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

Re: [SED-ML-discuss] Id uniqueness in SED-ML files

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

seems sensible to me.

Cheers,
David.



On Thu, Jul 7, 2016 at 7:40 AM, Chris Myers <my...@ec...> wrote:
> In these cases, I would like to see a scheme where you refer to a child id through its parent id.  For example, if the parentId is p and the child is c, then refer to it as “p.c”.  Effectively, this is what I’m doing to try to make things unique by calling the child “p_c”.  The problem with this scheme is that “_” is a valid id character, so a person wanting to make my life difficult could create another object called “p_c”.  This necessitates a program to spend a lot of effort every time it creates an id to check it against all other ids rather than just relevant ones.  I believe, for example, with scoping, the reference scheme I just mentioned, and consideration of types in references, you can greatly simplify this.
>
> For example, one could restrict the ids of DataGenerators to be unique with respect to all other DataGenerators, but if you want to name a curve with the same Id, it should be okay, since you would never refer to a Curve in the same reference that refers to a DataGenerator.  Also, the id for the Variable in the DataGenerator, should be locally scoped to that DataGenerator, so if you want to give it the same Id as the Species and not worry about another DataGenerator trying to also refer to this same species using the same Variable Id.  If we ever need to refer to the Variable in a DG, then, you could do so with the “.” scheme I described above.
>
> The nice thing about this proposal is that at least the scoping of ids is that I think all that changes is validation.  At least for jlibSEDML, I seem to be able to create duplicate ids and use them with no problems, but I do get validation errors, if I check for them.
>
> Cheers,
>
> Chris
>
>> On Jul 6, 2016, at 7:24 AM, Frank T. Bergmann <fbe...@ca...> wrote:
>>
>> in 1.2 you are able to refer to ranges in variables by using the '#'
>> + range.id syntax. In the 1.3 proposal this is extended to also allow
>> refering to datasources / slices and of datagenerators. so care should
>> be taken in relaxing the requirements. But in principle I agree that
>> there are many places where a unique id is not necessary.
>>
>> cheers
>> Frank
>>
>> On Wed, Jul 6, 2016 at 7:58 AM, Chris Myers <my...@ec...> wrote:
>>> Actually, I think we could go even a step further than this.  In all cases where ids are referenced, the type of the object being referenced is clear, so as long as each list has uniqueIds, we should be fine.  I cannot think of any situation where the type of object is not known.  Each reference to another object by Id, it is clear the type of the referenced object, so the id only needs to be unique within that type.
>>>
>>> This would substantially simplify id creation and maintenance allowing for larger SED-ML files to be created without the worry of id clashes.
>>>
>>> Chris
>>>
>>>
>>>> On Jul 5, 2016, at 11:08 PM, Chris Myers <my...@ec...> wrote:
>>>>
>>>> HI,
>>>>
>>>> I’m finding it extremely difficult to maintain id uniqueness in a large SED-ML file.  I would strongly suggest that Variables, Curves, DataSets, and any other child with an Id be locally scoped.  As far as I can tell, there is no use of their id’s outside their parent object.  This would greatly simplify things, since it would allow me to check id uniqueness by just looking at the top-level classes ids.
>>>>
>>>> Is there any problem that I’m missing with this?
>>>>
>>>> Chris
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>>> present their vision of the future. This family event has something for
>>> everyone, including kids. Get more information and register today.
>>> http://sdm.link/attshape
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>> ------------------------------------------------------------------------------
>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>> present their vision of the future. This family event has something for
>> everyone, including kids. Get more information and register today.
>> http://sdm.link/attshape
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss



-- 


David Nickerson
about.me/david.nickerson

Re: [SED-ML-discuss] Id uniqueness in SED-ML files

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

In these cases, I would like to see a scheme where you refer to a child id through its parent id.  For example, if the parentId is p and the child is c, then refer to it as “p.c”.  Effectively, this is what I’m doing to try to make things unique by calling the child “p_c”.  The problem with this scheme is that “_” is a valid id character, so a person wanting to make my life difficult could create another object called “p_c”.  This necessitates a program to spend a lot of effort every time it creates an id to check it against all other ids rather than just relevant ones.  I believe, for example, with scoping, the reference scheme I just mentioned, and consideration of types in references, you can greatly simplify this.

For example, one could restrict the ids of DataGenerators to be unique with respect to all other DataGenerators, but if you want to name a curve with the same Id, it should be okay, since you would never refer to a Curve in the same reference that refers to a DataGenerator.  Also, the id for the Variable in the DataGenerator, should be locally scoped to that DataGenerator, so if you want to give it the same Id as the Species and not worry about another DataGenerator trying to also refer to this same species using the same Variable Id.  If we ever need to refer to the Variable in a DG, then, you could do so with the “.” scheme I described above.

The nice thing about this proposal is that at least the scoping of ids is that I think all that changes is validation.  At least for jlibSEDML, I seem to be able to create duplicate ids and use them with no problems, but I do get validation errors, if I check for them.

Cheers,

Chris

> On Jul 6, 2016, at 7:24 AM, Frank T. Bergmann <fbe...@ca...> wrote:
> 
> in 1.2 you are able to refer to ranges in variables by using the '#'
> + range.id syntax. In the 1.3 proposal this is extended to also allow
> refering to datasources / slices and of datagenerators. so care should
> be taken in relaxing the requirements. But in principle I agree that
> there are many places where a unique id is not necessary.
> 
> cheers
> Frank
> 
> On Wed, Jul 6, 2016 at 7:58 AM, Chris Myers <my...@ec...> wrote:
>> Actually, I think we could go even a step further than this.  In all cases where ids are referenced, the type of the object being referenced is clear, so as long as each list has uniqueIds, we should be fine.  I cannot think of any situation where the type of object is not known.  Each reference to another object by Id, it is clear the type of the referenced object, so the id only needs to be unique within that type.
>> 
>> This would substantially simplify id creation and maintenance allowing for larger SED-ML files to be created without the worry of id clashes.
>> 
>> Chris
>> 
>> 
>>> On Jul 5, 2016, at 11:08 PM, Chris Myers <my...@ec...> wrote:
>>> 
>>> HI,
>>> 
>>> I’m finding it extremely difficult to maintain id uniqueness in a large SED-ML file.  I would strongly suggest that Variables, Curves, DataSets, and any other child with an Id be locally scoped.  As far as I can tell, there is no use of their id’s outside their parent object.  This would greatly simplify things, since it would allow me to check id uniqueness by just looking at the top-level classes ids.
>>> 
>>> Is there any problem that I’m missing with this?
>>> 
>>> Chris
>>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>> present their vision of the future. This family event has something for
>> everyone, including kids. Get more information and register today.
>> http://sdm.link/attshape
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> ------------------------------------------------------------------------------
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Id uniqueness in SED-ML files

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

+1

On 06/07/2016 14:24, Frank T. Bergmann wrote:
> in 1.2 you are able to refer to ranges in variables by using the '#'
> + range.id syntax. In the 1.3 proposal this is extended to also allow
> refering to datasources / slices and of datagenerators. so care should
> be taken in relaxing the requirements. But in principle I agree that
> there are many places where a unique id is not necessary.
>
> cheers
> Frank
>
> On Wed, Jul 6, 2016 at 7:58 AM, Chris Myers <my...@ec...> wrote:
>> Actually, I think we could go even a step further than this.  In all cases where ids are referenced, the type of the object being referenced is clear, so as long as each list has uniqueIds, we should be fine.  I cannot think of any situation where the type of object is not known.  Each reference to another object by Id, it is clear the type of the referenced object, so the id only needs to be unique within that type.
>>
>> This would substantially simplify id creation and maintenance allowing for larger SED-ML files to be created without the worry of id clashes.
>>
>> Chris
>>
>>
>>> On Jul 5, 2016, at 11:08 PM, Chris Myers <my...@ec...> wrote:
>>>
>>> HI,
>>>
>>> I’m finding it extremely difficult to maintain id uniqueness in a large SED-ML file.  I would strongly suggest that Variables, Curves, DataSets, and any other child with an Id be locally scoped.  As far as I can tell, there is no use of their id’s outside their parent object.  This would greatly simplify things, since it would allow me to check id uniqueness by just looking at the top-level classes ids.
>>>
>>> Is there any problem that I’m missing with this?
>>>
>>> Chris
>>>
>>
>> ------------------------------------------------------------------------------
>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>> present their vision of the future. This family event has something for
>> everyone, including kids. Get more information and register today.
>> http://sdm.link/attshape
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> ------------------------------------------------------------------------------
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Id uniqueness in SED-ML files

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

in 1.2 you are able to refer to ranges in variables by using the '#'
+ range.id syntax. In the 1.3 proposal this is extended to also allow
refering to datasources / slices and of datagenerators. so care should
be taken in relaxing the requirements. But in principle I agree that
there are many places where a unique id is not necessary.

cheers
Frank

On Wed, Jul 6, 2016 at 7:58 AM, Chris Myers <my...@ec...> wrote:
> Actually, I think we could go even a step further than this.  In all cases where ids are referenced, the type of the object being referenced is clear, so as long as each list has uniqueIds, we should be fine.  I cannot think of any situation where the type of object is not known.  Each reference to another object by Id, it is clear the type of the referenced object, so the id only needs to be unique within that type.
>
> This would substantially simplify id creation and maintenance allowing for larger SED-ML files to be created without the worry of id clashes.
>
> Chris
>
>
>> On Jul 5, 2016, at 11:08 PM, Chris Myers <my...@ec...> wrote:
>>
>> HI,
>>
>> I’m finding it extremely difficult to maintain id uniqueness in a large SED-ML file.  I would strongly suggest that Variables, Curves, DataSets, and any other child with an Id be locally scoped.  As far as I can tell, there is no use of their id’s outside their parent object.  This would greatly simplify things, since it would allow me to check id uniqueness by just looking at the top-level classes ids.
>>
>> Is there any problem that I’m missing with this?
>>
>> Chris
>>
>
>
> ------------------------------------------------------------------------------
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] Id uniqueness in SED-ML files

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

HI,

I’m finding it extremely difficult to maintain id uniqueness in a large SED-ML file.  I would strongly suggest that Variables, Curves, DataSets, and any other child with an Id be locally scoped.  As far as I can tell, there is no use of their id’s outside their parent object.  This would greatly simplify things, since it would allow me to check id uniqueness by just looking at the top-level classes ids.

Is there any problem that I’m missing with this?

Chris

Re: [SED-ML-discuss] Id uniqueness in SED-ML files

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

Actually, I think we could go even a step further than this.  In all cases where ids are referenced, the type of the object being referenced is clear, so as long as each list has uniqueIds, we should be fine.  I cannot think of any situation where the type of object is not known.  Each reference to another object by Id, it is clear the type of the referenced object, so the id only needs to be unique within that type.

This would substantially simplify id creation and maintenance allowing for larger SED-ML files to be created without the worry of id clashes.

Chris


> On Jul 5, 2016, at 11:08 PM, Chris Myers <my...@ec...> wrote:
> 
> HI,
> 
> I’m finding it extremely difficult to maintain id uniqueness in a large SED-ML file.  I would strongly suggest that Variables, Curves, DataSets, and any other child with an Id be locally scoped.  As far as I can tell, there is no use of their id’s outside their parent object.  This would greatly simplify things, since it would allow me to check id uniqueness by just looking at the top-level classes ids.
> 
> Is there any problem that I’m missing with this?
> 
> Chris
> 

Re: [SED-ML-discuss] SED-ML discussions at COMBINE 2015

[Herbert S. <hs...@gm...>]

Useful document for those not at the meeting, thanks!

Herbert

On Wed, Jun 8, 2016 at 7:11 PM, David Nickerson <dav...@gm...>
wrote:

> Forgot to mention that we have been adding to this document here at
> HARMONY, so do take a look if you are interested.
>
> Cheers,
> David.
>
> On Wed, Jun 8, 2016 at 12:13 PM, David Nickerson
> <dav...@gm...> wrote:
> > Hi all,
> >
> > A reminder that the SED-ML discussion at COMBINE last year is
> > available here:
> >
> https://docs.google.com/document/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit
> >
> > Cheers,
> > David.
>
>
>
> --
>
>
> David Nickerson
> about.me/david.nickerson
>
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
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> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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> SED...@li...
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>

Re: [SED-ML-discuss] SED-ML discussions at COMBINE 2015

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

Forgot to mention that we have been adding to this document here at
HARMONY, so do take a look if you are interested.

Cheers,
David.

On Wed, Jun 8, 2016 at 12:13 PM, David Nickerson
<dav...@gm...> wrote:
> Hi all,
>
> A reminder that the SED-ML discussion at COMBINE last year is
> available here:
> https://docs.google.com/document/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit
>
> Cheers,
> David.



-- 


David Nickerson
about.me/david.nickerson

[SED-ML-discuss] SED-ML test suite

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

A reminder to contribute test cases:
https://github.com/luciansmith/sedml-test-suite/


-- 


David Nickerson
about.me/david.nickerson

[SED-ML-discuss] SED-ML discussions at COMBINE 2015

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

Hi all,

A reminder that the SED-ML discussion at COMBINE last year is
available here:
https://docs.google.com/document/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit

Cheers,
David.

[SED-ML-discuss] Fwd: COMBINE 2016: Newcastle upon Tyne, UK

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

Dear all,



COMBINE 2016 will be held in Newcastle upon Tyne (UK), 19-23 September 2016.



Please find below the Call for Abstracts - the submission deadline is 8
July.



Thanks and we look forward to seeing you in Newcastle!



Best,

Paolo Zuliani and Anil Wipat

COMBINE 2016 Organisers

School of Computing Science

Newcastle University, UK





%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

== Call for Abstracts ==





COMBINE 2016: 7th Computational Modeling in Biology Network Workshop



19-23 September 2016, Newcastle upon Tyne, UK



http://co.mbine.org/events/COMBINE_2016





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. COMBINE 2016 will be a workshop-style event with oral
presentations,

posters, and breakout sessions. The five meeting days will include talks
about the COMBINE

standards and associated or related standardization efforts, as well as
presentations

of tools using these standards. Oral presentations will be selected from
the submitted

abstracts. In addition, poster sessions will allow people to inform each
other about their

software and other projects in a setting that fosters interaction and
in-depth discussion.





== IMPORTANT DATES ==

Abstract submission:        8 July 2016

Scholarship application:    8 July 2016

Notification:              15 July 2016

COMBINE Workshop:  19-23 September 2016





== KEYNOTE SPEAKERS ==

- Alfonso Bueno-Orovio (Oxford)

- Carole Goble (Manchester)

- Michael Hucka (Caltech)

- Dagmar Iber (ETH Zurich)

- Andrew Millar (Edinburgh)

- Chris J. Myers (Utah)

- Yujiang Wang (Newcastle)





== TOPICS OF INTEREST ==

Topics include, but are not limited to:

- Data exchange and model standards for systems biology

- Graphical notation standards for systems biology

- Standards for sharing and analysing biological pathway data

- Standards for computational biological models

More on the COMBINE standards at http://co.mbine.org/standards





== CALL FOR ABSTRACTS ==

We solicit high-quality abstracts, to be refereed by the COMBINE
Coordinators below, for either

oral or poster presentation at the Workshop. Abstracts will appear on
the COMBINE website only,

there will be no formal publication.



Please see the COMBINE website for submission instructions.





== TRAVEL SCHOLARSHIPS ==

PhD students and postdocs may apply for travel funds to attend COMBINE.
More information

on the COMBINE website.





== ACKNOWLEDGEMENTS ==

COMBINE 2016 is generously supported by:

- Engineering and Physical Sciences Research Council (UK) [AUDACIOUS
project EP/J004111/2]

- Interdisciplinary Computing and Complex BioSystems Group (ICOS)

- School of Computing Science, Newcastle University

- National Science Foundation (USA)





== LOCAL ORGANISERS ==

Paolo Zuliani & Anil Wipat, ICOS Group, School of Computing Science,
Newcastle University.





== COMBINE COORDINATORS ==

Gary Bader (Toronto)

Martin Golebiewski (Heidelberg)

Michael Hucka (Caltech)

Nicolas Le Novère (Babraham)

Chris J. Myers (Utah)

David Nickerson (Auckland)

Falk Schreiber (Monash)

Dagmar Waltemath (Rostock)



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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[SED-ML-discuss] US-based student travel support for COMBINE 2016

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

We have received funds from the National Science Foundation to help support travel, lodging, and registration fees for COMBINE 2016 which will be held in Newcastle UK from September 19th to 23rd for US-based students and postdoctoral researchers, as well as, participants from underrepresented groups working on systems and synthetic biology standards. To be considered for this support, please fill out the form linked from the meeting website:

http://co.mbine.org/events/COMBINE_2016

Applications will be considered as they are received until funds are exhausted.  Therefore, please submit your application as soon as possible and certainly before July 1st.

Thanks,

Chris Myers

Re: [SED-ML-discuss] Examples

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

Hi Chris,

There are some examples that can be run on Frank's SED-ML Web Tools,
links at the bottom of the front page:
http://sysbioapps.dyndns.org/SED-ML_Web_Tools. I think there is some
overlap with the examples from the spec.

Cheers,
David.


On Thu, May 26, 2016 at 9:45 AM, Chris Myers <my...@ec...> wrote:
> Is there a place to find the examples at the end of the specification for Level 1 Version 2?  I can only find Level 1 Version 1 examples.
>
> Chris
>
>
> ------------------------------------------------------------------------------
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> _______________________________________________
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> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss



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[SED-ML-discuss] Examples

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

Is there a place to find the examples at the end of the specification for Level 1 Version 2?  I can only find Level 1 Version 1 examples.

Chris

Re: [SED-ML-discuss] Stochastic simulation questions

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

Sounds like a good topic for Harmony.  Glad you will be there.  I hoping to push our SED-ML support forward there.  Already improved it a bit over the weekend.

Chris

> On May 23, 2016, at 2:41 AM, Frank T. Bergmann <fbe...@ca...> wrote:
> 
> Indeed, ever since introducing the concept of datagenerators that
> would yield multi-dimensional datasets we talked about ways of slicing
> the data in retrospect. However, none of the constructs have made it
> into the language so far. Primarily for lack of implementations. The
> most recent suggestion was to use the same data slicing mechanism as
> introduced with the SED-ML data proposal.
> 
> cheers
> Frank
> 
> On Mon, May 23, 2016 at 9:54 AM, Matthias König
> <kon...@go...> wrote:
>> Hi Chris,
>> as far as I understand sedml none of these things is supported in sedml. You
>> can calculate mean and sd over one timecourse but not for multiple or a
>> repeated task.
>> Matthias
>> 
>> On May 22, 2016 7:20 PM, "Chris Myers" <my...@ec...> wrote:
>> 
>> I assume then if you want the output to come from the repeated task, that
>> the dataGenerator would point to the repeatedTask.  However, how would you
>> then say I want to generate data to graph for a particular species for the
>> 3rd stochastic run?  Also, how would you say generate data to graph of the
>> mean and/or standard deviation of a particular species over all runs?
>> 
>> Chris
>> 
>>> On May 22, 2016, at 4:38 AM, Frank T. Bergmann <fbe...@ca...>
>>> wrote:
>>> 
>>> This is exactly what I do, I look at the list of outputs I have to
>>> reproduce for the datagenerators used, and then schedule only those
>>> tasks that need to run in order to produce the required data.
>>> 
>>> Frank
>>> 
>>> On Sun, May 22, 2016 at 6:05 AM, Chris Myers <my...@ec...> wrote:
>>>> I see.  I’m still struggling a little bit to understand how to organize
>>>> the simulations.  I thought that I would perform an analysis for each Task,
>>>> but now I have a Task and a RepeatedTask in the ListOfTasks, but it is only
>>>> the RepeatedTask that I want to run.  Do I need to somehow to determine
>>>> which Tasks are independent and which are dependent tasks?  I guess you can
>>>> perhaps look at the DataGenerators, but this feels like an awkward way to
>>>> organize your analysis, since many DataGenerators may use the same Task.  Is
>>>> there some description somewhere of an a workflow for processing a SED-ML
>>>> file?
>>>> 
>>>> Thanks,
>>>> 
>>>> Chris
>>>> 
>>>>> On May 21, 2016, at 4:45 PM, Frank T. Bergmann <fbe...@ca...>
>>>>> wrote:
>>>>> 
>>>>> Indeed a repeated task would be the way to go ... just having a
>>>>> uniformrange going from 1 ...100 with a subtask running an SSA would
>>>>> be doing what you want.
>>>>> 
>>>>> Cheers
>>>>> Frank
>>>>> 
>>>>> On Sat, May 21, 2016 at 6:10 PM, Chris Myers <my...@ec...> wrote:
>>>>>> Hi,
>>>>>> 
>>>>>> I’m trying to specify the number of runs in a stochastic simulation.  I
>>>>>> could not find a kisao term for this, so I could create an
>>>>>> algorithmParameter.  Is there one?  If not, am I supposed to specify a
>>>>>> repeated task?  Could someone let me know how to say perform 100 SSA runs in
>>>>>> SED-ML?
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> Chris
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> ------------------------------------------------------------------------------
>>>>>> Mobile security can be enabling, not merely restricting. Employees who
>>>>>> bring their own devices (BYOD) to work are irked by the imposition of
>>>>>> MDM
>>>>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>>>>> apps on BYO-devices by containerizing them, leaving personal data
>>>>>> untouched!
>>>>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>>>>> _______________________________________________
>>>>>> SED-ML-discuss mailing list
>>>>>> SED...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>> 
>>>>> 
>>>>> ------------------------------------------------------------------------------
>>>>> Mobile security can be enabling, not merely restricting. Employees who
>>>>> bring their own devices (BYOD) to work are irked by the imposition of
>>>>> MDM
>>>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>>>> apps on BYO-devices by containerizing them, leaving personal data
>>>>> untouched!
>>>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>>>> _______________________________________________
>>>>> SED-ML-discuss mailing list
>>>>> SED...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>> 
>>>> 
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Mobile security can be enabling, not merely restricting. Employees who
>>>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>>> apps on BYO-devices by containerizing them, leaving personal data
>>>> untouched!
>>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Mobile security can be enabling, not merely restricting. Employees who
>>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>> apps on BYO-devices by containerizing them, leaving personal data
>>> untouched!
>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> 
>> 
>> ------------------------------------------------------------------------------
>> Mobile security can be enabling, not merely restricting. Employees who
>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>> restrictions. Mobile Device Manager Plus allows you to control only the
>> apps on BYO-devices by containerizing them, leaving personal data untouched!
>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> 
>> 
>> ------------------------------------------------------------------------------
>> Mobile security can be enabling, not merely restricting. Employees who
>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>> restrictions. Mobile Device Manager Plus allows you to control only the
>> apps on BYO-devices by containerizing them, leaving personal data untouched!
>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> 
> 
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Stochastic simulation questions

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

Indeed, ever since introducing the concept of datagenerators that
would yield multi-dimensional datasets we talked about ways of slicing
the data in retrospect. However, none of the constructs have made it
into the language so far. Primarily for lack of implementations. The
most recent suggestion was to use the same data slicing mechanism as
introduced with the SED-ML data proposal.

cheers
Frank

On Mon, May 23, 2016 at 9:54 AM, Matthias König
<kon...@go...> wrote:
> Hi Chris,
> as far as I understand sedml none of these things is supported in sedml. You
> can calculate mean and sd over one timecourse but not for multiple or a
> repeated task.
> Matthias
>
> On May 22, 2016 7:20 PM, "Chris Myers" <my...@ec...> wrote:
>
> I assume then if you want the output to come from the repeated task, that
> the dataGenerator would point to the repeatedTask.  However, how would you
> then say I want to generate data to graph for a particular species for the
> 3rd stochastic run?  Also, how would you say generate data to graph of the
> mean and/or standard deviation of a particular species over all runs?
>
> Chris
>
>> On May 22, 2016, at 4:38 AM, Frank T. Bergmann <fbe...@ca...>
>> wrote:
>>
>> This is exactly what I do, I look at the list of outputs I have to
>> reproduce for the datagenerators used, and then schedule only those
>> tasks that need to run in order to produce the required data.
>>
>> Frank
>>
>> On Sun, May 22, 2016 at 6:05 AM, Chris Myers <my...@ec...> wrote:
>>> I see.  I’m still struggling a little bit to understand how to organize
>>> the simulations.  I thought that I would perform an analysis for each Task,
>>> but now I have a Task and a RepeatedTask in the ListOfTasks, but it is only
>>> the RepeatedTask that I want to run.  Do I need to somehow to determine
>>> which Tasks are independent and which are dependent tasks?  I guess you can
>>> perhaps look at the DataGenerators, but this feels like an awkward way to
>>> organize your analysis, since many DataGenerators may use the same Task.  Is
>>> there some description somewhere of an a workflow for processing a SED-ML
>>> file?
>>>
>>> Thanks,
>>>
>>> Chris
>>>
>>>> On May 21, 2016, at 4:45 PM, Frank T. Bergmann <fbe...@ca...>
>>>> wrote:
>>>>
>>>> Indeed a repeated task would be the way to go ... just having a
>>>> uniformrange going from 1 ...100 with a subtask running an SSA would
>>>> be doing what you want.
>>>>
>>>> Cheers
>>>> Frank
>>>>
>>>> On Sat, May 21, 2016 at 6:10 PM, Chris Myers <my...@ec...> wrote:
>>>>> Hi,
>>>>>
>>>>> I’m trying to specify the number of runs in a stochastic simulation.  I
>>>>> could not find a kisao term for this, so I could create an
>>>>> algorithmParameter.  Is there one?  If not, am I supposed to specify a
>>>>> repeated task?  Could someone let me know how to say perform 100 SSA runs in
>>>>> SED-ML?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Chris
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Mobile security can be enabling, not merely restricting. Employees who
>>>>> bring their own devices (BYOD) to work are irked by the imposition of
>>>>> MDM
>>>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>>>> apps on BYO-devices by containerizing them, leaving personal data
>>>>> untouched!
>>>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>>>> _______________________________________________
>>>>> SED-ML-discuss mailing list
>>>>> SED...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Mobile security can be enabling, not merely restricting. Employees who
>>>> bring their own devices (BYOD) to work are irked by the imposition of
>>>> MDM
>>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>>> apps on BYO-devices by containerizing them, leaving personal data
>>>> untouched!
>>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Mobile security can be enabling, not merely restricting. Employees who
>>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>> apps on BYO-devices by containerizing them, leaving personal data
>>> untouched!
>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>> ------------------------------------------------------------------------------
>> Mobile security can be enabling, not merely restricting. Employees who
>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>> restrictions. Mobile Device Manager Plus allows you to control only the
>> apps on BYO-devices by containerizing them, leaving personal data
>> untouched!
>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

Re: [SED-ML-discuss] Stochastic simulation questions

[Matthias K. <kon...@go...>]

Hi Chris,
as far as I understand sedml none of these things is supported in sedml.
You can calculate mean and sd over one timecourse but not for multiple or a
repeated task.
Matthias
On May 22, 2016 7:20 PM, "Chris Myers" <my...@ec...> wrote:

I assume then if you want the output to come from the repeated task, that
the dataGenerator would point to the repeatedTask.  However, how would you
then say I want to generate data to graph for a particular species for the
3rd stochastic run?  Also, how would you say generate data to graph of the
mean and/or standard deviation of a particular species over all runs?

Chris

> On May 22, 2016, at 4:38 AM, Frank T. Bergmann <fbe...@ca...>
wrote:
>
> This is exactly what I do, I look at the list of outputs I have to
> reproduce for the datagenerators used, and then schedule only those
> tasks that need to run in order to produce the required data.
>
> Frank
>
> On Sun, May 22, 2016 at 6:05 AM, Chris Myers <my...@ec...> wrote:
>> I see.  I’m still struggling a little bit to understand how to organize
the simulations.  I thought that I would perform an analysis for each Task,
but now I have a Task and a RepeatedTask in the ListOfTasks, but it is only
the RepeatedTask that I want to run.  Do I need to somehow to determine
which Tasks are independent and which are dependent tasks?  I guess you can
perhaps look at the DataGenerators, but this feels like an awkward way to
organize your analysis, since many DataGenerators may use the same Task.
Is there some description somewhere of an a workflow for processing a
SED-ML file?
>>
>> Thanks,
>>
>> Chris
>>
>>> On May 21, 2016, at 4:45 PM, Frank T. Bergmann <fbe...@ca...>
wrote:
>>>
>>> Indeed a repeated task would be the way to go ... just having a
>>> uniformrange going from 1 ...100 with a subtask running an SSA would
>>> be doing what you want.
>>>
>>> Cheers
>>> Frank
>>>
>>> On Sat, May 21, 2016 at 6:10 PM, Chris Myers <my...@ec...> wrote:
>>>> Hi,
>>>>
>>>> I’m trying to specify the number of runs in a stochastic simulation.
I could not find a kisao term for this, so I could create an
algorithmParameter.  Is there one?  If not, am I supposed to specify a
repeated task?  Could someone let me know how to say perform 100 SSA runs
in SED-ML?
>>>>
>>>> Thanks,
>>>>
>>>> Chris
>>>>
>>>>
>>>>
------------------------------------------------------------------------------
>>>> Mobile security can be enabling, not merely restricting. Employees who
>>>> bring their own devices (BYOD) to work are irked by the imposition of
MDM
>>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>>> apps on BYO-devices by containerizing them, leaving personal data
untouched!
>>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
------------------------------------------------------------------------------
>>> Mobile security can be enabling, not merely restricting. Employees who
>>> bring their own devices (BYOD) to work are irked by the imposition of
MDM
>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>> apps on BYO-devices by containerizing them, leaving personal data
untouched!
>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>>
------------------------------------------------------------------------------
>> Mobile security can be enabling, not merely restricting. Employees who
>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>> restrictions. Mobile Device Manager Plus allows you to control only the
>> apps on BYO-devices by containerizing them, leaving personal data
untouched!
>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss


------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
SED-ML-discuss mailing list
SED...@li...
https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] HARMONY 2016 Registration

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

Hi all,

HARMONY 2016 is rapidly approaching: June 7-11 in Auckland, New
Zealand, http://www.co.mbine.org/events/HARMONY_2016.

To help with planning, it would be great if everyone planning on
attending could register by this Friday, May 27. That will help us get
some preliminary numbers settled for the catering, meeting room
allocations, etc.

Registration information is available at:
http://www.co.mbine.org/events/HARMONY_2016#Registration.


Cheers,
David and the organisation team.

[SED-ML-discuss] Stochastic simulation questions

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

I assume then if you want the output to come from the repeated task, that the dataGenerator would point to the repeatedTask.  However, how would you then say I want to generate data to graph for a particular species for the 3rd stochastic run?  Also, how would you say generate data to graph of the mean and/or standard deviation of a particular species over all runs?

Chris

> On May 22, 2016, at 4:38 AM, Frank T. Bergmann <fbe...@ca...> wrote:
> 
> This is exactly what I do, I look at the list of outputs I have to
> reproduce for the datagenerators used, and then schedule only those
> tasks that need to run in order to produce the required data.
> 
> Frank
> 
> On Sun, May 22, 2016 at 6:05 AM, Chris Myers <my...@ec...> wrote:
>> I see.  I’m still struggling a little bit to understand how to organize the simulations.  I thought that I would perform an analysis for each Task, but now I have a Task and a RepeatedTask in the ListOfTasks, but it is only the RepeatedTask that I want to run.  Do I need to somehow to determine which Tasks are independent and which are dependent tasks?  I guess you can perhaps look at the DataGenerators, but this feels like an awkward way to organize your analysis, since many DataGenerators may use the same Task.  Is there some description somewhere of an a workflow for processing a SED-ML file?
>> 
>> Thanks,
>> 
>> Chris
>> 
>>> On May 21, 2016, at 4:45 PM, Frank T. Bergmann <fbe...@ca...> wrote:
>>> 
>>> Indeed a repeated task would be the way to go ... just having a
>>> uniformrange going from 1 ...100 with a subtask running an SSA would
>>> be doing what you want.
>>> 
>>> Cheers
>>> Frank
>>> 
>>> On Sat, May 21, 2016 at 6:10 PM, Chris Myers <my...@ec...> wrote:
>>>> Hi,
>>>> 
>>>> I’m trying to specify the number of runs in a stochastic simulation.  I could not find a kisao term for this, so I could create an algorithmParameter.  Is there one?  If not, am I supposed to specify a repeated task?  Could someone let me know how to say perform 100 SSA runs in SED-ML?
>>>> 
>>>> Thanks,
>>>> 
>>>> Chris
>>>> 
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Mobile security can be enabling, not merely restricting. Employees who
>>>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>>> apps on BYO-devices by containerizing them, leaving personal data untouched!
>>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>> 
>>> ------------------------------------------------------------------------------
>>> Mobile security can be enabling, not merely restricting. Employees who
>>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>> apps on BYO-devices by containerizing them, leaving personal data untouched!
>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> 
>> 
>> ------------------------------------------------------------------------------
>> Mobile security can be enabling, not merely restricting. Employees who
>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>> restrictions. Mobile Device Manager Plus allows you to control only the
>> apps on BYO-devices by containerizing them, leaving personal data untouched!
>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Number of runs in a stochastic simulation

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

This is exactly what I do, I look at the list of outputs I have to
reproduce for the datagenerators used, and then schedule only those
tasks that need to run in order to produce the required data.

Frank

On Sun, May 22, 2016 at 6:05 AM, Chris Myers <my...@ec...> wrote:
> I see.  I’m still struggling a little bit to understand how to organize the simulations.  I thought that I would perform an analysis for each Task, but now I have a Task and a RepeatedTask in the ListOfTasks, but it is only the RepeatedTask that I want to run.  Do I need to somehow to determine which Tasks are independent and which are dependent tasks?  I guess you can perhaps look at the DataGenerators, but this feels like an awkward way to organize your analysis, since many DataGenerators may use the same Task.  Is there some description somewhere of an a workflow for processing a SED-ML file?
>
> Thanks,
>
> Chris
>
>> On May 21, 2016, at 4:45 PM, Frank T. Bergmann <fbe...@ca...> wrote:
>>
>> Indeed a repeated task would be the way to go ... just having a
>> uniformrange going from 1 ...100 with a subtask running an SSA would
>> be doing what you want.
>>
>> Cheers
>> Frank
>>
>> On Sat, May 21, 2016 at 6:10 PM, Chris Myers <my...@ec...> wrote:
>>> Hi,
>>>
>>> I’m trying to specify the number of runs in a stochastic simulation.  I could not find a kisao term for this, so I could create an algorithmParameter.  Is there one?  If not, am I supposed to specify a repeated task?  Could someone let me know how to say perform 100 SSA runs in SED-ML?
>>>
>>> Thanks,
>>>
>>> Chris
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Mobile security can be enabling, not merely restricting. Employees who
>>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>> apps on BYO-devices by containerizing them, leaving personal data untouched!
>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>> ------------------------------------------------------------------------------
>> Mobile security can be enabling, not merely restricting. Employees who
>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>> restrictions. Mobile Device Manager Plus allows you to control only the
>> apps on BYO-devices by containerizing them, leaving personal data untouched!
>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Number of runs in a stochastic simulation

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

I see.  I’m still struggling a little bit to understand how to organize the simulations.  I thought that I would perform an analysis for each Task, but now I have a Task and a RepeatedTask in the ListOfTasks, but it is only the RepeatedTask that I want to run.  Do I need to somehow to determine which Tasks are independent and which are dependent tasks?  I guess you can perhaps look at the DataGenerators, but this feels like an awkward way to organize your analysis, since many DataGenerators may use the same Task.  Is there some description somewhere of an a workflow for processing a SED-ML file?

Thanks,

Chris

> On May 21, 2016, at 4:45 PM, Frank T. Bergmann <fbe...@ca...> wrote:
> 
> Indeed a repeated task would be the way to go ... just having a
> uniformrange going from 1 ...100 with a subtask running an SSA would
> be doing what you want.
> 
> Cheers
> Frank
> 
> On Sat, May 21, 2016 at 6:10 PM, Chris Myers <my...@ec...> wrote:
>> Hi,
>> 
>> I’m trying to specify the number of runs in a stochastic simulation.  I could not find a kisao term for this, so I could create an algorithmParameter.  Is there one?  If not, am I supposed to specify a repeated task?  Could someone let me know how to say perform 100 SSA runs in SED-ML?
>> 
>> Thanks,
>> 
>> Chris
>> 
>> 
>> ------------------------------------------------------------------------------
>> Mobile security can be enabling, not merely restricting. Employees who
>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>> restrictions. Mobile Device Manager Plus allows you to control only the
>> apps on BYO-devices by containerizing them, leaving personal data untouched!
>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Number of runs in a stochastic simulation

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

Indeed a repeated task would be the way to go ... just having a
uniformrange going from 1 ...100 with a subtask running an SSA would
be doing what you want.

Cheers
Frank

On Sat, May 21, 2016 at 6:10 PM, Chris Myers <my...@ec...> wrote:
> Hi,
>
> I’m trying to specify the number of runs in a stochastic simulation.  I could not find a kisao term for this, so I could create an algorithmParameter.  Is there one?  If not, am I supposed to specify a repeated task?  Could someone let me know how to say perform 100 SSA runs in SED-ML?
>
> Thanks,
>
> Chris
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] Number of runs in a stochastic simulation

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

Hi,

I’m trying to specify the number of runs in a stochastic simulation.  I could not find a kisao term for this, so I could create an algorithmParameter.  Is there one?  If not, am I supposed to specify a repeated task?  Could someone let me know how to say perform 100 SSA runs in SED-ML?

Thanks,

Chris

Re: [SED-ML-discuss] Soliciting ideas for HARMONY topics

[Herbert S. <hs...@gm...>]

I won't be at harmony and I think we are one of the few to have relatively
good support for SEDML. Could the workshop discuss the topics that were
raised at combine in Utah? Where are we in that regard?

Herbert

On Fri, Apr 1, 2016 at 5:08 AM, Brett G. Olivier <bre...@gm...>
wrote:

> Hi all
>
> I'd like to work on SED-ML support for constraint-based optimization, (FBA
> etc). Frank has starting doing some cool stuff with this and I'd like to
> formalize it (if necessary extend it) and try get a working implementation.
>
> Cheers
> Brett
>
> On Fri, Apr 1, 2016 at 1:38 PM, Dagmar Waltemath <
> dag...@un...> wrote:
>
>> Dear all,
>>
>> is anyone of you planning to attend HARMONY this year *and* interested
>> in a discussion of the proposal to extend SED-ML to cover SBML Qual
>> models?
>>
>> https://dx.doi.org/10.6084/m9.figshare.2075143.v1
>>
>> Do you have any other suggestions what to work on during HARMONY wrt
>> SED-ML?
>>
>> Dagmar
>>
>>
>>
>> On 03/20/2016 11:29 PM, David Nickerson wrote:
>> > Hi all,
>> >
>> > HARMONY 2016 is coming up (and registration is open:
>> > http://co.mbine.org/events/HARMONY_2016) and we are starting to
>> > collect topics for possible SED-ML related breakouts/sessions during
>> > the meeting.
>> >
>> > If you have any ideas for topics or burning issues that you would like
>> > to discuss, please let me know or raise them in on this list.
>> >
>> >
>> > Cheers,
>> > David.
>> >
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Transform Data into Opportunity.
>> Accelerate data analysis in your applications with
>> Intel Data Analytics Acceleration Library.
>> Click to learn more.
>> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>
>
> --
> "La vita è troppo breve per bere vino cattivo".
>
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>

Re: [SED-ML-discuss] Soliciting ideas for HARMONY topics

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

Hi all

I'd like to work on SED-ML support for constraint-based optimization, (FBA
etc). Frank has starting doing some cool stuff with this and I'd like to
formalize it (if necessary extend it) and try get a working implementation.

Cheers
Brett

On Fri, Apr 1, 2016 at 1:38 PM, Dagmar Waltemath <
dag...@un...> wrote:

> Dear all,
>
> is anyone of you planning to attend HARMONY this year *and* interested
> in a discussion of the proposal to extend SED-ML to cover SBML Qual models?
>
> https://dx.doi.org/10.6084/m9.figshare.2075143.v1
>
> Do you have any other suggestions what to work on during HARMONY wrt
> SED-ML?
>
> Dagmar
>
>
>
> On 03/20/2016 11:29 PM, David Nickerson wrote:
> > Hi all,
> >
> > HARMONY 2016 is coming up (and registration is open:
> > http://co.mbine.org/events/HARMONY_2016) and we are starting to
> > collect topics for possible SED-ML related breakouts/sessions during
> > the meeting.
> >
> > If you have any ideas for topics or burning issues that you would like
> > to discuss, please let me know or raise them in on this list.
> >
> >
> > Cheers,
> > David.
> >
>
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>


-- 
"La vita è troppo breve per bere vino cattivo".