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

[SED-ML-discuss] How to interpret ComputeChange & FunctionalRange & curves of repeatedTask in L1V2

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

Hi all,

I am currently implementing SEDML support for tellurium and a few things in
the SEDML specification are unclear for me.

[1] ComputeChange

The specification says: "The ComputeChange class permits to change the
numerical value of any element or attribute of a model based on a
calculation."
For me it is completely unclear when this calculation is performed.
Depending on the time of the actual evaluation different numerical values
are set in the model. After discussion with Lucian I understood the
ComputeChange as an InitialAssignmentRule in SBML.
But what happens if later model changes (of derived models) change the
variables used in the ComputeChange?

Here an example:
It is not clear what should happen if for instance later model versions
change variables which are used in the calculation of the computeChange,
i.e. something like
model1 = model "test"
model2 = model model1 with S1=0.3, S2=S1+4
model3 = model model2 with S1=10
What is the value of S2 in model 3?
If S2=S1+4 was impmented via an InitialAssignment than init(S2) in model3
is 14 instead of 4.3 (which was the computeChange set in model2). In my
understanding model3 should have an S2=4.3, because the computeChange
should be calculated based on the state of model2.
So what is the correct interpretation (S2=14 or S2=4.3 in model3).
It has to be clearly stated when the calculation of the ComputeChange has
to be performed (within every model or after all changes to all models)?

[2] FunctionalRange
Similar issue here. When is the computation of the functional range
performed? For instance in a repeatedTask where with every repeat values of
variables used in the calculation of the functional range change.
Is the complete functional range calculated
- at the beginning of the loop with the initial model state before any
repeat
- or with the actual variables of the model at the beginning of every
iteration of the loop (which could change with reset=false)
Both variants would give very differnent numerical values for the range.

[3] logX/logY/logZ on curves
Why are the logX,Y,Z not on the Plot, but on the curves?
What should be done if multiple curves have contradicting log settings in a
plot? I.e. two curves which have the same xDataReference but different log
settings.

<plot2D id="plot_0" name="Example plot">
  <listOfCurves>
    <curve logX="false" logY="false" xDataReference="plot_0_0_0"
yDataReference="plot_0_0_1"/>
    <curve logX="true" logY="false" xDataReference="plot_0_0_0"
yDataReference="plot_0_1_1"/>
  </listOfCurves>

[4] How to plot curves of repeatedTasks?
I could not really find any information on how to plot curves of
repeatedTasks. I interpreted it as following:
- when reset=True plot every repeat as a single curve in the plot (i.e.
Nrep lines per curve)
- when reset=False concatenate the repeats and plot one line (the repeats
are time slices of the complete simulation)
Is this correct?
And how would I encode the respective other thing in sedml, i.e.
- a repeatedTask with reset=False where every repeat should be a line in
the plot
- a repeatedTask with reset=True which is concatenated


Matthias

-- 
Matthias König
Junior Group Leader LiSym - Systems Medicine of the Liver
Humboldt-University Berlin, Institute for Theoretical Biology
  https://www.livermetabolism.com
kon...@go...
Tel: +49 30 20938450
Tel: +49 176 81168480

Re: [SED-ML-discuss] L1V1 -> L1V2 conversion & applyChanges

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

Thanks. Very helpful resource. The source is at
https://sourceforge.net/p/libsedml/code/HEAD/tree/
There are a multitude of examples of sem-dl and sedx in the repo, for
anybody looking for examples.
M



On Tue, Feb 23, 2016 at 11:02 PM, David Nickerson <dav...@gm...
> wrote:

> I believe this is the C# code Frank was referring to:
> http://libsedml.sourceforge.net/libSedML/Welcome.html
>
> Cheers,
> David.
>
> On Wed, Feb 24, 2016 at 10:57 AM, Matthias König
> <kon...@go...> wrote:
> > Hi Frank,
> > This helps a lot. Could you post a link to the c# source repository?
> > Thanks. M
> >
> > On Feb 23, 2016 7:25 PM, "Frank Bergmann" <fbe...@ca...> wrote:
> >>
> >>
> >> > On Feb 23, 2016, at 5:31 PM, Matthias König <kon...@go...
> >
> >> > wrote:
> >> >
> >> > Hi all,
> >> > I have some questions in regard to libsedml (python bindings)
> >> >
> >> > [1] Is there a conversion function to convert SedDocuments from L1V1
> to
> >> > L1V2 similar to libsbml? This would be very nice because than I have
> to
> >> > read/implement only one specification.
> >> > Should L1V1 still be supported or did the majority of the community
> >> > already move on to L1V2 so that I can just ignore L1V1?
> >> >
> >>
> >> L1V2 is a strict superset of L1V1, so if you just treat every model you
> >> read as if it were an L1V2 model, then your code will work no matter
> whether
> >> it is an l1v1 or l1v2 model. A converter as such is not necessary or
> even
> >> possible there is just no way to express the l1v2 features in l1v1.
> >>
> >> > [2] I looked for a helper function which gives me for a model id the
> XML
> >> > with all the applied changes. I.e. a function which reads the XML
> from the
> >> > model source, and applies all the changes defined to the XML (in the
> process
> >> > handling the model dependencies and the stepwise application of
> changes).
> >> > This would be a very helpful function which everybody working with
> sedml
> >> > needs and probably reimplements.
> >> > Something like
> >> > sedml_doc.getProcessedModelXML(model_id)
> >> >
> >>
> >> I take contributions for the C++ project. I currently do not have the
> time
> >> to add that. My C# library has all these features. so I could expose a
> SOAP
> >> service / REST endpoint, or a command line tool, that would make it
> possible
> >> to get the processed model.
> >>
> >> Cheers
> >> Frank
> >>
> >> > The best
> >> > Matthias
> >> >
> >> >
> >> > --
> >> > Matthias König
> >> > Junior Group Leader LiSym - Systems Medicine of the Liver
> >> > Humboldt-University Berlin, Institute for Theoretical Biology
> >> >   https://www.livermetabolism.com
> >> > kon...@go...
> >> > Tel: +49 30 20938450
> >> > Tel: +49 176 81168480
> >> >
> >> >
> ------------------------------------------------------------------------------
> >> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
> >> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> >> > Monitor end-to-end web transactions and take corrective actions now
> >> > Troubleshoot faster and improve end-user experience. Signup Now!
> >> >
> >> >
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
> >> > SED-ML-discuss mailing list
> >> > SED...@li...
> >> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> >> Monitor end-to-end web transactions and take corrective actions now
> >> Troubleshoot faster and improve end-user experience. Signup Now!
> >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> >> _______________________________________________
> >> SED-ML-discuss mailing list
> >> SED...@li...
> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> >
> >
> ------------------------------------------------------------------------------
> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> > Monitor end-to-end web transactions and take corrective actions now
> > Troubleshoot faster and improve end-user experience. Signup Now!
> > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
>
>
>
> --
>
>
> David Nickerson
> about.me/david.nickerson
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
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> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>



-- 
Matthias König
Junior Group Leader LiSym - Systems Medicine of the Liver
Humboldt-University Berlin, Institute for Theoretical Biology
  https://www.livermetabolism.com
kon...@go...
Tel: +49 30 20938450
Tel: +49 176 81168480

Re: [SED-ML-discuss] L1V1 -> L1V2 conversion & applyChanges

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

I believe this is the C# code Frank was referring to:
http://libsedml.sourceforge.net/libSedML/Welcome.html

Cheers,
David.

On Wed, Feb 24, 2016 at 10:57 AM, Matthias König
<kon...@go...> wrote:
> Hi Frank,
> This helps a lot. Could you post a link to the c# source repository?
> Thanks. M
>
> On Feb 23, 2016 7:25 PM, "Frank Bergmann" <fbe...@ca...> wrote:
>>
>>
>> > On Feb 23, 2016, at 5:31 PM, Matthias König <kon...@go...>
>> > wrote:
>> >
>> > Hi all,
>> > I have some questions in regard to libsedml (python bindings)
>> >
>> > [1] Is there a conversion function to convert SedDocuments from L1V1 to
>> > L1V2 similar to libsbml? This would be very nice because than I have to
>> > read/implement only one specification.
>> > Should L1V1 still be supported or did the majority of the community
>> > already move on to L1V2 so that I can just ignore L1V1?
>> >
>>
>> L1V2 is a strict superset of L1V1, so if you just treat every model you
>> read as if it were an L1V2 model, then your code will work no matter whether
>> it is an l1v1 or l1v2 model. A converter as such is not necessary or even
>> possible there is just no way to express the l1v2 features in l1v1.
>>
>> > [2] I looked for a helper function which gives me for a model id the XML
>> > with all the applied changes. I.e. a function which reads the XML from the
>> > model source, and applies all the changes defined to the XML (in the process
>> > handling the model dependencies and the stepwise application of changes).
>> > This would be a very helpful function which everybody working with sedml
>> > needs and probably reimplements.
>> > Something like
>> > sedml_doc.getProcessedModelXML(model_id)
>> >
>>
>> I take contributions for the C++ project. I currently do not have the time
>> to add that. My C# library has all these features. so I could expose a SOAP
>> service / REST endpoint, or a command line tool, that would make it possible
>> to get the processed model.
>>
>> Cheers
>> Frank
>>
>> > The best
>> > Matthias
>> >
>> >
>> > --
>> > Matthias König
>> > Junior Group Leader LiSym - Systems Medicine of the Liver
>> > Humboldt-University Berlin, Institute for Theoretical Biology
>> >   https://www.livermetabolism.com
>> > kon...@go...
>> > Tel: +49 30 20938450
>> > Tel: +49 176 81168480
>> >
>> > ------------------------------------------------------------------------------
>> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> > Monitor end-to-end web transactions and take corrective actions now
>> > Troubleshoot faster and improve end-user experience. Signup Now!
>> >
>> > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
>> > SED-ML-discuss mailing list
>> > SED...@li...
>> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> 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] L1V1 -> L1V2 conversion & applyChanges

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

Hi Frank,
This helps a lot. Could you post a link to the c# source repository?
Thanks. M
On Feb 23, 2016 7:25 PM, "Frank Bergmann" <fbe...@ca...> wrote:

>
> > On Feb 23, 2016, at 5:31 PM, Matthias König <kon...@go...>
> wrote:
> >
> > Hi all,
> > I have some questions in regard to libsedml (python bindings)
> >
> > [1] Is there a conversion function to convert SedDocuments from L1V1 to
> L1V2 similar to libsbml? This would be very nice because than I have to
> read/implement only one specification.
> > Should L1V1 still be supported or did the majority of the community
> already move on to L1V2 so that I can just ignore L1V1?
> >
>
> L1V2 is a strict superset of L1V1, so if you just treat every model you
> read as if it were an L1V2 model, then your code will work no matter
> whether it is an l1v1 or l1v2 model. A converter as such is not necessary
> or even possible there is just no way to express the l1v2 features in l1v1.
>
> > [2] I looked for a helper function which gives me for a model id the XML
> with all the applied changes. I.e. a function which reads the XML from the
> model source, and applies all the changes defined to the XML (in the
> process handling the model dependencies and the stepwise application of
> changes).
> > This would be a very helpful function which everybody working with sedml
> needs and probably reimplements.
> > Something like
> > sedml_doc.getProcessedModelXML(model_id)
> >
>
> I take contributions for the C++ project. I currently do not have the time
> to add that. My C# library has all these features. so I could expose a SOAP
> service / REST endpoint, or a command line tool, that would make it
> possible to get the processed model.
>
> Cheers
> Frank
>
> > The best
> > Matthias
> >
> >
> > --
> > Matthias König
> > Junior Group Leader LiSym - Systems Medicine of the Liver
> > Humboldt-University Berlin, Institute for Theoretical Biology
> >   https://www.livermetabolism.com
> > kon...@go...
> > Tel: +49 30 20938450
> > Tel: +49 176 81168480
> >
> ------------------------------------------------------------------------------
> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> > Monitor end-to-end web transactions and take corrective actions now
> > Troubleshoot faster and improve end-user experience. Signup Now!
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

Re: [SED-ML-discuss] L1V1 -> L1V2 conversion & applyChanges

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

> On Feb 23, 2016, at 5:31 PM, Matthias König <kon...@go...> wrote:
> 
> Hi all,
> I have some questions in regard to libsedml (python bindings)
> 
> [1] Is there a conversion function to convert SedDocuments from L1V1 to L1V2 similar to libsbml? This would be very nice because than I have to read/implement only one specification. 
> Should L1V1 still be supported or did the majority of the community already move on to L1V2 so that I can just ignore L1V1?
> 

L1V2 is a strict superset of L1V1, so if you just treat every model you read as if it were an L1V2 model, then your code will work no matter whether it is an l1v1 or l1v2 model. A converter as such is not necessary or even possible there is just no way to express the l1v2 features in l1v1. 

> [2] I looked for a helper function which gives me for a model id the XML with all the applied changes. I.e. a function which reads the XML from the model source, and applies all the changes defined to the XML (in the process handling the model dependencies and the stepwise application of changes).
> This would be a very helpful function which everybody working with sedml needs and probably reimplements. 
> Something like
> sedml_doc.getProcessedModelXML(model_id)
> 

I take contributions for the C++ project. I currently do not have the time to add that. My C# library has all these features. so I could expose a SOAP service / REST endpoint, or a command line tool, that would make it possible to get the processed model. 

Cheers
Frank

> The best
> Matthias
> 
> 
> -- 
> Matthias König
> Junior Group Leader LiSym - Systems Medicine of the Liver
> Humboldt-University Berlin, Institute for Theoretical Biology
>   https://www.livermetabolism.com
> kon...@go...
> Tel: +49 30 20938450
> Tel: +49 176 81168480
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] L1V1 -> L1V2 conversion & applyChanges

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

Hi all,
I have some questions in regard to libsedml (python bindings)

[1] Is there a conversion function to convert SedDocuments from L1V1 to
L1V2 similar to libsbml? This would be very nice because than I have to
read/implement only one specification.
Should L1V1 still be supported or did the majority of the community already
move on to L1V2 so that I can just ignore L1V1?

[2] I looked for a helper function which gives me for a model id the XML
with all the applied changes. I.e. a function which reads the XML from the
model source, and applies all the changes defined to the XML (in the
process handling the model dependencies and the stepwise application of
changes).
This would be a very helpful function which everybody working with sedml
needs and probably reimplements.
Something like
sedml_doc.getProcessedModelXML(model_id)

The best
Matthias


-- 
Matthias König
Junior Group Leader LiSym - Systems Medicine of the Liver
Humboldt-University Berlin, Institute for Theoretical Biology
  https://www.livermetabolism.com
kon...@go...
Tel: +49 30 20938450
Tel: +49 176 81168480

[SED-ML-discuss] Please comment on SED-ML extension to support qualitative (logical) models

[Claudine <cha...@ig...>]

Dear all,

We have worked out a draft proposal for SED-ML extension to support qualitative models (as specified in the SBML qual package). 

With this extension, we aim to encode simulation experiments on qualitative models. The current SED-ML does already provide the frame for the encoding of simulation experiments in computational biology. However, the nature of qualitative models is different to ODE-based models, which have been in the focus so far: Qualitative models are a class of discrete event systems, whose dynamics are represented by means of state transition graphs (STGs). These STGs represent, in the form of a graph, which nodes are the reachable states; the edges represent the state transitions.
The proposal at hand is the result of discussions at Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, February 2016. 

This is a first draft and we need feedback from you, the community, to turn it into a an official proposal to the SED-ML editors.

The PDF of the Draft Version 1 is kept at 10.6084/m9.figshare.2075143 for later reference. 

Please feel free to edit the following google doc to improve the proposal: 
https://docs.google.com/document/d/1WrLiOSxK58sxJwRDe-rXyCSpuvtiSQWjJd43WaBw_wE/edit?usp=sharing

We suggest to keep discussions on specific concepts on the SED-ML mailing list (please use the SED-ML list sed...@li...).


Greetings from the sunny side of Europe (edit from Dagmar!),
Claudine, Pedro, Aurélien & Dagmar

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

[1]
In my opinion `keep at most`,  `keep every`, keep exactly` and other
parameters which effect the number of points in the solution like
`absolute_tolerance` or `relative_tolerance` are all AlgorithmParameters
and should not be attributes of NonUniformTimeCourse.
This are all settings for the algorithm/software but do not describe any
inherent feature of a NonUniformTimeCourse. These features are: Start at
t_start, stop at t_end and give me >=0 timepoints in between (which are not
guaranteed to be equidistant).

[2]
In addition also the VariableOneStep is needed. The step size is not known
but a result of the adaptive step size of the integrator so that at the
next step the tolerances are fullfilled. I mainly would use this in the
case of hybrid simulations. Submodels are run for oneStep (so that the
tolerances are fullfilled) and than synchronized.

[3]
The definition of selections is missing on simulations, i.e. a list of ids
which are the columns in the simulation result.
Something like listOfSelections=['time', 'S1', 'r3'].
Selections can be species, parameters, reaction rates, ...
I  want to store only the variables I need in the data generators. It makes
no sense to store 40000 variables for all time points (and do this
repeatedly in the tasks).
The role of the DataGenerator is only to prepare the raw simulation results
for later output. What is missing is a way to define which data, i.e.
columns should be part of the raw simulation output.

[4] About the synchronicity:
Yes, this is the biggest issue.
For me it is completely fine to state clearly in the specifications that
this is an issue and the user has to take care of this/be aware of this
(just provide a warning when loading SED-ML "SED-ML contains
NonUniformTimecourse or VariableOneStep simulations, synchronicity can not
be guaranteed".)
How I handle this in my simulation workflow is to perform interpolations of
the two (many) time series to synchronize the time points. It should be
possible to describe these interpolations in SED-ML (but these can be added
later).
I prefer 10 times to be able to describe the subset of synchronized
NonUniformTimeCourse simulations in SED-ML instead of not being able to
describe anything but being save of synchronicity issues.


On Wed, Feb 3, 2016 at 2:52 AM, Dagmar Waltemath <
dag...@un...> wrote:

> Hi there,
>
> we do not have this default-statement in the spec, but I think it is a
> good idea to add it.
>
> It could be on page 43 (L1V2), just after:
> "The Algorithm class contains an optional list of parameters
> (algorithmParameter) that are used toparameterize the particular algorithm
> used in the simulation"
>
> or in Section 2.4.3.2 on the same page.
>
> Dagmar
>
>
>
>
> *Dagmar Waltemath*, Dept. of Systems Biology & Bioinformatics,
> University of Rostock, D-18051 Rostock, Germany
> Web: http://www.sbi.uni-rostock.de/sems
> <http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/>
> Skype: dagmar.waltemath
> ------------------------------
> *Von:* Lucian Smith [luc...@gm...]
> *Gesendet:* Mittwoch, 3. Februar 2016 00:13
> *An:* sed...@li...
> *Betreff:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse
>
> Well, there's a whole 'modelling and simulation algorithm characteristic'
> branch of KiSAO.  Would it make sense to add 'implementation version
> number' and 'implementation URL' to that list?
>
> 'Use the default settings except where otherwise noted' is probably
> currently assumed; it might be worth adding that statement to the SED-ML
> spec, though, assuming it doesn't already.
>
> -Lucian
>
> On Tue, Feb 2, 2016 at 3:09 PM, Matthias König <kon...@go...>
> wrote:
>
>> Would be nice to say something like:
>> - [1] I use cvode v2.8.2 with all default settings
>> - [2] I changed only BDF_max_order to 12
>>
>> [2] I can encode via the AlgorithmParameter with a suitable KISAO.
>> But how would I write [1] in SEDML?
>>
>> On Wed, Feb 3, 2016 at 12:03 AM, Lucian Smith <luc...@gm...>
>> wrote:
>>
>>> On Tue, Feb 2, 2016 at 2:50 PM, Pedro Mendes <
>>> ped...@ma...> wrote:
>>>
>>>> That would solve things. However it is impossible to antecipate if there
>>>> will be other algorithms with other orders. My feeling is that these
>>>> parameters are very specific from algorithm to algorithm and we can end
>>>> up with lots of special cases.
>>>>
>>>
>>> Is that a problem?  It's obviously not something that we can solve up
>>> front, but if we keep adding more and more terms to KiSAO, each addition
>>> permanently solves a new problem, and there's an obvious path to finding a
>>> solution for each new use-case.
>>>
>>> There are only two other solutions that I can see:  limit people to only
>>> using a certain subset of known algorithms; or letting people define
>>> parameters with free text.  The current situation is obviously not ideal,
>>> but those two options sound even *less* ideal, at least to me.  Is there
>>> some other option I'm not seeing?  Or is this just something to keep in
>>> mind as we go forward, and we try to see where we can mitigate the biggest
>>> problems?
>>>
>>> A similar situation, but more extreme, is with optimization algorithms,
>>>> which have all sorts of different algorithm parameters and it is
>>>> impossible to generalize there. (This will impact SED-ML later on when
>>>> we decide to include optimization or parameter estimation.
>>>>
>>>
>>> Again, while filling KiSAO with thousands of highly-specific terms
>>> doesn't sound ideal, I can't think of a better solution, either.  It's
>>> worth keeping in mind, at least.
>>>
>>> -Lucian
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
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>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
>>
>>
>> --
>> Matthias König
>> Email: kon...@go...
>> Tel: + 49 30 20938450
>> Tel: + 49 176 81168480
>>   https://www.livermetabolism.com/contact.html
>> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
>> Group König
>> Charité Berlin, Institute of Biochemistry, Computational Systems
>> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
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>>
>>
>
>
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-- 
Matthias König
Email: kon...@go...
Tel: + 49 30 20938450
Tel: + 49 176 81168480
  https://www.livermetabolism.com/contact.html
Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group
König
Charité Berlin, Institute of Biochemistry, Computational Systems
Biochemistry <http://www.charite.de/sysbio/people/koenig/>

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

Hi there,

we do not have this default-statement in the spec, but I think it is a good idea to add it.

It could be on page 43 (L1V2), just after:
"The Algorithm class contains an optional list of parameters (algorithmParameter) that are used toparameterize the particular algorithm used in the simulation"

or in Section 2.4.3.2 on the same page.

Dagmar




Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics,
University of Rostock, D-18051 Rostock, Germany
Web: http://www.sbi.uni-rostock.de/sems<http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/>
Skype: dagmar.waltemath
________________________________
Von: Lucian Smith [luc...@gm...]
Gesendet: Mittwoch, 3. Februar 2016 00:13
An: sed...@li...
Betreff: Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

Well, there's a whole 'modelling and simulation algorithm characteristic' branch of KiSAO.  Would it make sense to add 'implementation version number' and 'implementation URL' to that list?

'Use the default settings except where otherwise noted' is probably currently assumed; it might be worth adding that statement to the SED-ML spec, though, assuming it doesn't already.

-Lucian

On Tue, Feb 2, 2016 at 3:09 PM, Matthias König <kon...@go...<mailto:kon...@go...>> wrote:
Would be nice to say something like:
- [1] I use cvode v2.8.2 with all default settings
- [2] I changed only BDF_max_order to 12

[2] I can encode via the AlgorithmParameter with a suitable KISAO.
But how would I write [1] in SEDML?

On Wed, Feb 3, 2016 at 12:03 AM, Lucian Smith <luc...@gm...<mailto:luc...@gm...>> wrote:
On Tue, Feb 2, 2016 at 2:50 PM, Pedro Mendes <ped...@ma...<mailto:ped...@ma...>> wrote:
That would solve things. However it is impossible to antecipate if there
will be other algorithms with other orders. My feeling is that these
parameters are very specific from algorithm to algorithm and we can end
up with lots of special cases.

Is that a problem?  It's obviously not something that we can solve up front, but if we keep adding more and more terms to KiSAO, each addition permanently solves a new problem, and there's an obvious path to finding a solution for each new use-case.

There are only two other solutions that I can see:  limit people to only using a certain subset of known algorithms; or letting people define parameters with free text.  The current situation is obviously not ideal, but those two options sound even *less* ideal, at least to me.  Is there some other option I'm not seeing?  Or is this just something to keep in mind as we go forward, and we try to see where we can mitigate the biggest problems?

A similar situation, but more extreme, is with optimization algorithms,
which have all sorts of different algorithm parameters and it is
impossible to generalize there. (This will impact SED-ML later on when
we decide to include optimization or parameter estimation.

Again, while filling KiSAO with thousands of highly-specific terms doesn't sound ideal, I can't think of a better solution, either.  It's worth keeping in mind, at least.

-Lucian

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--
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Email: kon...@go...<mailto:kon...@go...>
Tel: + 49 30 20938450
Tel: + 49 176 81168480<tel:%2B%2049%20176%2081168480>
[X]  https://www.livermetabolism.com/contact.html
Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König
Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry<http://www.charite.de/sysbio/people/koenig/>

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Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

Ion, do you think these parameters are best stored as attributes to the
NonUniformTimeCourse class, or as generic Parameters, defined by KiSAO
terms?

-Lucian

On Tue, Feb 2, 2016 at 4:56 PM, Moraru,Ion <mo...@uc...> wrote:

> We should however include a couple of (optional) but fundamental settings
> for the output in the NonUniformTimeCourse class.  From our experience the
> basic ways users want to specify the output are:
>
> -          “keep at most” – sample solver output such as there are say no
> more than 1,000 time points saved
>
> -          “keep every” – sample solver output such as to save say every
> 1 out 5 integrator steps
>
> -          “keep exactly” – specify a list of exact timepoints where the
> solver should save data
>
>
>
> The other important issue which is somewhat non-trivial (and which was one
> of the reasons NonUniformTimeCourse was not included in SED-ML from the
> beginning) is the fact that DataGenerators reading in from various Tasks do
> not anymore have a guarantee of synchronicity or potentially not enough
> information for proper post-processing across Tasks (except in “keep
> exactly” scenario above).
>
>
>
> Ion
>
>
>
> *From:* Matthias König [mailto:kon...@go...]
> *Sent:* Tuesday, February 02, 2016 7:11 PM
> *To:* sed...@li...
> *Subject:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse
>
>
>
> @lucian
>
> As soon as there is a NonUniformTimeCourse and the Kisao terms everything
> is in place to be able to encode my simulations and tasks.
>
> How to encode all the default settings of the solver will be a problem for
> the future. Just adding the Kisao terms as they are needed is the pragmatic
> way to do it.
>
>
>
> On Wed, Feb 3, 2016 at 12:35 AM, Lucian Smith <luc...@gm...>
> wrote:
>
> Well, sure, but again, these XML-based exchange languages are for computer
> exchange, not so much hand-creation of XML documents.  Any solver that has
> save files has the capacity to write a SED-ML file with that same
> information (with everything that SED-ML supports, of course).  SED-ML is
> giving solvers the ability to load *other* solvers' save files,
> essentially.  If all you want is to be able to run the same thing on COPASI
> tomorrow that you ran on COPASI yesterday, the COPASI save file is
> obviously the way to go.
>
>
>
> However, I think I've lost what you're proposing.  Is there something
> SED-ML doesn't do, or that KiSAO doesn't cover, that you think it should,
> but that people have objected to?
>
>
>
> -Lucian
>
>
>
> On Tue, Feb 2, 2016 at 3:21 PM, Matthias König <kon...@go...>
> wrote:
>
> The problem is that a normal person/user does not know the settings the
> algorithms use. They mainly use some software/library which provides an
> interface to the algorithm. Within this interface there is only a limited
> number of parameters the user can change. So it would make a lot more sense
> to just record
> - what software/package was used with which integrator
>
> - plus the changes in a few standard parameters
>
> The software people have than to provide the list of parameters for their
> software.
>
> For instance it should be sufficient to record the software plus
> integrator (making up numbers, but is to illustrate my point)
>
> - COPASI Build 48, LSODA
>
> - roadrunner 1.5.0, gillespi
>
> - VCell 1.0, CVODE
>
> plus a very limited set of additional parameters which the normal user
> understands and can set in the software.
>
> The software people could provide a detailed listing of algorithm
> parameters for their software versions + integrators. It is not realistic
> that anybody will look up there BDF_max_order to write a SED-ML file (or
> how many of you know this for their last simulation?).
>
> M
>
>
>
>
>
> On Wed, Feb 3, 2016 at 12:09 AM, Matthias König <kon...@go...>
> wrote:
>
> Would be nice to say something like:
>
> - [1] I use cvode v2.8.2 with all default settings
>
> - [2] I changed only BDF_max_order to 12
>
>
> [2] I can encode via the AlgorithmParameter with a suitable KISAO.
> But how would I write [1] in SEDML?
>
>
>
> On Wed, Feb 3, 2016 at 12:03 AM, Lucian Smith <luc...@gm...>
> wrote:
>
> On Tue, Feb 2, 2016 at 2:50 PM, Pedro Mendes <
> ped...@ma...> wrote:
>
> That would solve things. However it is impossible to antecipate if there
> will be other algorithms with other orders. My feeling is that these
> parameters are very specific from algorithm to algorithm and we can end
> up with lots of special cases.
>
>
>
> Is that a problem?  It's obviously not something that we can solve up
> front, but if we keep adding more and more terms to KiSAO, each addition
> permanently solves a new problem, and there's an obvious path to finding a
> solution for each new use-case.
>
>
>
> There are only two other solutions that I can see:  limit people to only
> using a certain subset of known algorithms; or letting people define
> parameters with free text.  The current situation is obviously not ideal,
> but those two options sound even *less* ideal, at least to me.  Is there
> some other option I'm not seeing?  Or is this just something to keep in
> mind as we go forward, and we try to see where we can mitigate the biggest
> problems?
>
>
>
> A similar situation, but more extreme, is with optimization algorithms,
> which have all sorts of different algorithm parameters and it is
> impossible to generalize there. (This will impact SED-ML later on when
> we decide to include optimization or parameter estimation.
>
>
>
> Again, while filling KiSAO with thousands of highly-specific terms doesn't
> sound ideal, I can't think of a better solution, either.  It's worth
> keeping in mind, at least.
>
>
>
> -Lucian
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
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> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=7bQoDORX33B2KdaQ46o2ruQWFPfq64XpOsNU33hbTOQ&s=7QB02jw6mD0g4bJJ3n-2DgxSHHHkodsm64B64tTbygs&e=>
>
>
>
>
> --
>
> Matthias König
> Email: kon...@go...
> Tel: + 49 30 20938450
> Tel: + 49 176 81168480
>   https://www.livermetabolism.com/contact.html
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.livermetabolism.com_contact.html&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=7bQoDORX33B2KdaQ46o2ruQWFPfq64XpOsNU33hbTOQ&s=urtpbBSbHlwCX-L11lqrKxVihPSfDsXQNyL4W-VH52g&e=>
> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
> Group König
> Charité Berlin, Institute of Biochemistry, Computational Systems
> Biochemistry
>
>
>
>
> --
>
> Matthias König
> Email: kon...@go...
> Tel: + 49 30 20938450
> Tel: + 49 176 81168480
>   https://www.livermetabolism.com/contact.html
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.livermetabolism.com_contact.html&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=7bQoDORX33B2KdaQ46o2ruQWFPfq64XpOsNU33hbTOQ&s=urtpbBSbHlwCX-L11lqrKxVihPSfDsXQNyL4W-VH52g&e=>
> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
> Group König
> Charité Berlin, Institute of Biochemistry, Computational Systems
> Biochemistry
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
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> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=7bQoDORX33B2KdaQ46o2ruQWFPfq64XpOsNU33hbTOQ&s=7QB02jw6mD0g4bJJ3n-2DgxSHHHkodsm64B64tTbygs&e=>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
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> _______________________________________________
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> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=7bQoDORX33B2KdaQ46o2ruQWFPfq64XpOsNU33hbTOQ&s=7QB02jw6mD0g4bJJ3n-2DgxSHHHkodsm64B64tTbygs&e=>
>
>
>
>
> --
>
> Matthias König
> Email: kon...@go...
> Tel: + 49 30 20938450
> Tel: + 49 176 81168480
>   https://www.livermetabolism.com/contact.html
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.livermetabolism.com_contact.html&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=7bQoDORX33B2KdaQ46o2ruQWFPfq64XpOsNU33hbTOQ&s=urtpbBSbHlwCX-L11lqrKxVihPSfDsXQNyL4W-VH52g&e=>
> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
> Group König
> Charité Berlin, Institute of Biochemistry, Computational Systems
> Biochemistry
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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> Monitor end-to-end web transactions and take corrective actions now
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>
>

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

[Moraru,Ion <mo...@uc...>]

We should however include a couple of (optional) but fundamental settings for the output in the NonUniformTimeCourse class.  From our experience the basic ways users want to specify the output are:

-          “keep at most” – sample solver output such as there are say no more than 1,000 time points saved

-          “keep every” – sample solver output such as to save say every 1 out 5 integrator steps

-          “keep exactly” – specify a list of exact timepoints where the solver should save data

The other important issue which is somewhat non-trivial (and which was one of the reasons NonUniformTimeCourse was not included in SED-ML from the beginning) is the fact that DataGenerators reading in from various Tasks do not anymore have a guarantee of synchronicity or potentially not enough information for proper post-processing across Tasks (except in “keep exactly” scenario above).

Ion

From: Matthias König [mailto:kon...@go...]
Sent: Tuesday, February 02, 2016 7:11 PM
To: sed...@li...
Subject: Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

@lucian
As soon as there is a NonUniformTimeCourse and the Kisao terms everything is in place to be able to encode my simulations and tasks.
How to encode all the default settings of the solver will be a problem for the future. Just adding the Kisao terms as they are needed is the pragmatic way to do it.

On Wed, Feb 3, 2016 at 12:35 AM, Lucian Smith <luc...@gm...<mailto:luc...@gm...>> wrote:
Well, sure, but again, these XML-based exchange languages are for computer exchange, not so much hand-creation of XML documents.  Any solver that has save files has the capacity to write a SED-ML file with that same information (with everything that SED-ML supports, of course).  SED-ML is giving solvers the ability to load *other* solvers' save files, essentially.  If all you want is to be able to run the same thing on COPASI tomorrow that you ran on COPASI yesterday, the COPASI save file is obviously the way to go.

However, I think I've lost what you're proposing.  Is there something SED-ML doesn't do, or that KiSAO doesn't cover, that you think it should, but that people have objected to?

-Lucian

On Tue, Feb 2, 2016 at 3:21 PM, Matthias König <kon...@go...<mailto:kon...@go...>> wrote:
The problem is that a normal person/user does not know the settings the algorithms use. They mainly use some software/library which provides an interface to the algorithm. Within this interface there is only a limited number of parameters the user can change. So it would make a lot more sense to just record
- what software/package was used with which integrator
- plus the changes in a few standard parameters
The software people have than to provide the list of parameters for their software.
For instance it should be sufficient to record the software plus integrator (making up numbers, but is to illustrate my point)
- COPASI Build 48, LSODA
- roadrunner 1.5.0, gillespi
- VCell 1.0, CVODE
plus a very limited set of additional parameters which the normal user understands and can set in the software.
The software people could provide a detailed listing of algorithm parameters for their software versions + integrators. It is not realistic that anybody will look up there BDF_max_order to write a SED-ML file (or how many of you know this for their last simulation?).
M


On Wed, Feb 3, 2016 at 12:09 AM, Matthias König <kon...@go...<mailto:kon...@go...>> wrote:
Would be nice to say something like:
- [1] I use cvode v2.8.2 with all default settings
- [2] I changed only BDF_max_order to 12

[2] I can encode via the AlgorithmParameter with a suitable KISAO.
But how would I write [1] in SEDML?

On Wed, Feb 3, 2016 at 12:03 AM, Lucian Smith <luc...@gm...<mailto:luc...@gm...>> wrote:
On Tue, Feb 2, 2016 at 2:50 PM, Pedro Mendes <ped...@ma...<mailto:ped...@ma...>> wrote:
That would solve things. However it is impossible to antecipate if there
will be other algorithms with other orders. My feeling is that these
parameters are very specific from algorithm to algorithm and we can end
up with lots of special cases.

Is that a problem?  It's obviously not something that we can solve up front, but if we keep adding more and more terms to KiSAO, each addition permanently solves a new problem, and there's an obvious path to finding a solution for each new use-case.

There are only two other solutions that I can see:  limit people to only using a certain subset of known algorithms; or letting people define parameters with free text.  The current situation is obviously not ideal, but those two options sound even *less* ideal, at least to me.  Is there some other option I'm not seeing?  Or is this just something to keep in mind as we go forward, and we try to see where we can mitigate the biggest problems?

A similar situation, but more extreme, is with optimization algorithms,
which have all sorts of different algorithm parameters and it is
impossible to generalize there. (This will impact SED-ML later on when
we decide to include optimization or parameter estimation.

Again, while filling KiSAO with thousands of highly-specific terms doesn't sound ideal, I can't think of a better solution, either.  It's worth keeping in mind, at least.

-Lucian

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Email: kon...@go...<mailto:kon...@go...>
Tel: + 49 30 20938450
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Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König
Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry



--
Matthias König
Email: kon...@go...<mailto:kon...@go...>
Tel: + 49 30 20938450
Tel: + 49 176 81168480<tel:%2B%2049%20176%2081168480>
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Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König
Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry

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--
Matthias König
Email: kon...@go...<mailto:kon...@go...>
Tel: + 49 30 20938450
Tel: + 49 176 81168480
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Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

@lucian
As soon as there is a NonUniformTimeCourse and the Kisao terms everything
is in place to be able to encode my simulations and tasks.

How to encode all the default settings of the solver will be a problem for
the future. Just adding the Kisao terms as they are needed is the pragmatic
way to do it.

On Wed, Feb 3, 2016 at 12:35 AM, Lucian Smith <luc...@gm...>
wrote:

> Well, sure, but again, these XML-based exchange languages are for computer
> exchange, not so much hand-creation of XML documents.  Any solver that has
> save files has the capacity to write a SED-ML file with that same
> information (with everything that SED-ML supports, of course).  SED-ML is
> giving solvers the ability to load *other* solvers' save files,
> essentially.  If all you want is to be able to run the same thing on COPASI
> tomorrow that you ran on COPASI yesterday, the COPASI save file is
> obviously the way to go.
>
> However, I think I've lost what you're proposing.  Is there something
> SED-ML doesn't do, or that KiSAO doesn't cover, that you think it should,
> but that people have objected to?
>
> -Lucian
>
> On Tue, Feb 2, 2016 at 3:21 PM, Matthias König <kon...@go...>
> wrote:
>
>> The problem is that a normal person/user does not know the settings the
>> algorithms use. They mainly use some software/library which provides an
>> interface to the algorithm. Within this interface there is only a limited
>> number of parameters the user can change. So it would make a lot more sense
>> to just record
>> - what software/package was used with which integrator
>> - plus the changes in a few standard parameters
>> The software people have than to provide the list of parameters for their
>> software.
>>
>> For instance it should be sufficient to record the software plus
>> integrator (making up numbers, but is to illustrate my point)
>> - COPASI Build 48, LSODA
>> - roadrunner 1.5.0, gillespi
>> - VCell 1.0, CVODE
>> plus a very limited set of additional parameters which the normal user
>> understands and can set in the software.
>>
>> The software people could provide a detailed listing of algorithm
>> parameters for their software versions + integrators. It is not realistic
>> that anybody will look up there BDF_max_order to write a SED-ML file (or
>> how many of you know this for their last simulation?).
>> M
>>
>>
>>
>> On Wed, Feb 3, 2016 at 12:09 AM, Matthias König <kon...@go...
>> > wrote:
>>
>>> Would be nice to say something like:
>>> - [1] I use cvode v2.8.2 with all default settings
>>> - [2] I changed only BDF_max_order to 12
>>>
>>> [2] I can encode via the AlgorithmParameter with a suitable KISAO.
>>> But how would I write [1] in SEDML?
>>>
>>> On Wed, Feb 3, 2016 at 12:03 AM, Lucian Smith <luc...@gm...
>>> > wrote:
>>>
>>>> On Tue, Feb 2, 2016 at 2:50 PM, Pedro Mendes <
>>>> ped...@ma...> wrote:
>>>>
>>>>> That would solve things. However it is impossible to antecipate if
>>>>> there
>>>>> will be other algorithms with other orders. My feeling is that these
>>>>> parameters are very specific from algorithm to algorithm and we can end
>>>>> up with lots of special cases.
>>>>>
>>>>
>>>> Is that a problem?  It's obviously not something that we can solve up
>>>> front, but if we keep adding more and more terms to KiSAO, each addition
>>>> permanently solves a new problem, and there's an obvious path to finding a
>>>> solution for each new use-case.
>>>>
>>>> There are only two other solutions that I can see:  limit people to
>>>> only using a certain subset of known algorithms; or letting people define
>>>> parameters with free text.  The current situation is obviously not ideal,
>>>> but those two options sound even *less* ideal, at least to me.  Is there
>>>> some other option I'm not seeing?  Or is this just something to keep in
>>>> mind as we go forward, and we try to see where we can mitigate the biggest
>>>> problems?
>>>>
>>>> A similar situation, but more extreme, is with optimization algorithms,
>>>>> which have all sorts of different algorithm parameters and it is
>>>>> impossible to generalize there. (This will impact SED-ML later on when
>>>>> we decide to include optimization or parameter estimation.
>>>>>
>>>>
>>>> Again, while filling KiSAO with thousands of highly-specific terms
>>>> doesn't sound ideal, I can't think of a better solution, either.  It's
>>>> worth keeping in mind, at least.
>>>>
>>>> -Lucian
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>>>>
>>>>
>>>
>>>
>>> --
>>> Matthias König
>>> Email: kon...@go...
>>> Tel: + 49 30 20938450
>>> Tel: + 49 176 81168480
>>>   https://www.livermetabolism.com/contact.html
>>> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
>>> Group König
>>> Charité Berlin, Institute of Biochemistry, Computational Systems
>>> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>>>
>>
>>
>>
>> --
>> Matthias König
>> Email: kon...@go...
>> Tel: + 49 30 20938450
>> Tel: + 49 176 81168480
>>   https://www.livermetabolism.com/contact.html
>> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
>> Group König
>> Charité Berlin, Institute of Biochemistry, Computational Systems
>> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>>
>
>
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>


-- 
Matthias König
Email: kon...@go...
Tel: + 49 30 20938450
Tel: + 49 176 81168480
  https://www.livermetabolism.com/contact.html
Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group
König
Charité Berlin, Institute of Biochemistry, Computational Systems
Biochemistry <http://www.charite.de/sysbio/people/koenig/>

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

Well, sure, but again, these XML-based exchange languages are for computer
exchange, not so much hand-creation of XML documents.  Any solver that has
save files has the capacity to write a SED-ML file with that same
information (with everything that SED-ML supports, of course).  SED-ML is
giving solvers the ability to load *other* solvers' save files,
essentially.  If all you want is to be able to run the same thing on COPASI
tomorrow that you ran on COPASI yesterday, the COPASI save file is
obviously the way to go.

However, I think I've lost what you're proposing.  Is there something
SED-ML doesn't do, or that KiSAO doesn't cover, that you think it should,
but that people have objected to?

-Lucian

On Tue, Feb 2, 2016 at 3:21 PM, Matthias König <kon...@go...>
wrote:

> The problem is that a normal person/user does not know the settings the
> algorithms use. They mainly use some software/library which provides an
> interface to the algorithm. Within this interface there is only a limited
> number of parameters the user can change. So it would make a lot more sense
> to just record
> - what software/package was used with which integrator
> - plus the changes in a few standard parameters
> The software people have than to provide the list of parameters for their
> software.
>
> For instance it should be sufficient to record the software plus
> integrator (making up numbers, but is to illustrate my point)
> - COPASI Build 48, LSODA
> - roadrunner 1.5.0, gillespi
> - VCell 1.0, CVODE
> plus a very limited set of additional parameters which the normal user
> understands and can set in the software.
>
> The software people could provide a detailed listing of algorithm
> parameters for their software versions + integrators. It is not realistic
> that anybody will look up there BDF_max_order to write a SED-ML file (or
> how many of you know this for their last simulation?).
> M
>
>
>
> On Wed, Feb 3, 2016 at 12:09 AM, Matthias König <kon...@go...>
> wrote:
>
>> Would be nice to say something like:
>> - [1] I use cvode v2.8.2 with all default settings
>> - [2] I changed only BDF_max_order to 12
>>
>> [2] I can encode via the AlgorithmParameter with a suitable KISAO.
>> But how would I write [1] in SEDML?
>>
>> On Wed, Feb 3, 2016 at 12:03 AM, Lucian Smith <luc...@gm...>
>> wrote:
>>
>>> On Tue, Feb 2, 2016 at 2:50 PM, Pedro Mendes <
>>> ped...@ma...> wrote:
>>>
>>>> That would solve things. However it is impossible to antecipate if there
>>>> will be other algorithms with other orders. My feeling is that these
>>>> parameters are very specific from algorithm to algorithm and we can end
>>>> up with lots of special cases.
>>>>
>>>
>>> Is that a problem?  It's obviously not something that we can solve up
>>> front, but if we keep adding more and more terms to KiSAO, each addition
>>> permanently solves a new problem, and there's an obvious path to finding a
>>> solution for each new use-case.
>>>
>>> There are only two other solutions that I can see:  limit people to only
>>> using a certain subset of known algorithms; or letting people define
>>> parameters with free text.  The current situation is obviously not ideal,
>>> but those two options sound even *less* ideal, at least to me.  Is there
>>> some other option I'm not seeing?  Or is this just something to keep in
>>> mind as we go forward, and we try to see where we can mitigate the biggest
>>> problems?
>>>
>>> A similar situation, but more extreme, is with optimization algorithms,
>>>> which have all sorts of different algorithm parameters and it is
>>>> impossible to generalize there. (This will impact SED-ML later on when
>>>> we decide to include optimization or parameter estimation.
>>>>
>>>
>>> Again, while filling KiSAO with thousands of highly-specific terms
>>> doesn't sound ideal, I can't think of a better solution, either.  It's
>>> worth keeping in mind, at least.
>>>
>>> -Lucian
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
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>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
>>
>>
>> --
>> Matthias König
>> Email: kon...@go...
>> Tel: + 49 30 20938450
>> Tel: + 49 176 81168480
>>   https://www.livermetabolism.com/contact.html
>> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
>> Group König
>> Charité Berlin, Institute of Biochemistry, Computational Systems
>> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>>
>
>
>
> --
> Matthias König
> Email: kon...@go...
> Tel: + 49 30 20938450
> Tel: + 49 176 81168480
>   https://www.livermetabolism.com/contact.html
> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
> Group König
> Charité Berlin, Institute of Biochemistry, Computational Systems
> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

The problem is that a normal person/user does not know the settings the
algorithms use. They mainly use some software/library which provides an
interface to the algorithm. Within this interface there is only a limited
number of parameters the user can change. So it would make a lot more sense
to just record
- what software/package was used with which integrator
- plus the changes in a few standard parameters
The software people have than to provide the list of parameters for their
software.

For instance it should be sufficient to record the software plus integrator
(making up numbers, but is to illustrate my point)
- COPASI Build 48, LSODA
- roadrunner 1.5.0, gillespi
- VCell 1.0, CVODE
plus a very limited set of additional parameters which the normal user
understands and can set in the software.

The software people could provide a detailed listing of algorithm
parameters for their software versions + integrators. It is not realistic
that anybody will look up there BDF_max_order to write a SED-ML file (or
how many of you know this for their last simulation?).
M



On Wed, Feb 3, 2016 at 12:09 AM, Matthias König <kon...@go...>
wrote:

> Would be nice to say something like:
> - [1] I use cvode v2.8.2 with all default settings
> - [2] I changed only BDF_max_order to 12
>
> [2] I can encode via the AlgorithmParameter with a suitable KISAO.
> But how would I write [1] in SEDML?
>
> On Wed, Feb 3, 2016 at 12:03 AM, Lucian Smith <luc...@gm...>
> wrote:
>
>> On Tue, Feb 2, 2016 at 2:50 PM, Pedro Mendes <
>> ped...@ma...> wrote:
>>
>>> That would solve things. However it is impossible to antecipate if there
>>> will be other algorithms with other orders. My feeling is that these
>>> parameters are very specific from algorithm to algorithm and we can end
>>> up with lots of special cases.
>>>
>>
>> Is that a problem?  It's obviously not something that we can solve up
>> front, but if we keep adding more and more terms to KiSAO, each addition
>> permanently solves a new problem, and there's an obvious path to finding a
>> solution for each new use-case.
>>
>> There are only two other solutions that I can see:  limit people to only
>> using a certain subset of known algorithms; or letting people define
>> parameters with free text.  The current situation is obviously not ideal,
>> but those two options sound even *less* ideal, at least to me.  Is there
>> some other option I'm not seeing?  Or is this just something to keep in
>> mind as we go forward, and we try to see where we can mitigate the biggest
>> problems?
>>
>> A similar situation, but more extreme, is with optimization algorithms,
>>> which have all sorts of different algorithm parameters and it is
>>> impossible to generalize there. (This will impact SED-ML later on when
>>> we decide to include optimization or parameter estimation.
>>>
>>
>> Again, while filling KiSAO with thousands of highly-specific terms
>> doesn't sound ideal, I can't think of a better solution, either.  It's
>> worth keeping in mind, at least.
>>
>> -Lucian
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>
>
> --
> Matthias König
> Email: kon...@go...
> Tel: + 49 30 20938450
> Tel: + 49 176 81168480
>   https://www.livermetabolism.com/contact.html
> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
> Group König
> Charité Berlin, Institute of Biochemistry, Computational Systems
> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>



-- 
Matthias König
Email: kon...@go...
Tel: + 49 30 20938450
Tel: + 49 176 81168480
  https://www.livermetabolism.com/contact.html
Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group
König
Charité Berlin, Institute of Biochemistry, Computational Systems
Biochemistry <http://www.charite.de/sysbio/people/koenig/>

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

Well, there's a whole 'modelling and simulation algorithm characteristic'
branch of KiSAO.  Would it make sense to add 'implementation version
number' and 'implementation URL' to that list?

'Use the default settings except where otherwise noted' is probably
currently assumed; it might be worth adding that statement to the SED-ML
spec, though, assuming it doesn't already.

-Lucian

On Tue, Feb 2, 2016 at 3:09 PM, Matthias König <kon...@go...>
wrote:

> Would be nice to say something like:
> - [1] I use cvode v2.8.2 with all default settings
> - [2] I changed only BDF_max_order to 12
>
> [2] I can encode via the AlgorithmParameter with a suitable KISAO.
> But how would I write [1] in SEDML?
>
> On Wed, Feb 3, 2016 at 12:03 AM, Lucian Smith <luc...@gm...>
> wrote:
>
>> On Tue, Feb 2, 2016 at 2:50 PM, Pedro Mendes <
>> ped...@ma...> wrote:
>>
>>> That would solve things. However it is impossible to antecipate if there
>>> will be other algorithms with other orders. My feeling is that these
>>> parameters are very specific from algorithm to algorithm and we can end
>>> up with lots of special cases.
>>>
>>
>> Is that a problem?  It's obviously not something that we can solve up
>> front, but if we keep adding more and more terms to KiSAO, each addition
>> permanently solves a new problem, and there's an obvious path to finding a
>> solution for each new use-case.
>>
>> There are only two other solutions that I can see:  limit people to only
>> using a certain subset of known algorithms; or letting people define
>> parameters with free text.  The current situation is obviously not ideal,
>> but those two options sound even *less* ideal, at least to me.  Is there
>> some other option I'm not seeing?  Or is this just something to keep in
>> mind as we go forward, and we try to see where we can mitigate the biggest
>> problems?
>>
>> A similar situation, but more extreme, is with optimization algorithms,
>>> which have all sorts of different algorithm parameters and it is
>>> impossible to generalize there. (This will impact SED-ML later on when
>>> we decide to include optimization or parameter estimation.
>>>
>>
>> Again, while filling KiSAO with thousands of highly-specific terms
>> doesn't sound ideal, I can't think of a better solution, either.  It's
>> worth keeping in mind, at least.
>>
>> -Lucian
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>
>
> --
> Matthias König
> Email: kon...@go...
> Tel: + 49 30 20938450
> Tel: + 49 176 81168480
>   https://www.livermetabolism.com/contact.html
> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
> Group König
> Charité Berlin, Institute of Biochemistry, Computational Systems
> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
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> _______________________________________________
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> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

Would be nice to say something like:
- [1] I use cvode v2.8.2 with all default settings
- [2] I changed only BDF_max_order to 12

[2] I can encode via the AlgorithmParameter with a suitable KISAO.
But how would I write [1] in SEDML?

On Wed, Feb 3, 2016 at 12:03 AM, Lucian Smith <luc...@gm...>
wrote:

> On Tue, Feb 2, 2016 at 2:50 PM, Pedro Mendes <
> ped...@ma...> wrote:
>
>> That would solve things. However it is impossible to antecipate if there
>> will be other algorithms with other orders. My feeling is that these
>> parameters are very specific from algorithm to algorithm and we can end
>> up with lots of special cases.
>>
>
> Is that a problem?  It's obviously not something that we can solve up
> front, but if we keep adding more and more terms to KiSAO, each addition
> permanently solves a new problem, and there's an obvious path to finding a
> solution for each new use-case.
>
> There are only two other solutions that I can see:  limit people to only
> using a certain subset of known algorithms; or letting people define
> parameters with free text.  The current situation is obviously not ideal,
> but those two options sound even *less* ideal, at least to me.  Is there
> some other option I'm not seeing?  Or is this just something to keep in
> mind as we go forward, and we try to see where we can mitigate the biggest
> problems?
>
> A similar situation, but more extreme, is with optimization algorithms,
>> which have all sorts of different algorithm parameters and it is
>> impossible to generalize there. (This will impact SED-ML later on when
>> we decide to include optimization or parameter estimation.
>>
>
> Again, while filling KiSAO with thousands of highly-specific terms doesn't
> sound ideal, I can't think of a better solution, either.  It's worth
> keeping in mind, at least.
>
> -Lucian
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
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>
>


-- 
Matthias König
Email: kon...@go...
Tel: + 49 30 20938450
Tel: + 49 176 81168480
  https://www.livermetabolism.com/contact.html
Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group
König
Charité Berlin, Institute of Biochemistry, Computational Systems
Biochemistry <http://www.charite.de/sysbio/people/koenig/>

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

On Tue, Feb 2, 2016 at 2:52 PM, Matthias König <kon...@go...>
wrote:

>
> CVODE has many more internal parameters, which are normally set to
> defaults. With the exception of the error and warning settings all of the
> CVODE main solver settings could be algorithm parameters (one also need max
> order for BDF and ADAMS in CVODE).
> (from
> https://computation.llnl.gov/casc/sundials/documentation/cv_guide.pdf)
>
> [image: Inline image 1]
> M
>

I would be happy with adding all of these to KiSAO, where possible.
Obviously, some of them like 'user data' would need something a little bit
more involved ;-)  Would you be willing to go through these, find which
ones aren't in KiSAO now, and filling out tracker items for the ones we
could add?

-Lucian

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

On Tue, Feb 2, 2016 at 2:50 PM, Pedro Mendes <ped...@ma...>
wrote:

> That would solve things. However it is impossible to antecipate if there
> will be other algorithms with other orders. My feeling is that these
> parameters are very specific from algorithm to algorithm and we can end
> up with lots of special cases.
>

Is that a problem?  It's obviously not something that we can solve up
front, but if we keep adding more and more terms to KiSAO, each addition
permanently solves a new problem, and there's an obvious path to finding a
solution for each new use-case.

There are only two other solutions that I can see:  limit people to only
using a certain subset of known algorithms; or letting people define
parameters with free text.  The current situation is obviously not ideal,
but those two options sound even *less* ideal, at least to me.  Is there
some other option I'm not seeing?  Or is this just something to keep in
mind as we go forward, and we try to see where we can mitigate the biggest
problems?

A similar situation, but more extreme, is with optimization algorithms,
> which have all sorts of different algorithm parameters and it is
> impossible to generalize there. (This will impact SED-ML later on when
> we decide to include optimization or parameter estimation.
>

Again, while filling KiSAO with thousands of highly-specific terms doesn't
sound ideal, I can't think of a better solution, either.  It's worth
keeping in mind, at least.

-Lucian

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

CVODE has many more internal parameters, which are normally set to
defaults. With the exception of the error and warning settings all of the
CVODE main solver settings could be algorithm parameters (one also need max
order for BDF and ADAMS in CVODE).
(from https://computation.llnl.gov/casc/sundials/documentation/cv_guide.pdf)

[image: Inline image 1]
M


On Tue, Feb 2, 2016 at 11:35 PM, Lucian Smith <luc...@gm...>
wrote:

> Oh!  Well, that does make things more difficult.  Are 'adams' and 'bdf'
> the only two forms of 'maximum_order' that would be needed, or are there
> other (more obscure?) algorithms that also need multiple different
> 'maximum_order' settings?  And are the best generic terms for these
> settings 'adams' and 'bdf'?
>
> If distinguishing these two from each other is the only thing we need, I
> would assume that the best thing to do would be to request two new KiSAO
> terms that were both children of the new 'maximum_order' term:
>
> maximum_order
>   |_maximum_bdf_order
>   |_maximum_adams_order
>
> Would that solve things?  If so, I'll put in a new request.
>
> -Lucian
>
>
>
> On Tue, Feb 2, 2016 at 2:22 PM, Pedro Mendes <
> ped...@ma...> wrote:
>
>> The issue with the maximum_bdf_order and maximum_adams_order is that
>> they are needed in the same algorithm (LSODA) as this uses *both* bdf
>> and adams (unlike LSODE or CVODE for which you chose beforehand if you
>> want adams or bdf).
>>
>> Pedro
>>
>> On 02/02/2016 10:15 PM, Lucian Smith wrote:
>> > Those are there already, as of today:  I put in some requests for new
>> > KiSAO terms, which are all now accepted (see the top few of
>> >
>> https://sourceforge.net/p/kisao/feature-requests/search/?q=status%3Aclosed
>> )
>> >
>> > The only caveat is that there is a single 'maximum_order' KiSAO term,
>> > and whether (for roadrunner) you mean the adams or BDF version depends
>> > on which algorithm you're annotating.  The rest are straightforward.
>> > Next week, I should be able to update phrasedml to generate those SED-ML
>> > files for you (after I figure out what the new numbers actually are ;-).
>> >
>> > -Lucian
>> >
>> > On Tue, Feb 2, 2016 at 1:51 PM, Matthias König <
>> kon...@go...
>> > <mailto:kon...@go...>> wrote:
>> >
>> >     Sorry pressed to early.
>> >
>> >     I think everything else I need are Parameters in the
>> >     listOfAlgorithmParameters, namely the following
>> >
>> >     maximum_bdf_order: 5
>> >           maximum_adams_order: 12
>> >             maximum_num_steps: 20000
>> >             maximum_time_step: 0
>> >             minimum_time_step: 0
>> >             initial_time_step:
>> >
>> >
>> >     On Tue, Feb 2, 2016 at 10:50 PM, Matthias König
>> >     <kon...@go... <mailto:kon...@go...>> wrote:
>> >
>> >         listOfAlgorithmParameters
>> >
>> >         maximum_bdf_order: 5
>> >               maximum_adams_order: 12
>> >                 maximum_num_steps: 20000
>> >                 maximum_time_step: 0
>> >                 minimum_time_step: 0
>> >                 initial_time_step:
>> >
>> >
>> >
>> >         On Tue, Feb 2, 2016 at 7:37 PM, Lucian Smith
>> >         <luc...@gm... <mailto:luc...@gm...>>
>> >         wrote:
>> >
>> >             It's clearly important that whoever makes the diagrams use
>> >             what they're comfortable with!  I've made enough Google draw
>> >             UML diagrams by now that I can make them pretty quickly,
>> >             though of course you don't get the UML checking.  You can
>> >             export them to PDF, though, which is standard enough for
>> >             LaTeX to include.
>> >
>> >             Here's a draft UML diagram for Matthias's proposal.  And
>> >             clearly, great minds think alike, because I also had
>> >             Dagmar's idea of subclassing a base 'TimeCourse' abstract
>> class:
>> >
>> >
>> https://docs.google.com/drawings/d/1YqQ0h62UbEmBgrGvqGkHi9YhO1l3dUUsE3y7n83rMKw/edit?usp=sharing
>> >
>> >             -Lucian
>> >
>> >             On Tue, Feb 2, 2016 at 10:24 AM, Dagmar Waltemath
>> >             <dag...@un...
>> >             <mailto:dag...@un...>> wrote:
>> >
>> >                 Hi Lucian,
>> >
>> >                 it was me who insisted on using MagicDraw UML, because
>> >                 the last time I drew SBML UML diagrams this was in
>> >                 Google draw, so no means of checking the UML for
>> >                 consistency, and also not very automised, and not
>> >                 exportable to a standard format ;-).
>> >
>> >                 MagicDraw UML is not a free tool though, which is why
>> >                 the other editors didn't like it too much.
>> >
>> >                 Oh, and this is just to clarify, not an objection.
>> >
>> >                 Best, Dagmar
>> >
>> >
>> >                 *Dagmar Waltemath*, Dept. of Systems Biology &
>> >                 Bioinformatics,
>> >                 University of Rostock, D-18051 Rostock, Germany
>> >                 Web: http://www.sbi.uni-rostock.de/sems
>> >                 <
>> http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/>
>> >                 Skype: dagmar.waltemath
>> >
>>  ------------------------------------------------------------------------
>> >                 *Von:* Lucian Smith [luc...@gm...
>> >                 <mailto:luc...@gm...>]
>> >                 *Gesendet:* Dienstag, 2. Februar 2016 19:16
>> >                 *An:* sed...@li...
>> >                 <mailto:sed...@li...>
>> >                 *Betreff:* Re: [SED-ML-discuss] Feature request:
>> >                 NonUniformTimeCourse
>> >
>> >                 Sure, I can do that.  I like the idea of making a new
>> >                 base class which UniformTimeCourse inherits from.
>> >
>> >                 As far as the new spec goes, there are a lot of issues
>> >                 with the current UML diagrams, many of which have been
>> >                 filed in the sed-ml tracker.  I'm inclined to ditch them
>> >                 all and start from scratch, using UML templates from
>> >                 SBML.  Would anyone object to this? Are there features
>> >                 of the current SED-ML UML diagrams that people like
>> >                 better than the ones used in the SBML spec?
>> >
>> >                 -Lucian
>> >
>> >                 On Tue, Feb 2, 2016 at 9:37 AM, Moraru,Ion
>> >                 <mo...@uc... <mailto:mo...@uc...>> wrote:
>> >
>> >                     Same with VCell, has been supported for a decade by
>> >                     now…____
>> >
>> >                     __ __
>> >
>> >                     It is a feature on the list of add-ons to the next
>> >                     SED-ML version.  Perhaps Lucian, as a new Editor and
>> >                     full of energy, can spearhead a draft spec?____
>> >
>> >                     __ __
>> >
>> >                     Ion____
>> >
>> >                     __ __
>> >
>> >                     *From:*Herbert Sauro [mailto:hs...@gm...
>> >                     <mailto:hs...@gm...>]
>> >                     *Sent:* Tuesday, February 02, 2016 12:31 PM
>> >                     *To:* sed...@li...
>> >                     <mailto:sed...@li...>
>> >                     *Subject:* Re: [SED-ML-discuss] Feature request:
>> >                     NonUniformTimeCourse____
>> >
>> >                     __ __
>> >
>> >                     libRoadRunner already support variable time step so
>> >                     it would be very useful to have this in sedml.____
>> >
>> >                     __ __
>> >
>> >                     Herbert____
>> >
>> >                     __ __
>> >
>> >                     On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes
>> >                     <ped...@ma...
>> >                     <mailto:ped...@ma...>> wrote:____
>> >
>> >                         Matthias,
>> >
>> >                          > If tools like COPASI do not support
>> >                         variable_time_step simulation
>> >
>> >                         It will, the current snapshots being tested
>> >                         already have this feature,
>> >                         so it will be in the next release. It would be
>> >                         great if it would be
>> >                         supported in SED-ML.
>> >
>> >                         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.____
>> >
>> >
>> >
>>  ------------------------------------------------------------------------------
>> >                         Site24x7 APM Insight: Get Deep Visibility into
>> >                         Application Performance
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>> >                         at just $35/Month
>> >                         Monitor end-to-end web transactions and take
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>> >                         experience. Signup Now!
>> >
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> >                         <
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D267308311-26iu-3D_4140&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=muXLw0tJUSLN3opHI1lcLUoTTxgHFsFf0plt_ksm3ys&e=
>> >
>> >                         _______________________________________________
>> >                         SED-ML-discuss mailing list
>> >                         SED...@li...
>> >                         <mailto:SED...@li...>
>> >
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> >                         <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=
>> >____
>> >
>> >                     __ __
>> >
>> >
>> >
>>  ------------------------------------------------------------------------------
>> >                     Site24x7 APM Insight: Get Deep Visibility into
>> >                     Application Performance
>> >                     APM + Mobile APM + RUM: Monitor 3 App instances at
>> >                     just $35/Month
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>> >
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> >                     _______________________________________________
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>> >                     SED...@li...
>> >                     <mailto:SED...@li...>
>> >
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> >
>> >
>> >
>> >
>>  ------------------------------------------------------------------------------
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>> >                 SED...@li...
>> >                 <mailto:SED...@li...>
>> >
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> >
>> >
>> >
>> >
>>  ------------------------------------------------------------------------------
>> >             Site24x7 APM Insight: Get Deep Visibility into Application
>> >             Performance
>> >             APM + Mobile APM + RUM: Monitor 3 App instances at just
>> >             $35/Month
>> >             Monitor end-to-end web transactions and take corrective
>> >             actions now
>> >             Troubleshoot faster and improve end-user experience. Signup
>> Now!
>> >
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> >             _______________________________________________
>> >             SED-ML-discuss mailing list
>> >             SED...@li...
>> >             <mailto:SED...@li...>
>> >             https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> >
>> >
>> >
>> >
>> >         --
>> >         Matthias König
>> >         Email: kon...@go... <mailto:
>> kon...@go...>
>> >         Tel: + 49 30 20938450
>> >         Tel: + 49 176 81168480 <tel:%2B%2049%20176%2081168480>
>> >         https://www.livermetabolism.com/contact.html
>> >         Humboldt-University Berlin, Institute for Theoretical Biology,
>> >         Junior Group König
>> >         Charité Berlin, Institute of Biochemistry, Computational Systems
>> >         Biochemistry<http://www.charite.de/sysbio/people/koenig/>
>> >
>> >
>> >
>> >
>> >     --
>> >     Matthias König
>> >     Email: kon...@go... <mailto:kon...@go...>
>> >     Tel: + 49 30 20938450
>> >     Tel: + 49 176 81168480 <tel:%2B%2049%20176%2081168480>
>> >     https://www.livermetabolism.com/contact.html
>> >     Humboldt-University Berlin, Institute for Theoretical Biology,
>> >     Junior Group König
>> >     Charité Berlin, Institute of Biochemistry, Computational Systems
>> >     Biochemistry<http://www.charite.de/sysbio/people/koenig/>
>> >
>> >
>>  ------------------------------------------------------------------------------
>> >     Site24x7 APM Insight: Get Deep Visibility into Application
>> Performance
>> >     APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> >     Monitor end-to-end web transactions and take corrective actions now
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>> >     http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> >     _______________________________________________
>> >     SED-ML-discuss mailing list
>> >     SED...@li...
>> >     <mailto:SED...@li...>
>> >     https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> >
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> > Monitor end-to-end web transactions and take corrective actions now
>> > Troubleshoot faster and improve end-user experience. Signup Now!
>> > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> >
>> >
>> >
>> > _______________________________________________
>> > SED-ML-discuss mailing list
>> > SED...@li...
>> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> >
>>
>> --
>> 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.
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
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>> _______________________________________________
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>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>
>
>
> ------------------------------------------------------------------------------
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>
>


-- 
Matthias König
Email: kon...@go...
Tel: + 49 30 20938450
Tel: + 49 176 81168480
  https://www.livermetabolism.com/contact.html
Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group
König
Charité Berlin, Institute of Biochemistry, Computational Systems
Biochemistry <http://www.charite.de/sysbio/people/koenig/>

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

That would solve things. However it is impossible to antecipate if there 
will be other algorithms with other orders. My feeling is that these 
parameters are very specific from algorithm to algorithm and we can end 
up with lots of special cases.

A similar situation, but more extreme, is with optimization algorithms, 
which have all sorts of different algorithm parameters and it is 
impossible to generalize there. (This will impact SED-ML later on when 
we decide to include optimization or parameter estimation.

Pedro

On 02/02/2016 10:35 PM, Lucian Smith wrote:
> Oh!  Well, that does make things more difficult.  Are 'adams' and 'bdf'
> the only two forms of 'maximum_order' that would be needed, or are there
> other (more obscure?) algorithms that also need multiple different
> 'maximum_order' settings?  And are the best generic terms for these
> settings 'adams' and 'bdf'?
>
> If distinguishing these two from each other is the only thing we need, I
> would assume that the best thing to do would be to request two new KiSAO
> terms that were both children of the new 'maximum_order' term:
>
> maximum_order
>    |_maximum_bdf_order
>    |_maximum_adams_order
>
> Would that solve things?  If so, I'll put in a new request.
>
> -Lucian
>
>
>
> On Tue, Feb 2, 2016 at 2:22 PM, Pedro Mendes
> <ped...@ma... <mailto:ped...@ma...>>
> wrote:
>
>     The issue with the maximum_bdf_order and maximum_adams_order is that
>     they are needed in the same algorithm (LSODA) as this uses *both* bdf
>     and adams (unlike LSODE or CVODE for which you chose beforehand if you
>     want adams or bdf).
>
>     Pedro
>
>     On 02/02/2016 10:15 PM, Lucian Smith wrote:
>     > Those are there already, as of today:  I put in some requests for new
>     > KiSAO terms, which are all now accepted (see the top few of
>     >https://sourceforge.net/p/kisao/feature-requests/search/?q=status%3Aclosed)
>     >
>     > The only caveat is that there is a single 'maximum_order' KiSAO term,
>     > and whether (for roadrunner) you mean the adams or BDF version depends
>     > on which algorithm you're annotating.  The rest are straightforward.
>     > Next week, I should be able to update phrasedml to generate those SED-ML
>     > files for you (after I figure out what the new numbers actually are ;-).
>     >
>     > -Lucian
>     >
>     > On Tue, Feb 2, 2016 at 1:51 PM, Matthias König <kon...@go... <mailto:kon...@go...>
>     > <mailto:kon...@go... <mailto:kon...@go...>>> wrote:
>     >
>     >     Sorry pressed to early.
>     >
>     >     I think everything else I need are Parameters in the
>     >     listOfAlgorithmParameters, namely the following
>     >
>     >     maximum_bdf_order: 5
>     >           maximum_adams_order: 12
>     >             maximum_num_steps: 20000
>     >             maximum_time_step: 0
>     >             minimum_time_step: 0
>     >             initial_time_step:
>     >
>     >
>     >     On Tue, Feb 2, 2016 at 10:50 PM, Matthias König
>     >     <kon...@go... <mailto:kon...@go...>
>     <mailto:kon...@go... <mailto:kon...@go...>>>
>     wrote:
>     >
>     >         listOfAlgorithmParameters
>     >
>     >         maximum_bdf_order: 5
>     >               maximum_adams_order: 12
>     >                 maximum_num_steps: 20000
>     >                 maximum_time_step: 0
>     >                 minimum_time_step: 0
>     >                 initial_time_step:
>     >
>     >
>     >
>     >         On Tue, Feb 2, 2016 at 7:37 PM, Lucian Smith
>      >         <luc...@gm...
>     <mailto:luc...@gm...> <mailto:luc...@gm...
>     <mailto:luc...@gm...>>>
>     >         wrote:
>     >
>     >             It's clearly important that whoever makes the diagrams use
>     >             what they're comfortable with!  I've made enough Google draw
>     >             UML diagrams by now that I can make them pretty quickly,
>     >             though of course you don't get the UML checking.  You can
>     >             export them to PDF, though, which is standard enough for
>     >             LaTeX to include.
>     >
>     >             Here's a draft UML diagram for Matthias's proposal.  And
>     >             clearly, great minds think alike, because I also had
>     >             Dagmar's idea of subclassing a base 'TimeCourse' abstract class:
>     >
>     >https://docs.google.com/drawings/d/1YqQ0h62UbEmBgrGvqGkHi9YhO1l3dUUsE3y7n83rMKw/edit?usp=sharing
>     >
>     >             -Lucian
>     >
>     >             On Tue, Feb 2, 2016 at 10:24 AM, Dagmar Waltemath
>     >             <dag...@un... <mailto:dag...@un...>
>     >             <mailto:dag...@un...
>     <mailto:dag...@un...>>> wrote:
>     >
>     >                 Hi Lucian,
>     >
>     >                 it was me who insisted on using MagicDraw UML, because
>     >                 the last time I drew SBML UML diagrams this was in
>     >                 Google draw, so no means of checking the UML for
>     >                 consistency, and also not very automised, and not
>     >                 exportable to a standard format ;-).
>     >
>     >                 MagicDraw UML is not a free tool though, which is why
>     >                 the other editors didn't like it too much.
>     >
>     >                 Oh, and this is just to clarify, not an objection.
>     >
>     >                 Best, Dagmar
>     >
>     >
>      >                 *Dagmar Waltemath*, Dept. of Systems Biology &
>     >                 Bioinformatics,
>     >                 University of Rostock, D-18051 Rostock, Germany
>     >                 Web:http://www.sbi.uni-rostock.de/sems
>      >
>       <http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/>
>      >                 Skype: dagmar.waltemath
>      >
>       ------------------------------------------------------------------------
>      >                 *Von:* Lucian Smith [luc...@gm...
>     <mailto:luc...@gm...>
>      >                 <mailto:luc...@gm...
>     <mailto:luc...@gm...>>]
>      >                 *Gesendet:* Dienstag, 2. Februar 2016 19:16
>      >                 *An:* sed...@li...
>     <mailto:sed...@li...>
>      >                 <mailto:sed...@li...
>     <mailto:sed...@li...>>
>      >                 *Betreff:* Re: [SED-ML-discuss] Feature request:
>     >                 NonUniformTimeCourse
>     >
>     >                 Sure, I can do that.  I like the idea of making a new
>     >                 base class which UniformTimeCourse inherits from.
>     >
>     >                 As far as the new spec goes, there are a lot of issues
>     >                 with the current UML diagrams, many of which have been
>     >                 filed in the sed-ml tracker.  I'm inclined to ditch them
>     >                 all and start from scratch, using UML templates from
>     >                 SBML.  Would anyone object to this? Are there features
>     >                 of the current SED-ML UML diagrams that people like
>     >                 better than the ones used in the SBML spec?
>     >
>     >                 -Lucian
>     >
>     >                 On Tue, Feb 2, 2016 at 9:37 AM, Moraru,Ion
>     >                 <mo...@uc... <mailto:mo...@uc...> <mailto:mo...@uc...
>     <mailto:mo...@uc...>>> wrote:
>     >
>     >                     Same with VCell, has been supported for a decade by
>      >                     now…____
>      >
>      >                     __ __
>     >
>     >                     It is a feature on the list of add-ons to the next
>     >                     SED-ML version.  Perhaps Lucian, as a new Editor and
>      >                     full of energy, can spearhead a draft spec?____
>      >
>      >                     __ __
>      >
>      >                     Ion____
>      >
>      >                     __ __
>      >
>      >                     *From:*Herbert Sauro [mailto:hs...@gm...
>     <mailto:hs...@gm...>
>      >                     <mailto:hs...@gm...
>     <mailto:hs...@gm...>>]
>      >                     *Sent:* Tuesday, February 02, 2016 12:31 PM
>      >                     *To:* sed...@li...
>     <mailto:sed...@li...>
>      >                     <mailto:sed...@li...
>     <mailto:sed...@li...>>
>      >                     *Subject:* Re: [SED-ML-discuss] Feature request:
>      >                     NonUniformTimeCourse____
>      >
>      >                     __ __
>     >
>     >                     libRoadRunner already support variable time step so
>      >                     it would be very useful to have this in
>     sedml.____
>      >
>      >                     __ __
>      >
>      >                     Herbert____
>      >
>      >                     __ __
>     >
>     >                     On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes
>     >                     <ped...@ma... <mailto:ped...@ma...>
>      >                     <mailto:ped...@ma...
>     <mailto:ped...@ma...>>> wrote:____
>     >
>     >                         Matthias,
>     >
>     >                          > If tools like COPASI do not support
>     >                         variable_time_step simulation
>     >
>     >                         It will, the current snapshots being tested
>     >                         already have this feature,
>     >                         so it will be in the next release. It would be
>     >                         great if it would be
>     >                         supported in SED-ML.
>     >
>     >                         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.____
>     >
>     >
>     >                         ------------------------------------------------------------------------------
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>     >                         _______________________________________________
>     >                         SED-ML-discuss mailing list
>     >SED...@li...
>     <mailto:SED...@li...>
>      >
>       <mailto:SED...@li...
>     <mailto:SED...@li...>>
>      > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>      >
>       <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=>____
>      >
>      >                     __ __
>     >
>     >
>     >                     ------------------------------------------------------------------------------
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>     >                     APM + Mobile APM + RUM: Monitor 3 App instances at
>     >                     just $35/Month
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>     >                     corrective actions now
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>     >                     _______________________________________________
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>     >SED...@li...
>     <mailto:SED...@li...>
>      >                     <mailto:SED...@li...
>     <mailto:SED...@li...>>
>     >https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>     >
>     >
>     >
>     >                 ------------------------------------------------------------------------------
>     >                 Site24x7 APM Insight: Get Deep Visibility into
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>     >                 APM + Mobile APM + RUM: Monitor 3 App instances at just
>     >                 $35/Month
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>     >                 actions now
>     >                 Troubleshoot faster and improve end-user experience.
>     >                 Signup Now!
>     >http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>     >                 _______________________________________________
>     >                 SED-ML-discuss mailing list
>     >SED...@li...
>     <mailto:SED...@li...>
>      >                 <mailto:SED...@li...
>     <mailto:SED...@li...>>
>     >https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>     >
>     >
>     >
>     >             ------------------------------------------------------------------------------
>     >             Site24x7 APM Insight: Get Deep Visibility into Application
>     >             Performance
>     >             APM + Mobile APM + RUM: Monitor 3 App instances at just
>     >             $35/Month
>     >             Monitor end-to-end web transactions and take corrective
>     >             actions now
>     >             Troubleshoot faster and improve end-user experience. Signup Now!
>     >http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>     >             _______________________________________________
>     >             SED-ML-discuss mailing list
>     >SED...@li...
>     <mailto:SED...@li...>
>      >             <mailto:SED...@li...
>     <mailto:SED...@li...>>
>     >https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>     >
>     >
>     >
>     >
>     >         --
>     >         Matthias König
>      >         Email: kon...@go...
>     <mailto:kon...@go...> <mailto:kon...@go...
>     <mailto:kon...@go...>>
>     >         Tel:+ 49 30 20938450 <tel:%2B%2049%2030%2020938450>
>      >         Tel: + 49 176 81168480 <tel:%2B%2049%20176%2081168480>
>     <tel:%2B%2049%20176%2081168480>
>     >https://www.livermetabolism.com/contact.html
>     >         Humboldt-University Berlin, Institute for Theoretical Biology,
>     >         Junior Group König
>     >         Charité Berlin, Institute of Biochemistry, Computational Systems
>      >         Biochemistry<http://www.charite.de/sysbio/people/koenig/>
>      >
>      >
>      >
>      >
>      >     --
>      >     Matthias König
>      >     Email: kon...@go...
>     <mailto:kon...@go...> <mailto:kon...@go...
>     <mailto:kon...@go...>>
>     >     Tel:+ 49 30 20938450 <tel:%2B%2049%2030%2020938450>
>      >     Tel: + 49 176 81168480 <tel:%2B%2049%20176%2081168480>
>     <tel:%2B%2049%20176%2081168480>
>     >https://www.livermetabolism.com/contact.html
>     >     Humboldt-University Berlin, Institute for Theoretical Biology,
>     >     Junior Group König
>     >     Charité Berlin, Institute of Biochemistry, Computational Systems
>      >     Biochemistry<http://www.charite.de/sysbio/people/koenig/>
>     >
>     >     ------------------------------------------------------------------------------
>     >     Site24x7 APM Insight: Get Deep Visibility into Application Performance
>     >     APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>     >     Monitor end-to-end web transactions and take corrective actions now
>     >     Troubleshoot faster and improve end-user experience. Signup Now!
>     >http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>     >     _______________________________________________
>     >     SED-ML-discuss mailing list
>     >SED...@li...
>     <mailto:SED...@li...>
>      >     <mailto:SED...@li...
>     <mailto:SED...@li...>>
>     >https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>     >
>     >
>     >
>     >
>     > ------------------------------------------------------------------------------
>     > Site24x7 APM Insight: Get Deep Visibility into Application Performance
>     > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>     > Monitor end-to-end web transactions and take corrective actions now
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>     >
>     >
>     >
>     > _______________________________________________
>     > SED-ML-discuss mailing list
>     >SED...@li...
>     <mailto:SED...@li...>
>     >https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>     >
>
>     --
>     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.
>
>     ------------------------------------------------------------------------------
>     Site24x7 APM Insight: Get Deep Visibility into Application Performance
>     APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>     Monitor end-to-end web transactions and take corrective actions now
>     Troubleshoot faster and improve end-user experience. Signup Now!
>     http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>     _______________________________________________
>     SED-ML-discuss mailing list
>     SED...@li...
>     <mailto:SED...@li...>
>     https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>
>
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

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

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

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

Oh!  Well, that does make things more difficult.  Are 'adams' and 'bdf' the
only two forms of 'maximum_order' that would be needed, or are there other
(more obscure?) algorithms that also need multiple different
'maximum_order' settings?  And are the best generic terms for these
settings 'adams' and 'bdf'?

If distinguishing these two from each other is the only thing we need, I
would assume that the best thing to do would be to request two new KiSAO
terms that were both children of the new 'maximum_order' term:

maximum_order
  |_maximum_bdf_order
  |_maximum_adams_order

Would that solve things?  If so, I'll put in a new request.

-Lucian



On Tue, Feb 2, 2016 at 2:22 PM, Pedro Mendes <ped...@ma...>
wrote:

> The issue with the maximum_bdf_order and maximum_adams_order is that
> they are needed in the same algorithm (LSODA) as this uses *both* bdf
> and adams (unlike LSODE or CVODE for which you chose beforehand if you
> want adams or bdf).
>
> Pedro
>
> On 02/02/2016 10:15 PM, Lucian Smith wrote:
> > Those are there already, as of today:  I put in some requests for new
> > KiSAO terms, which are all now accepted (see the top few of
> >
> https://sourceforge.net/p/kisao/feature-requests/search/?q=status%3Aclosed
> )
> >
> > The only caveat is that there is a single 'maximum_order' KiSAO term,
> > and whether (for roadrunner) you mean the adams or BDF version depends
> > on which algorithm you're annotating.  The rest are straightforward.
> > Next week, I should be able to update phrasedml to generate those SED-ML
> > files for you (after I figure out what the new numbers actually are ;-).
> >
> > -Lucian
> >
> > On Tue, Feb 2, 2016 at 1:51 PM, Matthias König <kon...@go...
> > <mailto:kon...@go...>> wrote:
> >
> >     Sorry pressed to early.
> >
> >     I think everything else I need are Parameters in the
> >     listOfAlgorithmParameters, namely the following
> >
> >     maximum_bdf_order: 5
> >           maximum_adams_order: 12
> >             maximum_num_steps: 20000
> >             maximum_time_step: 0
> >             minimum_time_step: 0
> >             initial_time_step:
> >
> >
> >     On Tue, Feb 2, 2016 at 10:50 PM, Matthias König
> >     <kon...@go... <mailto:kon...@go...>> wrote:
> >
> >         listOfAlgorithmParameters
> >
> >         maximum_bdf_order: 5
> >               maximum_adams_order: 12
> >                 maximum_num_steps: 20000
> >                 maximum_time_step: 0
> >                 minimum_time_step: 0
> >                 initial_time_step:
> >
> >
> >
> >         On Tue, Feb 2, 2016 at 7:37 PM, Lucian Smith
> >         <luc...@gm... <mailto:luc...@gm...>>
> >         wrote:
> >
> >             It's clearly important that whoever makes the diagrams use
> >             what they're comfortable with!  I've made enough Google draw
> >             UML diagrams by now that I can make them pretty quickly,
> >             though of course you don't get the UML checking.  You can
> >             export them to PDF, though, which is standard enough for
> >             LaTeX to include.
> >
> >             Here's a draft UML diagram for Matthias's proposal.  And
> >             clearly, great minds think alike, because I also had
> >             Dagmar's idea of subclassing a base 'TimeCourse' abstract
> class:
> >
> >
> https://docs.google.com/drawings/d/1YqQ0h62UbEmBgrGvqGkHi9YhO1l3dUUsE3y7n83rMKw/edit?usp=sharing
> >
> >             -Lucian
> >
> >             On Tue, Feb 2, 2016 at 10:24 AM, Dagmar Waltemath
> >             <dag...@un...
> >             <mailto:dag...@un...>> wrote:
> >
> >                 Hi Lucian,
> >
> >                 it was me who insisted on using MagicDraw UML, because
> >                 the last time I drew SBML UML diagrams this was in
> >                 Google draw, so no means of checking the UML for
> >                 consistency, and also not very automised, and not
> >                 exportable to a standard format ;-).
> >
> >                 MagicDraw UML is not a free tool though, which is why
> >                 the other editors didn't like it too much.
> >
> >                 Oh, and this is just to clarify, not an objection.
> >
> >                 Best, Dagmar
> >
> >
> >                 *Dagmar Waltemath*, Dept. of Systems Biology &
> >                 Bioinformatics,
> >                 University of Rostock, D-18051 Rostock, Germany
> >                 Web: http://www.sbi.uni-rostock.de/sems
> >                 <
> http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/>
> >                 Skype: dagmar.waltemath
> >
>  ------------------------------------------------------------------------
> >                 *Von:* Lucian Smith [luc...@gm...
> >                 <mailto:luc...@gm...>]
> >                 *Gesendet:* Dienstag, 2. Februar 2016 19:16
> >                 *An:* sed...@li...
> >                 <mailto:sed...@li...>
> >                 *Betreff:* Re: [SED-ML-discuss] Feature request:
> >                 NonUniformTimeCourse
> >
> >                 Sure, I can do that.  I like the idea of making a new
> >                 base class which UniformTimeCourse inherits from.
> >
> >                 As far as the new spec goes, there are a lot of issues
> >                 with the current UML diagrams, many of which have been
> >                 filed in the sed-ml tracker.  I'm inclined to ditch them
> >                 all and start from scratch, using UML templates from
> >                 SBML.  Would anyone object to this? Are there features
> >                 of the current SED-ML UML diagrams that people like
> >                 better than the ones used in the SBML spec?
> >
> >                 -Lucian
> >
> >                 On Tue, Feb 2, 2016 at 9:37 AM, Moraru,Ion
> >                 <mo...@uc... <mailto:mo...@uc...>> wrote:
> >
> >                     Same with VCell, has been supported for a decade by
> >                     now…____
> >
> >                     __ __
> >
> >                     It is a feature on the list of add-ons to the next
> >                     SED-ML version.  Perhaps Lucian, as a new Editor and
> >                     full of energy, can spearhead a draft spec?____
> >
> >                     __ __
> >
> >                     Ion____
> >
> >                     __ __
> >
> >                     *From:*Herbert Sauro [mailto:hs...@gm...
> >                     <mailto:hs...@gm...>]
> >                     *Sent:* Tuesday, February 02, 2016 12:31 PM
> >                     *To:* sed...@li...
> >                     <mailto:sed...@li...>
> >                     *Subject:* Re: [SED-ML-discuss] Feature request:
> >                     NonUniformTimeCourse____
> >
> >                     __ __
> >
> >                     libRoadRunner already support variable time step so
> >                     it would be very useful to have this in sedml.____
> >
> >                     __ __
> >
> >                     Herbert____
> >
> >                     __ __
> >
> >                     On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes
> >                     <ped...@ma...
> >                     <mailto:ped...@ma...>> wrote:____
> >
> >                         Matthias,
> >
> >                          > If tools like COPASI do not support
> >                         variable_time_step simulation
> >
> >                         It will, the current snapshots being tested
> >                         already have this feature,
> >                         so it will be in the next release. It would be
> >                         great if it would be
> >                         supported in SED-ML.
> >
> >                         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.____
> >
> >
> >
>  ------------------------------------------------------------------------------
> >                         Site24x7 APM Insight: Get Deep Visibility into
> >                         Application Performance
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> >                         at just $35/Month
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> >                         experience. Signup Now!
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> >                         <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D267308311-26iu-3D_4140&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=muXLw0tJUSLN3opHI1lcLUoTTxgHFsFf0plt_ksm3ys&e=
> >
> >                         _______________________________________________
> >                         SED-ML-discuss mailing list
> >                         SED...@li...
> >                         <mailto:SED...@li...>
> >
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >                         <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=
> >____
> >
> >                     __ __
> >
> >
> >
>  ------------------------------------------------------------------------------
> >                     Site24x7 APM Insight: Get Deep Visibility into
> >                     Application Performance
> >                     APM + Mobile APM + RUM: Monitor 3 App instances at
> >                     just $35/Month
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> >                     Signup Now!
> >
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> >                     <mailto:SED...@li...>
> >
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> >
> >
> >
>  ------------------------------------------------------------------------------
> >                 Site24x7 APM Insight: Get Deep Visibility into
> >                 Application Performance
> >                 APM + Mobile APM + RUM: Monitor 3 App instances at just
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> >                 SED...@li...
> >                 <mailto:SED...@li...>
> >
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> >
> >
> >
>  ------------------------------------------------------------------------------
> >             Site24x7 APM Insight: Get Deep Visibility into Application
> >             Performance
> >             APM + Mobile APM + RUM: Monitor 3 App instances at just
> >             $35/Month
> >             Monitor end-to-end web transactions and take corrective
> >             actions now
> >             Troubleshoot faster and improve end-user experience. Signup
> Now!
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> >             _______________________________________________
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> >             SED...@li...
> >             <mailto:SED...@li...>
> >             https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> >
> >
> >
> >         --
> >         Matthias König
> >         Email: kon...@go... <mailto:kon...@go...
> >
> >         Tel: + 49 30 20938450
> >         Tel: + 49 176 81168480 <tel:%2B%2049%20176%2081168480>
> >         https://www.livermetabolism.com/contact.html
> >         Humboldt-University Berlin, Institute for Theoretical Biology,
> >         Junior Group König
> >         Charité Berlin, Institute of Biochemistry, Computational Systems
> >         Biochemistry<http://www.charite.de/sysbio/people/koenig/>
> >
> >
> >
> >
> >     --
> >     Matthias König
> >     Email: kon...@go... <mailto:kon...@go...>
> >     Tel: + 49 30 20938450
> >     Tel: + 49 176 81168480 <tel:%2B%2049%20176%2081168480>
> >     https://www.livermetabolism.com/contact.html
> >     Humboldt-University Berlin, Institute for Theoretical Biology,
> >     Junior Group König
> >     Charité Berlin, Institute of Biochemistry, Computational Systems
> >     Biochemistry<http://www.charite.de/sysbio/people/koenig/>
> >
> >
>  ------------------------------------------------------------------------------
> >     Site24x7 APM Insight: Get Deep Visibility into Application
> Performance
> >     APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> >     Monitor end-to-end web transactions and take corrective actions now
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> >     <mailto:SED...@li...>
> >     https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Site24x7 APM Insight: Get Deep Visibility into Application Performance
> > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
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> >
> >
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
>
> --
> 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.
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

@Lucian great. Saw your Kisao post and had the feeling it covers everything
I need.
As soon as there are NonUniformTimeCourse & Kisao terms available I wanted
to implement better SED-ML support in roadrunner/tellurium.
phrasedml would be the scripting language to generate the SEDML files in
the workflow.

On Tue, Feb 2, 2016 at 11:15 PM, Lucian Smith <luc...@gm...>
wrote:

> Those are there already, as of today:  I put in some requests for new
> KiSAO terms, which are all now accepted (see the top few of
> https://sourceforge.net/p/kisao/feature-requests/search/?q=status%3Aclosed
> )
>
> The only caveat is that there is a single 'maximum_order' KiSAO term, and
> whether (for roadrunner) you mean the adams or BDF version depends on which
> algorithm you're annotating.  The rest are straightforward.  Next week, I
> should be able to update phrasedml to generate those SED-ML files for you
> (after I figure out what the new numbers actually are ;-).
>
> -Lucian
>
> On Tue, Feb 2, 2016 at 1:51 PM, Matthias König <kon...@go...>
> wrote:
>
>> Sorry pressed to early.
>>
>> I think everything else I need are Parameters in the
>> listOfAlgorithmParameters, namely the following
>>
>> maximum_bdf_order: 5
>>      maximum_adams_order: 12
>>        maximum_num_steps: 20000
>>        maximum_time_step: 0
>>        minimum_time_step: 0
>>        initial_time_step:
>>
>>
>> On Tue, Feb 2, 2016 at 10:50 PM, Matthias König <kon...@go...
>> > wrote:
>>
>>> listOfAlgorithmParameters
>>>
>>> maximum_bdf_order: 5
>>>      maximum_adams_order: 12
>>>        maximum_num_steps: 20000
>>>        maximum_time_step: 0
>>>        minimum_time_step: 0
>>>        initial_time_step:
>>>
>>>
>>>
>>> On Tue, Feb 2, 2016 at 7:37 PM, Lucian Smith <luc...@gm...>
>>> wrote:
>>>
>>>> It's clearly important that whoever makes the diagrams use what they're
>>>> comfortable with!  I've made enough Google draw UML diagrams by now that I
>>>> can make them pretty quickly, though of course you don't get the UML
>>>> checking.  You can export them to PDF, though, which is standard enough for
>>>> LaTeX to include.
>>>>
>>>> Here's a draft UML diagram for Matthias's proposal.  And clearly, great
>>>> minds think alike, because I also had Dagmar's idea of subclassing a base
>>>> 'TimeCourse' abstract class:
>>>>
>>>>
>>>> https://docs.google.com/drawings/d/1YqQ0h62UbEmBgrGvqGkHi9YhO1l3dUUsE3y7n83rMKw/edit?usp=sharing
>>>>
>>>> -Lucian
>>>>
>>>> On Tue, Feb 2, 2016 at 10:24 AM, Dagmar Waltemath <
>>>> dag...@un...> wrote:
>>>>
>>>>> Hi Lucian,
>>>>>
>>>>> it was me who insisted on using MagicDraw UML, because the last time I
>>>>> drew SBML UML diagrams this was in Google draw, so no means of checking the
>>>>> UML for consistency, and also not very automised, and not exportable to a
>>>>> standard format ;-).
>>>>>
>>>>> MagicDraw UML is not a free tool though, which is why the other
>>>>> editors didn't like it too much.
>>>>>
>>>>> Oh, and this is just to clarify, not an objection.
>>>>>
>>>>> Best, Dagmar
>>>>>
>>>>>
>>>>> *Dagmar Waltemath*, Dept. of Systems Biology & Bioinformatics,
>>>>> University of Rostock, D-18051 Rostock, Germany
>>>>> Web: http://www.sbi.uni-rostock.de/sems
>>>>> <http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/>
>>>>> Skype: dagmar.waltemath
>>>>> ------------------------------
>>>>> *Von:* Lucian Smith [luc...@gm...]
>>>>> *Gesendet:* Dienstag, 2. Februar 2016 19:16
>>>>> *An:* sed...@li...
>>>>> *Betreff:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse
>>>>>
>>>>> Sure, I can do that.  I like the idea of making a new base class which
>>>>> UniformTimeCourse inherits from.
>>>>>
>>>>> As far as the new spec goes, there are a lot of issues with the
>>>>> current UML diagrams, many of which have been filed in the sed-ml tracker.
>>>>> I'm inclined to ditch them all and start from scratch, using UML templates
>>>>> from SBML.  Would anyone object to this?  Are there features of the current
>>>>> SED-ML UML diagrams that people like better than the ones used in the SBML
>>>>> spec?
>>>>>
>>>>> -Lucian
>>>>>
>>>>> On Tue, Feb 2, 2016 at 9:37 AM, Moraru,Ion <mo...@uc...> wrote:
>>>>>
>>>>>> Same with VCell, has been supported for a decade by now…
>>>>>>
>>>>>>
>>>>>>
>>>>>> It is a feature on the list of add-ons to the next SED-ML version.
>>>>>> Perhaps Lucian, as a new Editor and full of energy, can spearhead a draft
>>>>>> spec?
>>>>>>
>>>>>>
>>>>>>
>>>>>> Ion
>>>>>>
>>>>>>
>>>>>>
>>>>>> *From:* Herbert Sauro [mailto:hs...@gm...]
>>>>>> *Sent:* Tuesday, February 02, 2016 12:31 PM
>>>>>> *To:* sed...@li...
>>>>>> *Subject:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse
>>>>>>
>>>>>>
>>>>>>
>>>>>> libRoadRunner already support variable time step so it would be very
>>>>>> useful to have this in sedml.
>>>>>>
>>>>>>
>>>>>>
>>>>>> Herbert
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes <
>>>>>> ped...@ma...> wrote:
>>>>>>
>>>>>> Matthias,
>>>>>>
>>>>>> > If tools like COPASI do not support variable_time_step simulation
>>>>>>
>>>>>> It will, the current snapshots being tested already have this feature,
>>>>>> so it will be in the next release. It would be great if it would be
>>>>>> supported in SED-ML.
>>>>>>
>>>>>> 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.
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D267308311-26iu-3D_4140&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=muXLw0tJUSLN3opHI1lcLUoTTxgHFsFf0plt_ksm3ys&e=>
>>>>>> _______________________________________________
>>>>>> SED-ML-discuss mailing list
>>>>>> SED...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>>> _______________________________________________
>>>>>> SED-ML-discuss mailing list
>>>>>> SED...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>> _______________________________________________
>>>>> SED-ML-discuss mailing list
>>>>> SED...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
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>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>
>>>>
>>>
>>>
>>> --
>>> Matthias König
>>> Email: kon...@go...
>>> Tel: + 49 30 20938450
>>> Tel: + 49 176 81168480
>>>   https://www.livermetabolism.com/contact.html
>>> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
>>> Group König
>>> Charité Berlin, Institute of Biochemistry, Computational Systems
>>> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>>>
>>
>>
>>
>> --
>> Matthias König
>> Email: kon...@go...
>> Tel: + 49 30 20938450
>> Tel: + 49 176 81168480
>>   https://www.livermetabolism.com/contact.html
>> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
>> Group König
>> Charité Berlin, Institute of Biochemistry, Computational Systems
>> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
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> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>


-- 
Matthias König
Email: kon...@go...
Tel: + 49 30 20938450
Tel: + 49 176 81168480
  https://www.livermetabolism.com/contact.html
Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group
König
Charité Berlin, Institute of Biochemistry, Computational Systems
Biochemistry <http://www.charite.de/sysbio/people/koenig/>

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

The issue with the maximum_bdf_order and maximum_adams_order is that 
they are needed in the same algorithm (LSODA) as this uses *both* bdf 
and adams (unlike LSODE or CVODE for which you chose beforehand if you 
want adams or bdf).

Pedro

On 02/02/2016 10:15 PM, Lucian Smith wrote:
> Those are there already, as of today:  I put in some requests for new
> KiSAO terms, which are all now accepted (see the top few of
> https://sourceforge.net/p/kisao/feature-requests/search/?q=status%3Aclosed)
>
> The only caveat is that there is a single 'maximum_order' KiSAO term,
> and whether (for roadrunner) you mean the adams or BDF version depends
> on which algorithm you're annotating.  The rest are straightforward.
> Next week, I should be able to update phrasedml to generate those SED-ML
> files for you (after I figure out what the new numbers actually are ;-).
>
> -Lucian
>
> On Tue, Feb 2, 2016 at 1:51 PM, Matthias König <kon...@go...
> <mailto:kon...@go...>> wrote:
>
>     Sorry pressed to early.
>
>     I think everything else I need are Parameters in the
>     listOfAlgorithmParameters, namely the following
>
>     maximum_bdf_order: 5
>           maximum_adams_order: 12
>             maximum_num_steps: 20000
>             maximum_time_step: 0
>             minimum_time_step: 0
>             initial_time_step:
>
>
>     On Tue, Feb 2, 2016 at 10:50 PM, Matthias König
>     <kon...@go... <mailto:kon...@go...>> wrote:
>
>         listOfAlgorithmParameters
>
>         maximum_bdf_order: 5
>               maximum_adams_order: 12
>                 maximum_num_steps: 20000
>                 maximum_time_step: 0
>                 minimum_time_step: 0
>                 initial_time_step:
>
>
>
>         On Tue, Feb 2, 2016 at 7:37 PM, Lucian Smith
>         <luc...@gm... <mailto:luc...@gm...>>
>         wrote:
>
>             It's clearly important that whoever makes the diagrams use
>             what they're comfortable with!  I've made enough Google draw
>             UML diagrams by now that I can make them pretty quickly,
>             though of course you don't get the UML checking.  You can
>             export them to PDF, though, which is standard enough for
>             LaTeX to include.
>
>             Here's a draft UML diagram for Matthias's proposal.  And
>             clearly, great minds think alike, because I also had
>             Dagmar's idea of subclassing a base 'TimeCourse' abstract class:
>
>             https://docs.google.com/drawings/d/1YqQ0h62UbEmBgrGvqGkHi9YhO1l3dUUsE3y7n83rMKw/edit?usp=sharing
>
>             -Lucian
>
>             On Tue, Feb 2, 2016 at 10:24 AM, Dagmar Waltemath
>             <dag...@un...
>             <mailto:dag...@un...>> wrote:
>
>                 Hi Lucian,
>
>                 it was me who insisted on using MagicDraw UML, because
>                 the last time I drew SBML UML diagrams this was in
>                 Google draw, so no means of checking the UML for
>                 consistency, and also not very automised, and not
>                 exportable to a standard format ;-).
>
>                 MagicDraw UML is not a free tool though, which is why
>                 the other editors didn't like it too much.
>
>                 Oh, and this is just to clarify, not an objection.
>
>                 Best, Dagmar
>
>
>                 *Dagmar Waltemath*, Dept. of Systems Biology &
>                 Bioinformatics,
>                 University of Rostock, D-18051 Rostock, Germany
>                 Web: http://www.sbi.uni-rostock.de/sems
>                 <http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/>
>                 Skype: dagmar.waltemath
>                 ------------------------------------------------------------------------
>                 *Von:* Lucian Smith [luc...@gm...
>                 <mailto:luc...@gm...>]
>                 *Gesendet:* Dienstag, 2. Februar 2016 19:16
>                 *An:* sed...@li...
>                 <mailto:sed...@li...>
>                 *Betreff:* Re: [SED-ML-discuss] Feature request:
>                 NonUniformTimeCourse
>
>                 Sure, I can do that.  I like the idea of making a new
>                 base class which UniformTimeCourse inherits from.
>
>                 As far as the new spec goes, there are a lot of issues
>                 with the current UML diagrams, many of which have been
>                 filed in the sed-ml tracker.  I'm inclined to ditch them
>                 all and start from scratch, using UML templates from
>                 SBML.  Would anyone object to this? Are there features
>                 of the current SED-ML UML diagrams that people like
>                 better than the ones used in the SBML spec?
>
>                 -Lucian
>
>                 On Tue, Feb 2, 2016 at 9:37 AM, Moraru,Ion
>                 <mo...@uc... <mailto:mo...@uc...>> wrote:
>
>                     Same with VCell, has been supported for a decade by
>                     now…____
>
>                     __ __
>
>                     It is a feature on the list of add-ons to the next
>                     SED-ML version.  Perhaps Lucian, as a new Editor and
>                     full of energy, can spearhead a draft spec?____
>
>                     __ __
>
>                     Ion____
>
>                     __ __
>
>                     *From:*Herbert Sauro [mailto:hs...@gm...
>                     <mailto:hs...@gm...>]
>                     *Sent:* Tuesday, February 02, 2016 12:31 PM
>                     *To:* sed...@li...
>                     <mailto:sed...@li...>
>                     *Subject:* Re: [SED-ML-discuss] Feature request:
>                     NonUniformTimeCourse____
>
>                     __ __
>
>                     libRoadRunner already support variable time step so
>                     it would be very useful to have this in sedml.____
>
>                     __ __
>
>                     Herbert____
>
>                     __ __
>
>                     On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes
>                     <ped...@ma...
>                     <mailto:ped...@ma...>> wrote:____
>
>                         Matthias,
>
>                          > If tools like COPASI do not support
>                         variable_time_step simulation
>
>                         It will, the current snapshots being tested
>                         already have this feature,
>                         so it will be in the next release. It would be
>                         great if it would be
>                         supported in SED-ML.
>
>                         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.____
>
>
>                         ------------------------------------------------------------------------------
>                         Site24x7 APM Insight: Get Deep Visibility into
>                         Application Performance
>                         APM + Mobile APM + RUM: Monitor 3 App instances
>                         at just $35/Month
>                         Monitor end-to-end web transactions and take
>                         corrective actions now
>                         Troubleshoot faster and improve end-user
>                         experience. Signup Now!
>                         http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>                         <https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D267308311-26iu-3D_4140&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=muXLw0tJUSLN3opHI1lcLUoTTxgHFsFf0plt_ksm3ys&e=>
>                         _______________________________________________
>                         SED-ML-discuss mailing list
>                         SED...@li...
>                         <mailto:SED...@li...>
>                         https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>                         <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=>____
>
>                     __ __
>
>
>                     ------------------------------------------------------------------------------
>                     Site24x7 APM Insight: Get Deep Visibility into
>                     Application Performance
>                     APM + Mobile APM + RUM: Monitor 3 App instances at
>                     just $35/Month
>                     Monitor end-to-end web transactions and take
>                     corrective actions now
>                     Troubleshoot faster and improve end-user experience.
>                     Signup Now!
>                     http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>                     _______________________________________________
>                     SED-ML-discuss mailing list
>                     SED...@li...
>                     <mailto:SED...@li...>
>                     https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
>                 ------------------------------------------------------------------------------
>                 Site24x7 APM Insight: Get Deep Visibility into
>                 Application Performance
>                 APM + Mobile APM + RUM: Monitor 3 App instances at just
>                 $35/Month
>                 Monitor end-to-end web transactions and take corrective
>                 actions now
>                 Troubleshoot faster and improve end-user experience.
>                 Signup Now!
>                 http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>                 _______________________________________________
>                 SED-ML-discuss mailing list
>                 SED...@li...
>                 <mailto:SED...@li...>
>                 https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
>             ------------------------------------------------------------------------------
>             Site24x7 APM Insight: Get Deep Visibility into Application
>             Performance
>             APM + Mobile APM + RUM: Monitor 3 App instances at just
>             $35/Month
>             Monitor end-to-end web transactions and take corrective
>             actions now
>             Troubleshoot faster and improve end-user experience. Signup Now!
>             http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>             _______________________________________________
>             SED-ML-discuss mailing list
>             SED...@li...
>             <mailto:SED...@li...>
>             https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
>
>         --
>         Matthias König
>         Email: kon...@go... <mailto:kon...@go...>
>         Tel: + 49 30 20938450
>         Tel: + 49 176 81168480 <tel:%2B%2049%20176%2081168480>
>         https://www.livermetabolism.com/contact.html
>         Humboldt-University Berlin, Institute for Theoretical Biology,
>         Junior Group König
>         Charité Berlin, Institute of Biochemistry, Computational Systems
>         Biochemistry<http://www.charite.de/sysbio/people/koenig/>
>
>
>
>
>     --
>     Matthias König
>     Email: kon...@go... <mailto:kon...@go...>
>     Tel: + 49 30 20938450
>     Tel: + 49 176 81168480 <tel:%2B%2049%20176%2081168480>
>     https://www.livermetabolism.com/contact.html
>     Humboldt-University Berlin, Institute for Theoretical Biology,
>     Junior Group König
>     Charité Berlin, Institute of Biochemistry, Computational Systems
>     Biochemistry<http://www.charite.de/sysbio/people/koenig/>
>
>     ------------------------------------------------------------------------------
>     Site24x7 APM Insight: Get Deep Visibility into Application Performance
>     APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>     Monitor end-to-end web transactions and take corrective actions now
>     Troubleshoot faster and improve end-user experience. Signup Now!
>     http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>     _______________________________________________
>     SED-ML-discuss mailing list
>     SED...@li...
>     <mailto:SED...@li...>
>     https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>
>
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

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

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

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

Those are there already, as of today:  I put in some requests for new KiSAO
terms, which are all now accepted (see the top few of
https://sourceforge.net/p/kisao/feature-requests/search/?q=status%3Aclosed)

The only caveat is that there is a single 'maximum_order' KiSAO term, and
whether (for roadrunner) you mean the adams or BDF version depends on which
algorithm you're annotating.  The rest are straightforward.  Next week, I
should be able to update phrasedml to generate those SED-ML files for you
(after I figure out what the new numbers actually are ;-).

-Lucian

On Tue, Feb 2, 2016 at 1:51 PM, Matthias König <kon...@go...>
wrote:

> Sorry pressed to early.
>
> I think everything else I need are Parameters in the
> listOfAlgorithmParameters, namely the following
>
> maximum_bdf_order: 5
>      maximum_adams_order: 12
>        maximum_num_steps: 20000
>        maximum_time_step: 0
>        minimum_time_step: 0
>        initial_time_step:
>
>
> On Tue, Feb 2, 2016 at 10:50 PM, Matthias König <kon...@go...>
> wrote:
>
>> listOfAlgorithmParameters
>>
>> maximum_bdf_order: 5
>>      maximum_adams_order: 12
>>        maximum_num_steps: 20000
>>        maximum_time_step: 0
>>        minimum_time_step: 0
>>        initial_time_step:
>>
>>
>>
>> On Tue, Feb 2, 2016 at 7:37 PM, Lucian Smith <luc...@gm...>
>> wrote:
>>
>>> It's clearly important that whoever makes the diagrams use what they're
>>> comfortable with!  I've made enough Google draw UML diagrams by now that I
>>> can make them pretty quickly, though of course you don't get the UML
>>> checking.  You can export them to PDF, though, which is standard enough for
>>> LaTeX to include.
>>>
>>> Here's a draft UML diagram for Matthias's proposal.  And clearly, great
>>> minds think alike, because I also had Dagmar's idea of subclassing a base
>>> 'TimeCourse' abstract class:
>>>
>>>
>>> https://docs.google.com/drawings/d/1YqQ0h62UbEmBgrGvqGkHi9YhO1l3dUUsE3y7n83rMKw/edit?usp=sharing
>>>
>>> -Lucian
>>>
>>> On Tue, Feb 2, 2016 at 10:24 AM, Dagmar Waltemath <
>>> dag...@un...> wrote:
>>>
>>>> Hi Lucian,
>>>>
>>>> it was me who insisted on using MagicDraw UML, because the last time I
>>>> drew SBML UML diagrams this was in Google draw, so no means of checking the
>>>> UML for consistency, and also not very automised, and not exportable to a
>>>> standard format ;-).
>>>>
>>>> MagicDraw UML is not a free tool though, which is why the other editors
>>>> didn't like it too much.
>>>>
>>>> Oh, and this is just to clarify, not an objection.
>>>>
>>>> Best, Dagmar
>>>>
>>>>
>>>> *Dagmar Waltemath*, Dept. of Systems Biology & Bioinformatics,
>>>> University of Rostock, D-18051 Rostock, Germany
>>>> Web: http://www.sbi.uni-rostock.de/sems
>>>> <http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/>
>>>> Skype: dagmar.waltemath
>>>> ------------------------------
>>>> *Von:* Lucian Smith [luc...@gm...]
>>>> *Gesendet:* Dienstag, 2. Februar 2016 19:16
>>>> *An:* sed...@li...
>>>> *Betreff:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse
>>>>
>>>> Sure, I can do that.  I like the idea of making a new base class which
>>>> UniformTimeCourse inherits from.
>>>>
>>>> As far as the new spec goes, there are a lot of issues with the current
>>>> UML diagrams, many of which have been filed in the sed-ml tracker.  I'm
>>>> inclined to ditch them all and start from scratch, using UML templates from
>>>> SBML.  Would anyone object to this?  Are there features of the current
>>>> SED-ML UML diagrams that people like better than the ones used in the SBML
>>>> spec?
>>>>
>>>> -Lucian
>>>>
>>>> On Tue, Feb 2, 2016 at 9:37 AM, Moraru,Ion <mo...@uc...> wrote:
>>>>
>>>>> Same with VCell, has been supported for a decade by now…
>>>>>
>>>>>
>>>>>
>>>>> It is a feature on the list of add-ons to the next SED-ML version.
>>>>> Perhaps Lucian, as a new Editor and full of energy, can spearhead a draft
>>>>> spec?
>>>>>
>>>>>
>>>>>
>>>>> Ion
>>>>>
>>>>>
>>>>>
>>>>> *From:* Herbert Sauro [mailto:hs...@gm...]
>>>>> *Sent:* Tuesday, February 02, 2016 12:31 PM
>>>>> *To:* sed...@li...
>>>>> *Subject:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse
>>>>>
>>>>>
>>>>>
>>>>> libRoadRunner already support variable time step so it would be very
>>>>> useful to have this in sedml.
>>>>>
>>>>>
>>>>>
>>>>> Herbert
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes <
>>>>> ped...@ma...> wrote:
>>>>>
>>>>> Matthias,
>>>>>
>>>>> > If tools like COPASI do not support variable_time_step simulation
>>>>>
>>>>> It will, the current snapshots being tested already have this feature,
>>>>> so it will be in the next release. It would be great if it would be
>>>>> supported in SED-ML.
>>>>>
>>>>> 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.
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D267308311-26iu-3D_4140&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=muXLw0tJUSLN3opHI1lcLUoTTxgHFsFf0plt_ksm3ys&e=>
>>>>> _______________________________________________
>>>>> SED-ML-discuss mailing list
>>>>> SED...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>>> Monitor end-to-end web transactions and take corrective actions now
>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>>> _______________________________________________
>>>>> SED-ML-discuss mailing list
>>>>> SED...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
>>
>>
>> --
>> Matthias König
>> Email: kon...@go...
>> Tel: + 49 30 20938450
>> Tel: + 49 176 81168480
>>   https://www.livermetabolism.com/contact.html
>> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
>> Group König
>> Charité Berlin, Institute of Biochemistry, Computational Systems
>> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>>
>
>
>
> --
> Matthias König
> Email: kon...@go...
> Tel: + 49 30 20938450
> Tel: + 49 176 81168480
>   https://www.livermetabolism.com/contact.html
> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
> Group König
> Charité Berlin, Institute of Biochemistry, Computational Systems
> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>

Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse

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

Sorry pressed to early.

I think everything else I need are Parameters in the
listOfAlgorithmParameters, namely the following

maximum_bdf_order: 5
     maximum_adams_order: 12
       maximum_num_steps: 20000
       maximum_time_step: 0
       minimum_time_step: 0
       initial_time_step:


On Tue, Feb 2, 2016 at 10:50 PM, Matthias König <kon...@go...>
wrote:

> listOfAlgorithmParameters
>
> maximum_bdf_order: 5
>      maximum_adams_order: 12
>        maximum_num_steps: 20000
>        maximum_time_step: 0
>        minimum_time_step: 0
>        initial_time_step:
>
>
>
> On Tue, Feb 2, 2016 at 7:37 PM, Lucian Smith <luc...@gm...>
> wrote:
>
>> It's clearly important that whoever makes the diagrams use what they're
>> comfortable with!  I've made enough Google draw UML diagrams by now that I
>> can make them pretty quickly, though of course you don't get the UML
>> checking.  You can export them to PDF, though, which is standard enough for
>> LaTeX to include.
>>
>> Here's a draft UML diagram for Matthias's proposal.  And clearly, great
>> minds think alike, because I also had Dagmar's idea of subclassing a base
>> 'TimeCourse' abstract class:
>>
>>
>> https://docs.google.com/drawings/d/1YqQ0h62UbEmBgrGvqGkHi9YhO1l3dUUsE3y7n83rMKw/edit?usp=sharing
>>
>> -Lucian
>>
>> On Tue, Feb 2, 2016 at 10:24 AM, Dagmar Waltemath <
>> dag...@un...> wrote:
>>
>>> Hi Lucian,
>>>
>>> it was me who insisted on using MagicDraw UML, because the last time I
>>> drew SBML UML diagrams this was in Google draw, so no means of checking the
>>> UML for consistency, and also not very automised, and not exportable to a
>>> standard format ;-).
>>>
>>> MagicDraw UML is not a free tool though, which is why the other editors
>>> didn't like it too much.
>>>
>>> Oh, and this is just to clarify, not an objection.
>>>
>>> Best, Dagmar
>>>
>>>
>>> *Dagmar Waltemath*, Dept. of Systems Biology & Bioinformatics,
>>> University of Rostock, D-18051 Rostock, Germany
>>> Web: http://www.sbi.uni-rostock.de/sems
>>> <http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/>
>>> Skype: dagmar.waltemath
>>> ------------------------------
>>> *Von:* Lucian Smith [luc...@gm...]
>>> *Gesendet:* Dienstag, 2. Februar 2016 19:16
>>> *An:* sed...@li...
>>> *Betreff:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse
>>>
>>> Sure, I can do that.  I like the idea of making a new base class which
>>> UniformTimeCourse inherits from.
>>>
>>> As far as the new spec goes, there are a lot of issues with the current
>>> UML diagrams, many of which have been filed in the sed-ml tracker.  I'm
>>> inclined to ditch them all and start from scratch, using UML templates from
>>> SBML.  Would anyone object to this?  Are there features of the current
>>> SED-ML UML diagrams that people like better than the ones used in the SBML
>>> spec?
>>>
>>> -Lucian
>>>
>>> On Tue, Feb 2, 2016 at 9:37 AM, Moraru,Ion <mo...@uc...> wrote:
>>>
>>>> Same with VCell, has been supported for a decade by now…
>>>>
>>>>
>>>>
>>>> It is a feature on the list of add-ons to the next SED-ML version.
>>>> Perhaps Lucian, as a new Editor and full of energy, can spearhead a draft
>>>> spec?
>>>>
>>>>
>>>>
>>>> Ion
>>>>
>>>>
>>>>
>>>> *From:* Herbert Sauro [mailto:hs...@gm...]
>>>> *Sent:* Tuesday, February 02, 2016 12:31 PM
>>>> *To:* sed...@li...
>>>> *Subject:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse
>>>>
>>>>
>>>>
>>>> libRoadRunner already support variable time step so it would be very
>>>> useful to have this in sedml.
>>>>
>>>>
>>>>
>>>> Herbert
>>>>
>>>>
>>>>
>>>> On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes <
>>>> ped...@ma...> wrote:
>>>>
>>>> Matthias,
>>>>
>>>> > If tools like COPASI do not support variable_time_step simulation
>>>>
>>>> It will, the current snapshots being tested already have this feature,
>>>> so it will be in the next release. It would be great if it would be
>>>> supported in SED-ML.
>>>>
>>>> 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.
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D267308311-26iu-3D_4140&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=muXLw0tJUSLN3opHI1lcLUoTTxgHFsFf0plt_ksm3ys&e=>
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>>> Monitor end-to-end web transactions and take corrective actions now
>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>
>
> --
> Matthias König
> Email: kon...@go...
> Tel: + 49 30 20938450
> Tel: + 49 176 81168480
>   https://www.livermetabolism.com/contact.html
> Humboldt-University Berlin, Institute for Theoretical Biology, Junior
> Group König
> Charité Berlin, Institute of Biochemistry, Computational Systems
> Biochemistry <http://www.charite.de/sysbio/people/koenig/>
>



-- 
Matthias König
Email: kon...@go...
Tel: + 49 30 20938450
Tel: + 49 176 81168480
  https://www.livermetabolism.com/contact.html
Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group
König
Charité Berlin, Institute of Biochemistry, Computational Systems
Biochemistry <http://www.charite.de/sysbio/people/koenig/>