributes which perhaps a tool is allowed to ignore.  I would like to make SED-ML my simulation option storage mechanism but my excitement to actually execute this diminishes considerably if I must use a ton of custom annotations.

> "how to scale the plots, whether to have a log axis, should the legend be visible. "
> 
> As for the log axis, this is part of the current version.
> 
Great.

> "How about using an x-axis other than time? "
> 
> Same thing. You can report whatever variable Vs whatever variable. Curves are not necessarily timecourses.
> 
Great.

Chris

> Best regards
> 
> On 10/09/13 19:27, Chris J. Myers wrote:
>> Unfortunately, I will not arrive in Paris until after this session, so I will give you my feedback by email.  About a year ago, we implemented support for importing SED-ML files into iBioSim.  More specifically, the subset of SED-ML that is used in the SBML test suite.  This worked reasonably well, and we then considered potentially using SED-ML to describe internally the information that we store about our simulations, but we ran into several snags and have abandoned this for now.  Note that my comments are at least a year old, so some of these items may have been addressed, and others may have been our own ignorance of how to use SED-ML.  Also, this is likely not a complete list and some things are very specific to iBioSim.  However, you may find some of the limitations useful to know about.  Here are the items that we could not describe in SED-ML without using custom annotations:
>> 
>> 1) Our SBML models are often converted to new models at various levels of abstraction.  Describing this process of conversion would not be easy to express.  We need to be able to say though which abstraction we are using.  This is likely a custom annotation.
>> 
>> 2) It would be nice to know a general class of analysis algorithm being used (i.e., ODE, monte carlo, markovian, FBA, etc.)  as well as the more specific type of analyzer used.  Ideally, this can be handled by KISAO, but the support for KISAO did not make this very easy to do.  This may have been fixed by now.
>> 
>> 3) Since we develop new simulation methodologies, we are often creating new ones.  This would require a lot of back in forth with KISAO which is not very appealing especially since we abandon or consolidate methods as time goes by.  Perhaps, it is good to have custom analysis method term with a string for the custom method.  We also have methods like produce GraphViz file or xHTML file, etc.  Are these analysis methods for KISAO?  Not so sure that custom with string is not better for those as well.  Or in those, maybe term for display model and then a custom field for type of display.
>> 
>> 4) We also have several options for an analysis that there is no field for, such as whether runs should be generated or just statistics, whether to use number of steps or a print interval (also have a minimal print interval for non-uniform stepping).  We need to be able to specify both minimum and maximum allowed time steps, absolute error, random seed, and number of runs.  Some of these may be supported but I pretty sure they are not all supported.
>> 
>> 5) I mentioned that we have various model abstraction techniques, things like applying steady state approximations, etc.  There is no way to specify these and their corresponding parameters.
>> 
>> 6) We have means to modify parameters and initial values for simulation, but I was not enamored with the method for this in SED-ML.  I feel like something like replacements and deletions in comp may work better.
>> 
>> 7) We have a visualization tool that allows us to play back a simulation on a schematic, so we need a way to associate colors gradients to values from the simulation.
>> 
>> 8) The graphing support in SED-ML is lacking things like colors to use, shapes to use, whether the points should be connected or not, or the shapes should be visible or filled.  Also, how to scale the plots, whether to have a log axis, should the legend be visible.  How about using an x-axis other than time?  We also support histograms for some types of data like the probability of each type of constraint being violated, and I don't think there is support for that.
>> 
>> I should probably look at SED-ML again and re-evaluate, but last time it seemed like our SED-ML file would be more custom annotation than SED-ML file which is why we abandoned it.  I'm not sure which items above are common across tools, but it would be interesting to see if there is at least some commonality that can be weaved into SED-ML.
>> 
>> Cheers,
>> 
>> Chris
>> 
>> On Sep 5, 2013, at 5:04 PM, David Nickerson <dav...@gm...> wrote:
>> 
>>> Hi all,
>>> 
>>> At the upcoming COMBINE meeting, we have a session on Wednesday
>>> morning focussed on the future of SED-ML. The current focus of
>>> developing SED-ML is on the use of data and parameter estimation, each
>>> of which have their own session on Wednesday, but we would like to
>>> start getting feature requests together to plan how SED-ML will
>>> evolve.
>>> 
>>> Due to the wide ranging scope of activities under the COMBINE umbrella
>>> it is hard to know what features are important. Therefore we would
>>> like to invite you to briefly present any simulation experiments that
>>> you would like to see supported by SED-ML. For example, tasks that
>>> your simulation tool might be able to do now but can not be described
>>> in SED-ML; simulations based on models making use of the various SBML
>>> packages that are being developed (or even models in straight SBML);
>>> NeuroML models or simulators; etc.
>>> 
>>> In this manner we hope to start collecting feature requests that will
>>> help stimulate discussion on the directions SED-ML needs to evolve in
>>> order to best support the community. And don't worry if you are not
>>> familiar with SED-ML's current capabilities, by presenting your wishes
>>> for simulation experiment descriptions we will be able to give you an
>>> idea of whether they are features that can currently be encoded in
>>> SED-ML or will require new features.
>>> 
>>> Please let me know if you would like to present in this session or
>>> alternatively let me know any ideas or requirements you may have for
>>> the adoption of SED-ML for specific tasks that we could discuss during
>>> this session.
>>> 
>>> 
>>> Thanks,
>>> David, on behalf of the SED-ML editors.
>>> 
>>> 
>>> PS - you were chosen to receive this invitation because you are
>>> chairing a session on one of the standards (or SBML packages) that we
>>> would like to hear from or because you are known to be developing
>>> tools that do (or could) make use of SED-ML. Please let me know if
>>> there is anyone else attending COMBINE that you think would have
>>> something to contribute to this session.
>> 
>> 
>> ------------------------------------------------------------------------------
>> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
>> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
>> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
>> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/22/13.
>> http://pubads.g.doubleclick.net/gampad/clk?id=64545871&iu=/4140/ostg.clktrk
>> _______________________________________________
>> sed-ml-editors mailing list
>> sed...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-editors
>> 
> 
> 
> -- 
> 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/
> 
> 

Re: [SED-ML-discuss] [sed-ml-editors] Discussion on the future of SED-ML

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

Hi Chris

On point 8).

"things like colors to use, shapes to use, whether the points should be connected or not, or the shapes should be visible or filled"

This was voluntarily omitted from the initial version of SED-ML. We did not aim to precise how to visually present the results, but which result to present (which variable versus which variables etc.) The results can be presented as a graph, but also as a movie etc. The words "plot", "curve", "surface" etc. are extremely misleading. For instance the timecourse of a variable X can perfectly be represented by an animated cylinder which height changes over time.

"how to scale the plots, whether to have a log axis, should the legend be visible. "

As for the log axis, this is part of the current version.

"How about using an x-axis other than time? "

Same thing. You can report whatever variable Vs whatever variable. Curves are not necessarily timecourses.

Best regards

On 10/09/13 19:27, Chris J. Myers wrote:
> Unfortunately, I will not arrive in Paris until after this session, so I will give you my feedback by email.  About a year ago, we implemented support for importing SED-ML files into iBioSim.  More specifically, the subset of SED-ML that is used in the SBML test suite.  This worked reasonably well, and we then considered potentially using SED-ML to describe internally the information that we store about our simulations, but we ran into several snags and have abandoned this for now.  Note that my comments are at least a year old, so some of these items may have been addressed, and others may have been our own ignorance of how to use SED-ML.  Also, this is likely not a complete list and some things are very specific to iBioSim.  However, you may find some of the limitations useful to know about.  Here are the items that we could not describe in SED-ML without using custom annotations:
>
> 1) Our SBML models are often converted to new models at various levels of abstraction.  Describing this process of conversion would not be easy to express.  We need to be able to say though which abstraction we are using.  This is likely a custom annotation.
>
> 2) It would be nice to know a general class of analysis algorithm being used (i.e., ODE, monte carlo, markovian, FBA, etc.)  as well as the more specific type of analyzer used.  Ideally, this can be handled by KISAO, but the support for KISAO did not make this very easy to do.  This may have been fixed by now.
>
> 3) Since we develop new simulation methodologies, we are often creating new ones.  This would require a lot of back in forth with KISAO which is not very appealing especially since we abandon or consolidate methods as time goes by.  Perhaps, it is good to have custom analysis method term with a string for the custom method.  We also have methods like produce GraphViz file or xHTML file, etc.  Are these analysis methods for KISAO?  Not so sure that custom with string is not better for those as well.  Or in those, maybe term for display model and then a custom field for type of display.
>
> 4) We also have several options for an analysis that there is no field for, such as whether runs should be generated or just statistics, whether to use number of steps or a print interval (also have a minimal print interval for non-uniform stepping).  We need to be able to specify both minimum and maximum allowed time steps, absolute error, random seed, and number of runs.  Some of these may be supported but I pretty sure they are not all supported.
>
> 5) I mentioned that we have various model abstraction techniques, things like applying steady state approximations, etc.  There is no way to specify these and their corresponding parameters.
>
> 6) We have means to modify parameters and initial values for simulation, but I was not enamored with the method for this in SED-ML.  I feel like something like replacements and deletions in comp may work better.
>
> 7) We have a visualization tool that allows us to play back a simulation on a schematic, so we need a way to associate colors gradients to values from the simulation.
>
> 8) The graphing support in SED-ML is lacking things like colors to use, shapes to use, whether the points should be connected or not, or the shapes should be visible or filled.  Also, how to scale the plots, whether to have a log axis, should the legend be visible.  How about using an x-axis other than time?  We also support histograms for some types of data like the probability of each type of constraint being violated, and I don't think there is support for that.
>
> I should probably look at SED-ML again and re-evaluate, but last time it seemed like our SED-ML file would be more custom annotation than SED-ML file which is why we abandoned it.  I'm not sure which items above are common across tools, but it would be interesting to see if there is at least some commonality that can be weaved into SED-ML.
>
> Cheers,
>
> Chris
>
> On Sep 5, 2013, at 5:04 PM, David Nickerson <dav...@gm...> wrote:
>
>> Hi all,
>>
>> At the upcoming COMBINE meeting, we have a session on Wednesday
>> morning focussed on the future of SED-ML. The current focus of
>> developing SED-ML is on the use of data and parameter estimation, each
>> of which have their own session on Wednesday, but we would like to
>> start getting feature requests together to plan how SED-ML will
>> evolve.
>>
>> Due to the wide ranging scope of activities under the COMBINE umbrella
>> it is hard to know what features are important. Therefore we would
>> like to invite you to briefly present any simulation experiments that
>> you would like to see supported by SED-ML. For example, tasks that
>> your simulation tool might be able to do now but can not be described
>> in SED-ML; simulations based on models making use of the various SBML
>> packages that are being developed (or even models in straight SBML);
>> NeuroML models or simulators; etc.
>>
>> In this manner we hope to start collecting feature requests that will
>> help stimulate discussion on the directions SED-ML needs to evolve in
>> order to best support the community. And don't worry if you are not
>> familiar with SED-ML's current capabilities, by presenting your wishes
>> for simulation experiment descriptions we will be able to give you an
>> idea of whether they are features that can currently be encoded in
>> SED-ML or will require new features.
>>
>> Please let me know if you would like to present in this session or
>> alternatively let me know any ideas or requirements you may have for
>> the adoption of SED-ML for specific tasks that we could discuss during
>> this session.
>>
>>
>> Thanks,
>> David, on behalf of the SED-ML editors.
>>
>>
>> PS - you were chosen to receive this invitation because you are
>> chairing a session on one of the standards (or SBML packages) that we
>> would like to hear from or because you are known to be developing
>> tools that do (or could) make use of SED-ML. Please let me know if
>> there is anyone else attending COMBINE that you think would have
>> something to contribute to this session.
>
>
> ------------------------------------------------------------------------------
> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99!
> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint
> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes
> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/22/13.
> http://pubads.g.doubleclick.net/gampad/clk?id=64545871&iu=/4140/ostg.clktrk
> _______________________________________________
> sed-ml-editors mailing list
> sed...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-editors
>


-- 
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/

[SED-ML-discuss] COMBINE 2013

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

Hi all,

The programme for COMBINE this September in Paris is starting to fill
out: http://co.mbine.org/events/COMBINE_2013 and features some
interesting discussion sessions for SED-ML and its future development.

The registration deadline is fast approaching (9 September), so if you
intend to join us in Paris please register as soon as possible. You
are also encouraged to book your accommodation quickly as this will be
a very busy week in Paris and hotels are rapidly filling.


Cheers,
David.

[SED-ML-discuss] [Combine-announce] 4th annual COMBINE forum (COMBINE 2013)

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

######################################################################
#####            4th annual COMBINE forum (COMBINE 2013)         #####
#####            16-20 September, Institut Curie, Paris          #####
######################################################################

* Monday 16th September: Open symposium on modelling approaches in systems 
biology
* Tuesday 17th-Friday 20th September: Workshop on COMBINE standards
http://co.mbine.org/events/COMBINE_2013

The deadline to register for COMBINE 2013 is set to *Friday 9 September* 
2013. http://binom.curie.fr/combine2013

The "Computational Modeling in Biology" Network (COMBINE) is an initiative 
to coordinate the development of the various community standards and 
formats in systems biology and related fields. An important activity of 
COMBINE is to organise common meetings, where the developers of the 
different standards can meet and work together. The annual COMBINE forum is 
a workshop-style event with oral presentations, discussions, posters and 
breakout sessions. The meeting includes talks about the COMBINE standards 
and associated or related standardization efforts, as well as presentations 
of tools using these standards.

The first day of the meeting, Monday 16th September, will be dedicated to 
presentations of modelling approaches in biology either not currently 
covered by our efforts, or using them in new or innovative ways. Invited 
speakers are:
Michael Hucka, Caltech
Vincent Danos, CNRS, University Paris-Diderot, University of Edinburgh
Denis Thieffry, École Normale Supérieure
Andrei Zinovyev, Institut Curie
Andrew Davison, CNRS
Marc Lavielle, INRIA, University Paris-Sud
Benjamin Ribba, INRIA
Hiroaki Kitano, SBI, OIST
Dirk Drasdo, INRIA, University of Leipzig

In addition, short presentations will be selected from the submitted abstracts.

The remaining four meeting days, from Tuesday 17th to Friday 20th 
September, will include talks about the COMBINE standards and associated or 
related standardization efforts and discussion sessions. Main discussion 
themes will be "Mathematical Modelling", "Simulation and analysis", 
"Interoperability", "Visualization".

More information at http://co.mbine.org/events/COMBINE_2013 and 
registration at http://binom.curie.fr/combine2013

-- 
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] [Combine-announce] Registration to COMBINE 2013

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

Dear Colleagues,

We are about to announce the preliminary agenda for COMBINE 2013. The first 
day will be a scientific conference featuring an impressive line-up of 
speakers presenting different modelling approaches used in biology. From 
Tuesday 17 to Friday 20, we will have several rooms available for 
presentations, discussions, quiet hacking etc.

We will post the agenda of the main room soon. It will be refined as we go. 
It would be very useful for us to have an overview of who will attend. So 
please, register as soon as you are know you are coming.

http://binom.curie.fr/combine2013

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...
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[SED-ML-discuss] Fwd: [Combine-announce] COMBINE 2013 registration

[Dagmar W. <dag...@un...>]

Dear colleagues,

please note that the registration for COMBINE 2013 is now open (see link 
below).

The COMBINE meeting is the annual forum for discussions about standards 
related to modeling in biology. The first meeting day is dedicated to 
presentations of modelling approaches in biology (see the website for 
the list of invited speakers). The remaining four days include oral 
presentations about the COMBINE standards, posters, and breakout 
sessions for discussion and development.

The SED-ML editors look forward to meeting you in Paris in September 
this year, for discussions about recent SED-ML developments (e.g., 
nested tasks, encoding of parameter estimations); updates on the SED-ML 
specification, libraries and tools; and in particular future visions 
(more types of experiments that we want to cover, incorporation of links 
to data, cooperation with NuML etc).

You'll find detailed information about COMBINE 2013 on the following 
website: http://co.mbine.org/events/COMBINE_2013

Dagmar Waltemath,
on behalf of the editors.



-------- Original Message --------
Subject: 	[[cellml-discussion] ] [Combine-announce] COMBINE 2013 
registration
Date: 	Thu, 27 Jun 2013 14:21:13 +0100
From: 	Nicolas Le Novere <n.l...@gm...>
Reply-To: 	<cel...@li...>
To: 	<com...@mb...>



Dear colleagues,

The registration for COMBINE 2013 is now open. You can register at:
http://binom.curie.fr/combine2013/

More information about the meeting are added on a regular basis at:
http://co.mbine.org/events/COMBINE_2013

I am looking forward to see you in Paris!

-- 
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] [Combine-announce] COMBINE 2013 registration

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

Dear colleagues,

The registration for COMBINE 2013 is now open. You can register at:
http://binom.curie.fr/combine2013/

More information about the meeting are added on a regular basis at:
http://co.mbine.org/events/COMBINE_2013

I am looking forward to see you in Paris!

-- 
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/



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Com...@eb...
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[SED-ML-discuss] taskReference on variable and nested tasks

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

Hi all,

There is a problem with the current text of the L1V2 draft specification:

2.3.5.2 says that the taskReference attribute on Variable can only refer 
to Tasks (not AbstractTasks / RepeatedTasks). This is okay if you define 
a RepeatedTask with explicitly listed subtasks, because then the 
variables can refer directly to the tasks defined to be subtasks, but if 
you use the short hand notation by putting modelReference and 
simulationReference attributes directly on the RepeatedTask, there is 
now no Task for the variable to refer to.

One solution could be to allow the taskReference on a Variable to refer 
to a RepeatedTask, but only if the RepeatedTask has modelReference and 
simulationReference attributes. However, I think that the costs of the 
added complexity (both in terms of all the rules modellers need to 
remember about what is and isn't valid, and for implementers to deal 
with) from the short hand probably outweigh the benefits of slightly 
more succinct RepeatedTask definitions, so I would suggest simply 
getting rid of the short hand notation.

Best wishes,
Andrew

Re: [SED-ML-discuss] RepeatedTask questions

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

On Jun 4, 2013, at 8:32 PM, Frank Bergmann wrote:

> Hello Dan, 
> 
>> Hello all in SED-ML-discuss,
>> 
>> I have another question about RepeatedTasks, please: should it be possible to also iterate over Parameters? If yes, should we add a ListOfParameters field to FunctionalRange, just like ComputeChange has?
>> 
> 
> Indeed … you are correct … I shall change the spelling that indicates that the 'FunctionalRange' is not just similar to the ComputeChange class but does in fact inherit from it. Personally … I'm still not sure when I ever would want to use the listOfParameters … It seems less trouble to just encode the value … I shall update the spec accordingly … 

Looking over the spec, that inheritance would be almost what we want. However, only almost … (since the FunctionalRange has no 'target' and its math element is in a 'function' element. So direct inheritance does not work in that case. So it would seem that the thing to do is to add the listOfParameters, if that is what people feel is necessary. 

Thanks
Frank

Re: [SED-ML-discuss] RepeatedTask questions

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

Hello Dan, 

> Hello all in SED-ML-discuss,
> 
> I have another question about RepeatedTasks, please: should it be possible to also iterate over Parameters? If yes, should we add a ListOfParameters field to FunctionalRange, just like ComputeChange has?
> 

Indeed … you are correct … I shall change the spelling that indicates that the 'FunctionalRange' is not just similar to the ComputeChange class but does in fact inherit from it. Personally … I'm still not sure when I ever would want to use the listOfParameters … It seems less trouble to just encode the value … I shall update the spec accordingly … 

> Also, a second question: suppose that I wish to just replace the value of a variable with another value. I could simply create a ChangeAttribute object or I could use RepeatedTask to create a SetValue object and associate it with a VectorRange containing the new value.
> Which is the right way to go? The first option seems more elegant but from an implementation standpoint the second may actually be simpler because it avoids the need to discriminate between one vs. many values for each variable.
> 

There is a difference here … the ChangeAttribute, would only modify a model once. Once specified that model (with the updated parameter) will always be there for other tasks. Everything that you do with setValue, has a different scope, in that the change only applies for 1) the duration of the repeated task execution or 2) just one iteration of the repeated task. So it would depend on what you want to do. 

All the best
Frank


> Thank you,
> Dan Vasilescu
> CCAM / UCONN
> 
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[SED-ML-discuss] RepeatedTask questions

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

Hello all in SED-ML-discuss,

I have another question about RepeatedTasks, please: should it be possible to also iterate over Parameters? If yes, should we add a ListOfParameters field to FunctionalRange, just like ComputeChange has?

Also, a second question: suppose that I wish to just replace the value of a variable with another value. I could simply create a ChangeAttribute object or I could use RepeatedTask to create a SetValue object and associate it with a VectorRange containing the new value.
Which is the right way to go? The first option seems more elegant but from an implementation standpoint the second may actually be simpler because it avoids the need to discriminate between one vs. many values for each variable.

Thank you,
Dan Vasilescu
CCAM / UCONN

[SED-ML-discuss] Suggestion: Remove 'rough SED-ML workflow' from specification

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

Hi all,

I have a suggestion for improving the readability of the SED-ML 
specification: that the 'rough SED-ML workflow' shown in Figure 1.7 (in 
the latest version) and the next few figures showing a process diagram 
be removed; I don't think they are likely to be helpful to anyone, and 
they are a distraction that makes it harder to understand how SED-ML is 
actually defined.

The sequence shown is only one possible way someone might want to work. 
For example, according to the workflow file, someone building a SED-ML 
file needs to specify the models to use before they specify the 
simulation parameters, but this is completely arbitrary - someone might 
have a reason to specify the simulation parameters first.

SED-ML is supposed to be a specification for how to describe simulation 
experiments. It is not our place to stipulate what workflow is used to 
create those simulation experiment descriptions - and given an 
understanding of what needs to go in the description, it is trivial for 
most people to work out what workflow they need.

SED-ML should be usable for people using a range of different workflows, 
and trying to specify which one is only going to lead to confusion.

Best wishes,
Andrew