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From: Herbert S. <hs...@gm...> - 2015-12-21 21:22:43
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I've got a feeling the same goes for SBML. Herbert On Mon, Dec 21, 2015 at 1:13 PM, David Nickerson <dav...@gm...> wrote: > > I think in CellML there is no way to determine what kind of ODE it is > > without some kind of annotation. > > yep - there is nothing in CellML itself to inform you anything about > the biology, just the math. (There is a "reaction" construct, but that > is deprecated and not supported by the CellML API.) > > > ------------------------------------------------------------------------------ > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > |
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From: David N. <dav...@gm...> - 2015-12-21 21:14:18
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> I think in CellML there is no way to determine what kind of ODE it is > without some kind of annotation. yep - there is nothing in CellML itself to inform you anything about the biology, just the math. (There is a "reaction" construct, but that is deprecated and not supported by the CellML API.) |
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From: Herbert S. <hs...@gm...> - 2015-12-21 04:41:41
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I was thinking of the situation where the differential equations have nothing to do with reactions and species, for example someone might encode the lorenz attractor as three rate rules. It doesn't make much sense to decompose these into a set of reactions and species even though one could - I have just to see what they looked like . I've not kept up with SBML but can one have rate rules that are associated with general state variables and NOT species, or must all variables be species? This was something I wanted to be able to distinguish when SBML 1 was developed but it never became part of the standard. Is it possible now to distinguish species variables from generic state variables? I think in CellML there is no way to determine what kind of ODE it is without some kind of annotation. I had a look at that paper a while ago but wasn't able to spend long enough to decipher the theory. Doesn't any one have the paper explained in more simpler terms? I think I might have understood it has something to do with determining the Jacobian but not sure? Herbert On Sun, Dec 20, 2015 at 6:03 PM, Chris J. Myers <my...@ec...> wrote: > I don’t think so. The BioCham method I believe assumes that values that > are targets of ODEs are species and other values are constants. You really > should take a look: > > http://www.sciencedirect.com/science/article/pii/S0304397514006197 > > Chris > > On Dec 20, 2015, at 3:53 PM, Herbert Sauro <hs...@gm...> wrote: > > Wouldn't you need CellML annotation to identify the differential equations > that correspond to rate of change of species, assuming they in turn have > been constructed such that they can be separated? > > Herbert > > On Sun, Dec 20, 2015 at 2:50 PM, Chris J. Myers <my...@ec...> > wrote: > >> One could use the BioCham approach to extract the reactions from the math >> like Mike does with the matlab to sbml converter. >> >> Chris >> >> Sent from my iPhone >> >> On Dec 20, 2015, at 2:29 PM, Lucian Smith <luc...@gm...> >> wrote: >> >> That was actually going to be the next part of my question: stochastic >> Reactions are a 'standard thing' in SBML, but I believe nobody ever tries >> to interpret the 'rate rules' in a stochastic manner. If they did, that >> could presumably be applied to the CellML side of things. Conversely, if >> CellML *did* have some sort of stochastic interpretation, the reverse could >> be true. >> >> For now, it sounds like I should just not try to generate stochastic >> tests for CellML at all, and stick to reactions for SBML models. Although >> if we want to explicitly claim that the SBML RateRule construct is 'immune' >> to stochastic simulations, I should include that, too. >> >> -Lucian >> >> On Sun, Dec 20, 2015 at 12:09 PM, David Nickerson < >> dav...@gm...> wrote: >> >>> Hi Lucian, >>> >>> Short answer - I'm not aware of any simulator that would know what to >>> do with a CellML model and a Monte Carlo simulation. >>> >>> Long answer - something intelligent sounding about the math being >>> directly encoded in CellML vs the process description of SBML being >>> used to generate the math depending on your simulation algorithm (I >>> don't know if you can do a stochastic simulation of an SBML model that >>> only consists of math, no reactions?). Andrew Miller did have a >>> proposal for something along these lines with SED-ML, but requires >>> extra information provided for the CellML (or SBML) model >>> (distributions, ranges, etc.). >>> >>> >>> Cheers, >>> Andre. >>> >>> >>> On Sat, Dec 19, 2015 at 8:04 AM, Lucian Smith <luc...@gm...> >>> wrote: >>> > So, SBML has a tradition of allowing the user to encode a single >>> model, and >>> > allows you to simulate it deterministically or stochastically. Does >>> CellML >>> > have the same capability? I'm obviously asking from the perspective of >>> > SED-ML--if the KiSAO terms for Monte Carlo simulation would mean >>> anything to >>> > a CellML simulator. >>> > >>> > -Lucian >>> > >>> > >>> ------------------------------------------------------------------------------ >>> > >>> > _______________________________________________ >>> > SED-ML-discuss mailing list >>> > SED...@li... >>> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> > >>> >>> >>> >>> -- >>> >>> >>> David Nickerson >>> about.me/david.nickerson >>> >>> >>> ------------------------------------------------------------------------------ >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > ------------------------------------------------------------------------------ > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > |
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From: Chris J. M. <my...@ec...> - 2015-12-21 02:03:32
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I don’t think so. The BioCham method I believe assumes that values that are targets of ODEs are species and other values are constants. You really should take a look: http://www.sciencedirect.com/science/article/pii/S0304397514006197 <http://www.sciencedirect.com/science/article/pii/S0304397514006197> Chris > On Dec 20, 2015, at 3:53 PM, Herbert Sauro <hs...@gm...> wrote: > > Wouldn't you need CellML annotation to identify the differential equations that correspond to rate of change of species, assuming they in turn have been constructed such that they can be separated? > > Herbert > > On Sun, Dec 20, 2015 at 2:50 PM, Chris J. Myers <my...@ec... <mailto:my...@ec...>> wrote: > One could use the BioCham approach to extract the reactions from the math like Mike does with the matlab to sbml converter. > > Chris > > Sent from my iPhone > > On Dec 20, 2015, at 2:29 PM, Lucian Smith <luc...@gm... <mailto:luc...@gm...>> wrote: > >> That was actually going to be the next part of my question: stochastic Reactions are a 'standard thing' in SBML, but I believe nobody ever tries to interpret the 'rate rules' in a stochastic manner. If they did, that could presumably be applied to the CellML side of things. Conversely, if CellML *did* have some sort of stochastic interpretation, the reverse could be true. >> >> For now, it sounds like I should just not try to generate stochastic tests for CellML at all, and stick to reactions for SBML models. Although if we want to explicitly claim that the SBML RateRule construct is 'immune' to stochastic simulations, I should include that, too. >> >> -Lucian >> >> On Sun, Dec 20, 2015 at 12:09 PM, David Nickerson <dav...@gm... <mailto:dav...@gm...>> wrote: >> Hi Lucian, >> >> Short answer - I'm not aware of any simulator that would know what to >> do with a CellML model and a Monte Carlo simulation. >> >> Long answer - something intelligent sounding about the math being >> directly encoded in CellML vs the process description of SBML being >> used to generate the math depending on your simulation algorithm (I >> don't know if you can do a stochastic simulation of an SBML model that >> only consists of math, no reactions?). Andrew Miller did have a >> proposal for something along these lines with SED-ML, but requires >> extra information provided for the CellML (or SBML) model >> (distributions, ranges, etc.). >> >> >> Cheers, >> Andre. >> >> >> On Sat, Dec 19, 2015 at 8:04 AM, Lucian Smith <luc...@gm... <mailto:luc...@gm...>> wrote: >> > So, SBML has a tradition of allowing the user to encode a single model, and >> > allows you to simulate it deterministically or stochastically. Does CellML >> > have the same capability? I'm obviously asking from the perspective of >> > SED-ML--if the KiSAO terms for Monte Carlo simulation would mean anything to >> > a CellML simulator. >> > >> > -Lucian >> > >> > ------------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > SED-ML-discuss mailing list >> > SED...@li... <mailto:SED...@li...> >> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >> > >> >> >> >> -- >> >> >> David Nickerson >> about.me/david.nickerson <http://about.me/david.nickerson> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... <mailto:SED...@li...> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... <mailto:SED...@li...> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... <mailto:SED...@li...> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> > > > ------------------------------------------------------------------------------ > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: Herbert S. <hs...@gm...> - 2015-12-20 22:53:59
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Wouldn't you need CellML annotation to identify the differential equations that correspond to rate of change of species, assuming they in turn have been constructed such that they can be separated? Herbert On Sun, Dec 20, 2015 at 2:50 PM, Chris J. Myers <my...@ec...> wrote: > One could use the BioCham approach to extract the reactions from the math > like Mike does with the matlab to sbml converter. > > Chris > > Sent from my iPhone > > On Dec 20, 2015, at 2:29 PM, Lucian Smith <luc...@gm...> > wrote: > > That was actually going to be the next part of my question: stochastic > Reactions are a 'standard thing' in SBML, but I believe nobody ever tries > to interpret the 'rate rules' in a stochastic manner. If they did, that > could presumably be applied to the CellML side of things. Conversely, if > CellML *did* have some sort of stochastic interpretation, the reverse could > be true. > > For now, it sounds like I should just not try to generate stochastic tests > for CellML at all, and stick to reactions for SBML models. Although if we > want to explicitly claim that the SBML RateRule construct is 'immune' to > stochastic simulations, I should include that, too. > > -Lucian > > On Sun, Dec 20, 2015 at 12:09 PM, David Nickerson < > dav...@gm...> wrote: > >> Hi Lucian, >> >> Short answer - I'm not aware of any simulator that would know what to >> do with a CellML model and a Monte Carlo simulation. >> >> Long answer - something intelligent sounding about the math being >> directly encoded in CellML vs the process description of SBML being >> used to generate the math depending on your simulation algorithm (I >> don't know if you can do a stochastic simulation of an SBML model that >> only consists of math, no reactions?). Andrew Miller did have a >> proposal for something along these lines with SED-ML, but requires >> extra information provided for the CellML (or SBML) model >> (distributions, ranges, etc.). >> >> >> Cheers, >> Andre. >> >> >> On Sat, Dec 19, 2015 at 8:04 AM, Lucian Smith <luc...@gm...> >> wrote: >> > So, SBML has a tradition of allowing the user to encode a single model, >> and >> > allows you to simulate it deterministically or stochastically. Does >> CellML >> > have the same capability? I'm obviously asking from the perspective of >> > SED-ML--if the KiSAO terms for Monte Carlo simulation would mean >> anything to >> > a CellML simulator. >> > >> > -Lucian >> > >> > >> ------------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > SED-ML-discuss mailing list >> > SED...@li... >> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > >> >> >> >> -- >> >> >> David Nickerson >> about.me/david.nickerson >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > |
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From: Chris J. M. <my...@ec...> - 2015-12-20 22:51:05
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One could use the BioCham approach to extract the reactions from the math like Mike does with the matlab to sbml converter. Chris Sent from my iPhone > On Dec 20, 2015, at 2:29 PM, Lucian Smith <luc...@gm...> wrote: > > That was actually going to be the next part of my question: stochastic Reactions are a 'standard thing' in SBML, but I believe nobody ever tries to interpret the 'rate rules' in a stochastic manner. If they did, that could presumably be applied to the CellML side of things. Conversely, if CellML *did* have some sort of stochastic interpretation, the reverse could be true. > > For now, it sounds like I should just not try to generate stochastic tests for CellML at all, and stick to reactions for SBML models. Although if we want to explicitly claim that the SBML RateRule construct is 'immune' to stochastic simulations, I should include that, too. > > -Lucian > >> On Sun, Dec 20, 2015 at 12:09 PM, David Nickerson <dav...@gm...> wrote: >> Hi Lucian, >> >> Short answer - I'm not aware of any simulator that would know what to >> do with a CellML model and a Monte Carlo simulation. >> >> Long answer - something intelligent sounding about the math being >> directly encoded in CellML vs the process description of SBML being >> used to generate the math depending on your simulation algorithm (I >> don't know if you can do a stochastic simulation of an SBML model that >> only consists of math, no reactions?). Andrew Miller did have a >> proposal for something along these lines with SED-ML, but requires >> extra information provided for the CellML (or SBML) model >> (distributions, ranges, etc.). >> >> >> Cheers, >> Andre. >> >> >> On Sat, Dec 19, 2015 at 8:04 AM, Lucian Smith <luc...@gm...> wrote: >> > So, SBML has a tradition of allowing the user to encode a single model, and >> > allows you to simulate it deterministically or stochastically. Does CellML >> > have the same capability? I'm obviously asking from the perspective of >> > SED-ML--if the KiSAO terms for Monte Carlo simulation would mean anything to >> > a CellML simulator. >> > >> > -Lucian >> > >> > ------------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > SED-ML-discuss mailing list >> > SED...@li... >> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > >> >> >> >> -- >> >> >> David Nickerson >> about.me/david.nickerson >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > ------------------------------------------------------------------------------ > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: Lucian S. <luc...@gm...> - 2015-12-20 21:29:24
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That was actually going to be the next part of my question: stochastic Reactions are a 'standard thing' in SBML, but I believe nobody ever tries to interpret the 'rate rules' in a stochastic manner. If they did, that could presumably be applied to the CellML side of things. Conversely, if CellML *did* have some sort of stochastic interpretation, the reverse could be true. For now, it sounds like I should just not try to generate stochastic tests for CellML at all, and stick to reactions for SBML models. Although if we want to explicitly claim that the SBML RateRule construct is 'immune' to stochastic simulations, I should include that, too. -Lucian On Sun, Dec 20, 2015 at 12:09 PM, David Nickerson <dav...@gm... > wrote: > Hi Lucian, > > Short answer - I'm not aware of any simulator that would know what to > do with a CellML model and a Monte Carlo simulation. > > Long answer - something intelligent sounding about the math being > directly encoded in CellML vs the process description of SBML being > used to generate the math depending on your simulation algorithm (I > don't know if you can do a stochastic simulation of an SBML model that > only consists of math, no reactions?). Andrew Miller did have a > proposal for something along these lines with SED-ML, but requires > extra information provided for the CellML (or SBML) model > (distributions, ranges, etc.). > > > Cheers, > Andre. > > > On Sat, Dec 19, 2015 at 8:04 AM, Lucian Smith <luc...@gm...> > wrote: > > So, SBML has a tradition of allowing the user to encode a single model, > and > > allows you to simulate it deterministically or stochastically. Does > CellML > > have the same capability? I'm obviously asking from the perspective of > > SED-ML--if the KiSAO terms for Monte Carlo simulation would mean > anything to > > a CellML simulator. > > > > -Lucian > > > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > > SED-ML-discuss mailing list > > SED...@li... > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > > -- > > > David Nickerson > about.me/david.nickerson > > > ------------------------------------------------------------------------------ > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > |
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From: David N. <dav...@gm...> - 2015-12-20 20:10:22
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Hi Lucian, Short answer - I'm not aware of any simulator that would know what to do with a CellML model and a Monte Carlo simulation. Long answer - something intelligent sounding about the math being directly encoded in CellML vs the process description of SBML being used to generate the math depending on your simulation algorithm (I don't know if you can do a stochastic simulation of an SBML model that only consists of math, no reactions?). Andrew Miller did have a proposal for something along these lines with SED-ML, but requires extra information provided for the CellML (or SBML) model (distributions, ranges, etc.). Cheers, Andre. On Sat, Dec 19, 2015 at 8:04 AM, Lucian Smith <luc...@gm...> wrote: > So, SBML has a tradition of allowing the user to encode a single model, and > allows you to simulate it deterministically or stochastically. Does CellML > have the same capability? I'm obviously asking from the perspective of > SED-ML--if the KiSAO terms for Monte Carlo simulation would mean anything to > a CellML simulator. > > -Lucian > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > -- David Nickerson about.me/david.nickerson |
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From: Frank B. <fbe...@ca...> - 2015-12-18 19:59:07
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Hello Lucian, indeed, we definitely would need the L1V3 slicing construct or something similar for this. Also remember that currently we don’t have access to the calculation of either mean or stddev within the allowed mathml subset. So for the time being, I would perform a two step approach, step1 simulate, and then later analyze the data (which would not need to happen within sedml). cheers Frank > On Dec 18, 2015, at 8:37 PM, Lucian Smith <luc...@gm...> wrote: > > If one is running a stochastic test, and you want to figure out if you're doing it properly, you must run the same test many times, and compare means and standard deviations to expected means and standard deviations. Is there anything in SED-ML today that would let you calculate the mean of several runs of timecourse data, or will we have to wait for Frank's 'slice' construct for that? > > -Lucian > ------------------------------------------------------------------------------ > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: Lucian S. <luc...@gm...> - 2015-12-18 19:37:10
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If one is running a stochastic test, and you want to figure out if you're doing it properly, you must run the same test many times, and compare means and standard deviations to expected means and standard deviations. Is there anything in SED-ML today that would let you calculate the mean of several runs of timecourse data, or will we have to wait for Frank's 'slice' construct for that? -Lucian |
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From: Lucian S. <luc...@gm...> - 2015-12-18 19:05:04
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So, SBML has a tradition of allowing the user to encode a single model, and allows you to simulate it deterministically or stochastically. Does CellML have the same capability? I'm obviously asking from the perspective of SED-ML--if the KiSAO terms for Monte Carlo simulation would mean anything to a CellML simulator. -Lucian |
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From: Jonathan C. <jon...@cs...> - 2015-12-18 14:26:26
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On 18/12/2015 03:09, David Nickerson wrote: >>> I'm sure at one point there was discussion on how to address variables >>> in a model using generic terms (such as ontology terms) or perhaps >>> something like an "independent variable" symbol, but as yet nothing >>> concrete proposed for addition to SED-ML. Jonathan Cooper and >>> colleagues have a system where they use biological ontology terms in >>> their simulation experiment protocols to identify source variables in >>> the model so that a given protocol can be used with multiple models >>> and software can easily determine the correct model entities to pull >>> out. >> >> That sounds pretty clever--are they able to pull this off with XPaths? >> Something like 'the parent of the element with this attribute ID'? Or is >> this a system that lives above SED-ML, and is translated for different >> models on the fly? > Its currently a system that lives outside SED-ML and used by their > tools (I think more like "the variable that is intracellular calcium > ion concentration"). The idea is to pull some of their ideas into > future versions of SED-ML. One day :) > That's right. The protocol (currently in our own language) references ontology terms, and the tool finds the model variable(s) annotated with this term using bqbiol:is as predicate. You can have a play with it at https://chaste.cs.ox.ac.uk/WebLab Best wishes, Jonathan |
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From: Frank B. <fbe...@ca...> - 2015-12-18 06:43:32
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Indeed, one has to reference time explicitly when using CellML models. The only reason for the introduction of the time symbol for SBML was, that no xpath expression to the SBML time element existed. cheers Frank > On Dec 18, 2015, at 2:27 AM, Lucian Smith <luc...@gm...> wrote: > > SED-ML defines 'time' as 'urn:sedml:symbol:time', so that systems like SBML which don't define time explicitly can still work. CellML, on the other hand, does define time explicitly. But if you're using a SED-ML file in conjunction with a CellML model, is it wrong to use 'urn:sedml:symbol:time'? Do you have to use an explicit reference to the CellML 'time' variable, or could the SED-ML interpreter be expected to work that out? > > -Lucian > ------------------------------------------------------------------------------ > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: David N. <dav...@gm...> - 2015-12-18 03:09:58
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>> I'm sure at one point there was discussion on how to address variables >> in a model using generic terms (such as ontology terms) or perhaps >> something like an "independent variable" symbol, but as yet nothing >> concrete proposed for addition to SED-ML. Jonathan Cooper and >> colleagues have a system where they use biological ontology terms in >> their simulation experiment protocols to identify source variables in >> the model so that a given protocol can be used with multiple models >> and software can easily determine the correct model entities to pull >> out. > > > That sounds pretty clever--are they able to pull this off with XPaths? > Something like 'the parent of the element with this attribute ID'? Or is > this a system that lives above SED-ML, and is translated for different > models on the fly? Its currently a system that lives outside SED-ML and used by their tools (I think more like "the variable that is intracellular calcium ion concentration"). The idea is to pull some of their ideas into future versions of SED-ML. One day :) Cheers, David. |
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From: Lucian S. <luc...@gm...> - 2015-12-18 03:05:28
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On Thu, Dec 17, 2015 at 5:56 PM, David Nickerson <dav...@gm...> wrote: > Hi Lucian, > > Its a bit of an indirect path, but the spec basically says to look on > the website to see the list of predefined symbols that can be used. If > you find the table on the website (which actually seems impossible to > link directly to, but its under the "information" tab), you'll see > there that urn:sedml:symbol:time is an SBML specific symbol. So it > would have no meaning in the context of a CellML model. > Aha, thanks. So, my CellML versions of my tests would have to change that bit, then. > I'm sure at one point there was discussion on how to address variables > in a model using generic terms (such as ontology terms) or perhaps > something like an "independent variable" symbol, but as yet nothing > concrete proposed for addition to SED-ML. Jonathan Cooper and > colleagues have a system where they use biological ontology terms in > their simulation experiment protocols to identify source variables in > the model so that a given protocol can be used with multiple models > and software can easily determine the correct model entities to pull > out. > That sounds pretty clever--are they able to pull this off with XPaths? Something like 'the parent of the element with this attribute ID'? Or is this a system that lives above SED-ML, and is translated for different models on the fly? -Lucian |
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From: David N. <dav...@gm...> - 2015-12-18 01:57:17
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Hi Lucian, Its a bit of an indirect path, but the spec basically says to look on the website to see the list of predefined symbols that can be used. If you find the table on the website (which actually seems impossible to link directly to, but its under the "information" tab), you'll see there that urn:sedml:symbol:time is an SBML specific symbol. So it would have no meaning in the context of a CellML model. I'm sure at one point there was discussion on how to address variables in a model using generic terms (such as ontology terms) or perhaps something like an "independent variable" symbol, but as yet nothing concrete proposed for addition to SED-ML. Jonathan Cooper and colleagues have a system where they use biological ontology terms in their simulation experiment protocols to identify source variables in the model so that a given protocol can be used with multiple models and software can easily determine the correct model entities to pull out. Cheers, David. On Fri, Dec 18, 2015 at 2:27 PM, Lucian Smith <luc...@gm...> wrote: > SED-ML defines 'time' as 'urn:sedml:symbol:time', so that systems like SBML > which don't define time explicitly can still work. CellML, on the other > hand, does define time explicitly. But if you're using a SED-ML file in > conjunction with a CellML model, is it wrong to use 'urn:sedml:symbol:time'? > Do you have to use an explicit reference to the CellML 'time' variable, or > could the SED-ML interpreter be expected to work that out? > > -Lucian > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > -- David Nickerson about.me/david.nickerson |
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From: Lucian S. <luc...@gm...> - 2015-12-18 01:27:54
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SED-ML defines 'time' as 'urn:sedml:symbol:time', so that systems like SBML which don't define time explicitly can still work. CellML, on the other hand, does define time explicitly. But if you're using a SED-ML file in conjunction with a CellML model, is it wrong to use 'urn:sedml:symbol:time'? Do you have to use an explicit reference to the CellML 'time' variable, or could the SED-ML interpreter be expected to work that out? -Lucian |
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From: David N. <dav...@gm...> - 2015-12-18 00:42:10
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This is a call for votes for electing one new SED-ML Editor to replace Jonathan Cooper, whose current three year term ends at the end of this year. Every member of the SED-ML forum (as determined by membership of the sed...@li... mailing list) is entitled to vote. Please vote for one candidate using the voting form at: http://goo.gl/forms/pwdwIjDhTz Voting will end on January 8, 2016. Thank you in advance for your participation in this important process! David, on behalf of the SED-ML editors. -- David Nickerson about.me/david.nickerson |
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From: David N. <dav...@gm...> - 2015-12-09 02:30:08
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Hi all, Just a reminder to be sure to nominate your candidate(s) for SED-ML editor. Nominations close this coming Monday, December 14. Cheers, David. On Wed, Dec 2, 2015 at 9:42 AM, David Nickerson <dav...@gm...> wrote: > Hi all, > > This is a call for nominations for one SED-ML editor to replace > Jonathan Cooper, whose term ends on the 31st of December 2015. The > length of a SED-ML Editor's term is 3 years, starting from the 1st of > January 2016. > > The current editors are Jonathan Cooper (to be replaced), Ion Moraru > (until 2016), Sven Sahle (until 2016), Brett Olivier (until 2017), and > David Nickerson (until 2017). The editor to be replaced is not > suitable to be nominated. > > We would like to ask you to nominate suitable candidates. You may > nominate anyone (including yourself) who you think is qualified to act > as an editor. You can fill out this survey multiple times in order to > nominate multiple candidates. > > The nomination form is at: http://goo.gl/forms/exTTMuaMS0 > > The call for nominations will close on December 14 2015. > > > Cheers, > David, on behalf of the SED-ML Editors. -- David Nickerson about.me/david.nickerson |
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From: Martin S. <ma...@bi...> - 2015-12-07 09:47:46
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Actually, my main goal was to create some sed-ml scripts :) People (including me) regularly complain that there are no sed-ml simulation descriptions available for $whatever. Therefore, I wrote a simple script [1] to generate simulation descriptions for models from the biomodels database using the sed-ml webtools (as that quickly produced a large amount of sed-ml files with minimal efforts). As I also hear complains about the limited amount of combine archives available I decided to also bundle model and simulation description into combine archives. Finally, I run the simulation job using the sed-ml webtools to obtain the simulation results. Best, Martin [1] https://github.com/binfalse/SED-ML-Depository/blob/master/generator.sh On 12/03/2015 08:19 PM, Lucian Smith wrote: > That's great! Thanks for the pointer. Is the intent here to recreate the > actual figures from the papers those models came from, or just to get > something interesting out of them (or both)? > > -Lucian > > On Wed, Dec 2, 2015 at 11:49 PM, Martin Scharm <ma...@bi...> wrote: > >> Coincidentally, I created a github repository of SED-ML scripts about a >> month ago: https://github.com/binfalse/SED-ML-Depository >> >> This "depository" contains a SED-ML script for every model of the >> curated branch of the Biomodels Database. (sorry don't have CellML, yet) >> There are also COMBINE archives encoding for a simulation job (SBML >> file plus SED-ML file) and the corresponding simulation results, as >> obtained by running the simulation study in the SED-ML WebTools. >> >> Not sure if that's going to help you, but feel free to use anything from >> that repository. I'm also happy to add anyone as a collaborator! :) >> >> Best wishes, >> Martin >> >> On 12/03/2015 01:31 AM, David Nickerson wrote: >>> Thanks Lucian - that is a great start. Now we just need to fill that >>> contributions folder up :) >>> >>> I think it is fine to include Antimony or phraSED-ML in the >>> description (or any other domain specific simple text format people >>> use). >>> >>> >>> Cheers, >>> David. >>> >>> On Thu, Dec 3, 2015 at 1:15 PM, Lucian Smith <luc...@gm...> >> wrote: >>>> I agree that we can model the suite after the SBML test suite, but it >> should >>>> both be its own thing, and have CellML models in it, too. In fact, I >> think >>>> that each directory/test should basically be modeling-language >> agnostic--the >>>> point is to test SED-ML, not the modeling. >>>> >>>> I put together a bare-bones repository with a single test in it on >> github so >>>> we can have an actual thing to talk about: >>>> >>>> https://github.com/luciansmith/sedml-test-suite/ >>>> >>>> If anyone wants access to it, I'll gladly add them to the >> 'collaborators' >>>> list, which I think should work? Github and I don't get along all that >> well >>>> ;-) >>>> >>>> I modeled everything off of the SBML test suite, with some changes: I >> now >>>> have an 'info' file instead of the '.m' file in the SBML test suite, >> which >>>> was an artifact of how the tests used to be created. There's no longer >> a >>>> 'settings' file, since everything there in the SBML test suite is here >>>> covered by SED-ML itself. >>>> >>>> All suggestions welcome! >>>> >>>> -Lucian >>>> >>>> >>>> On Dec 2, 2015 12:54 AM, "Alan Garny" <ala...@in...> wrote: >>>>> >>>>> +1 regarding David’s suggestion of a GitHub repository for a SED-ML >> test >>>>> suite and a test suite that is not SBML centric. And, as much as >> possible, I >>>>> would be happy to contribute to it when it comes to CellML. >>>>> >>>>> >>>>> >>>>> Alan >>>>> >>>>> On 02/12/2015, 03:07, "David Nickerson" <dav...@gm...> >> wrote: >>>>> >>>>>>> To make this effective, I think it would be nice to integrate with >> the >>>>>>> SBML Test Suite, since comparing simulation results is again what >> you will >>>>>>> need to do. You already have some SED-ML files there, so it would >> mostly be >>>>>>> adding some more sophisticated ones. >>>>>>> >>>>>> >>>>>> I think that since we need to cater to a broader community than SBML, >>>>>> the SED-ML test suite should be independent from the SBML test suite, >>>>>> but it would be fine to be using the same framework if that can be >>>>>> easily adapted and used in such a manner. I have an inking that >>>>>> discussing this in the past with SBML developers that this might not >>>>>> be such a straightforward task... >>>>>> >>>>>>>> It seems like it would be really helpful to have a >>>>>>>> collectively-agreed-on test suite that put SED-ML through its >> paces, to make >>>>>>>> sure everyone agreed that the same file meant the same thing to >> everyone. >>>>>>>> At least, I assume that this doesn't already exist and I missed it? >>>>>>>> >>>>>> >>>>>> No, nothing like that exists in a general sense. I know a few tools >>>>>> that probably have their own internal tests, but nothing commonly used >>>>>> by more than one tool. >>>>>> >>>>>>>> Assuming it doesn't, two questions: if I started putting such a >> thing >>>>>>>> together, would making it have the same format as the SBML Test >> Suite work >>>>>>>> for everyone--directory-demarked sets of files with input files, >> expected >>>>>>>> output files, and a setup file that listed with 'tags' what >> different >>>>>>>> aspects of SED-ML were being tested in each? Is that overkill, not >> enough, >>>>>>>> just right? >>>>>> >>>>>> I think that makes sense, and if you, Lucian, are willing and able to >>>>>> set something like that up then it would be a great resource for the >>>>>> community. As long as it is something that is easy to maintain and add >>>>>> to over time, then I'd imagine once the initial hurdle of setting it >>>>>> up is achieved, then we should be able to keep improving it with >>>>>> future releases of the specification. >>>>>> >>>>>>>> Secondly, if you have files you're using that you'd be willing to >> send >>>>>>>> in/deposit/point me to somewhere, that'd be great! >>>>>> >>>>>> Something like a github repo where we could submit pull requests to >>>>>> bring in more tests or corrections to existing tests would seem to be >>>>>> a good way to get the community contributing tests. Would provide a >>>>>> good forum to discuss the "correctness" of specific tests as well :) >>>>>> >>>>>> >>>>>> Cheers, >>>>>> David. >>>>>> >>>>> >>>>>>> >> ------------------------------------------------------------------------------ >>>>>> Go from Idea to Many App Stores Faster with Intel(R) XDK >>>>>> Give your users amazing mobile app experiences with Intel(R) XDK. >>>>>> Use one codebase in this all-in-one HTML5 development environment. >>>>>> Design, debug & build mobile apps & 2D/3D high-impact games for >> multiple >>>>>> OSs. >>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 >>>>>> _______________________________________________ >>>>>> SED-ML-discuss mailing list >>>>>> SED...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>> >>>>> >>>>> >>>>> >> ------------------------------------------------------------------------------ >>>>> Go from Idea to Many App Stores Faster with Intel(R) XDK >>>>> Give your users amazing mobile app experiences with Intel(R) XDK. >>>>> Use one codebase in this all-in-one HTML5 development environment. >>>>> Design, debug & build mobile apps & 2D/3D high-impact games for >> multiple >>>>> OSs. >>>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 >>>>> _______________________________________________ >>>>> SED-ML-discuss mailing list >>>>> SED...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>>> >> ------------------------------------------------------------------------------ >>>> Go from Idea to Many App Stores Faster with Intel(R) XDK >>>> Give your users amazing mobile app experiences with Intel(R) XDK. >>>> Use one codebase in this all-in-one HTML5 development environment. >>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple >>>> OSs. >>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>> >>> >>> >> >> >> >> ------------------------------------------------------------------------------ >> Go from Idea to Many App Stores Faster with Intel(R) XDK >> Give your users amazing mobile app experiences with Intel(R) XDK. >> Use one codebase in this all-in-one HTML5 development environment. >> Design, debug & build mobile apps & 2D/3D high-impact games for multiple >> OSs. >> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > > > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > |
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From: Matthias K. <kon...@go...> - 2015-12-07 08:48:58
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Hi all, [1] I tried to validate a SED-ML files with the online resource on http://www.sbsi.ed.ac.uk/html/sedml/index.html. This did not work (see mails below, uploading a file results in server errors). I tried to contact Richard Adams, but the provided Email Address is not valid any more. I am not sure who is responsible for maintaining resource. SED-ML Web Tools validation & simulation worked very nice. [2] Is there a list of tools which support: * Reading a SBML, * Loading a SED-ML * Running simulation * Showing plots in the simplest possible manner, i.e. either 3 clicks (loading sbml, loading sedml, running simulation), or 3 lines of code (loading, loading, running). I found so far * COPASI (standalone, working) * SED-ML Web Tools (web, working) * JWS online (web, timing out on uploading SEDML) Matthias ---------- Forwarded message ---------- From: Mail Delivery Subsystem <mai...@go...> Date: Mon, Dec 7, 2015 at 9:00 AM Subject: Delivery Status Notification (Failure) To: kon...@go... Delivery to the following recipient failed permanently: ric...@ed... Technical details of permanent failure: Google tried to deliver your message, but it was rejected by the server for the recipient domain ed.ac.uk by renko.ucs.ed.ac.uk. [129.215.13.3]. The error that the other server returned was: 550 5.1.1 <ric...@ed...>... recipient 'richard.adams' not known at domain ed.ac.uk ----- Original message ----- DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=googlemail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=0ylDB+Mf56jy7mEMIV0JO9naJDtz+Wu1boOulrEUMVM=; b=JI+uTQmg+5woh59q2nwN9uLc/TJwtyqY9a7Jg33EzzVVfsM7cdD/pbIfvYyhWrvi1F xwrnpztr5ralh1SLG7ea30yxu+KbYph3cgfA+8NWGJVSdGCmc4LxJafmC1VhMK5/95UW rPFTMOZeGNDGQLEn+cNPaQwUgA37o85IHbHHrVXbpvfx7nGpYTUiEuAm8qcsMHnmzVjr UPZWgZLhUdzLM7Vw7lw5sDyqIuik5R70aKFlidYgwzliQjoIjO5OMy6UV6ThXZcuFu6M XSAPD7DZGewKPSBL9/CsX0xMS6Eoua7pvDEwaKBhBJh8uWwxZSuR6/LBeigkNr0vhz5U /62Q== MIME-Version: 1.0 X-Received: by 10.107.25.77 with SMTP id 74mr24204065ioz.196.1449475220452; Mon, 07 Dec 2015 00:00:20 -0800 (PST) Received: by 10.79.3.2 with HTTP; Mon, 7 Dec 2015 00:00:20 -0800 (PST) Date: Mon, 7 Dec 2015 09:00:20 +0100 Message-ID: <CAEUx3ETtpx9hV_Y4tYQMhowmomtkbZt0+9wvL=nxC2j9X= 7x...@ma...> Subject: SBML Validation page not working From: =?UTF-8?Q?Matthias_K=C3=B6nig?= <kon...@go...> To: ric...@ed... Content-Type: multipart/mixed; boundary=001a113fd4c0a0631005264a3f12 Dear Richard Adams,I just tried to validate a file with the SBML validator on http://www.sbsi.ed.ac.uk/html/sedml/index.html. Unfortunately this is not working (file is attached, errors below). The best Matthias König HTTP Status 500 - Unable to compile class for JSP: *type* Exception report *message* *Unable to compile class for JSP: * *description* *The server encountered an internal error that prevented it from fulfilling this request.* *exception* org.apache.jasper.JasperException: Unable to compile class for JSP: An error occurred at line: [31] in the generated java file: [/localdisk/tomcats/sbsi/work/Catalina/sbsi/ROOT/org/apache/jsp/ValidateSBSIError_jsp.java] The method getJspApplicationContext(ServletContext) is undefined for the type JspFactory An error occurred at line: [42] in the generated java file: [/localdisk/tomcats/sbsi/work/Catalina/sbsi/ROOT/org/apache/jsp/ValidateSBSIError_jsp.java] The method getDispatcherType() is undefined for the type HttpServletRequest Stacktrace: org.apache.jasper.compiler.DefaultErrorHandler.javacError(DefaultErrorHandler.java:103) org.apache.jasper.compiler.ErrorDispatcher.javacError(ErrorDispatcher.java:199) org.apache.jasper.compiler.JDTCompiler.generateClass(JDTCompiler.java:450) org.apache.jasper.compiler.Compiler.compile(Compiler.java:361) org.apache.jasper.compiler.Compiler.compile(Compiler.java:336) org.apache.jasper.compiler.Compiler.compile(Compiler.java:323) org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:564) org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:357) org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:396) org.apache.jasper.servlet.JspServlet.service(JspServlet.java:340) javax.servlet.http.HttpServlet.service(HttpServlet.java:725) org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) uk.ac.ed.csbe.sbsiWebApp.utilities.AbstractSBSIServlet.forward(AbstractSBSIServlet.java:43) ----- Message truncated ----- -- -------------------------------------------------------------- Matthias König Computational Systems Biochemistry Institute of Biochemistry Charité - Universitätsmedizin Berlin http://www.charite.de/sysbio/people/koenig/ Tel: + 49 30 450528449 Tel: + 49 176 81168480 -------------------------------------------------------------- |
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From: Lucian S. <luc...@gm...> - 2015-12-03 19:19:15
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That's great! Thanks for the pointer. Is the intent here to recreate the actual figures from the papers those models came from, or just to get something interesting out of them (or both)? -Lucian On Wed, Dec 2, 2015 at 11:49 PM, Martin Scharm <ma...@bi...> wrote: > Coincidentally, I created a github repository of SED-ML scripts about a > month ago: https://github.com/binfalse/SED-ML-Depository > > This "depository" contains a SED-ML script for every model of the > curated branch of the Biomodels Database. (sorry don't have CellML, yet) > There are also COMBINE archives encoding for a simulation job (SBML > file plus SED-ML file) and the corresponding simulation results, as > obtained by running the simulation study in the SED-ML WebTools. > > Not sure if that's going to help you, but feel free to use anything from > that repository. I'm also happy to add anyone as a collaborator! :) > > Best wishes, > Martin > > On 12/03/2015 01:31 AM, David Nickerson wrote: > > Thanks Lucian - that is a great start. Now we just need to fill that > > contributions folder up :) > > > > I think it is fine to include Antimony or phraSED-ML in the > > description (or any other domain specific simple text format people > > use). > > > > > > Cheers, > > David. > > > > On Thu, Dec 3, 2015 at 1:15 PM, Lucian Smith <luc...@gm...> > wrote: > >> I agree that we can model the suite after the SBML test suite, but it > should > >> both be its own thing, and have CellML models in it, too. In fact, I > think > >> that each directory/test should basically be modeling-language > agnostic--the > >> point is to test SED-ML, not the modeling. > >> > >> I put together a bare-bones repository with a single test in it on > github so > >> we can have an actual thing to talk about: > >> > >> https://github.com/luciansmith/sedml-test-suite/ > >> > >> If anyone wants access to it, I'll gladly add them to the > 'collaborators' > >> list, which I think should work? Github and I don't get along all that > well > >> ;-) > >> > >> I modeled everything off of the SBML test suite, with some changes: I > now > >> have an 'info' file instead of the '.m' file in the SBML test suite, > which > >> was an artifact of how the tests used to be created. There's no longer > a > >> 'settings' file, since everything there in the SBML test suite is here > >> covered by SED-ML itself. > >> > >> All suggestions welcome! > >> > >> -Lucian > >> > >> > >> On Dec 2, 2015 12:54 AM, "Alan Garny" <ala...@in...> wrote: > >>> > >>> +1 regarding David’s suggestion of a GitHub repository for a SED-ML > test > >>> suite and a test suite that is not SBML centric. And, as much as > possible, I > >>> would be happy to contribute to it when it comes to CellML. > >>> > >>> > >>> > >>> Alan > >>> > >>> On 02/12/2015, 03:07, "David Nickerson" <dav...@gm...> > wrote: > >>> > >>>>> To make this effective, I think it would be nice to integrate with > the > >>>>> SBML Test Suite, since comparing simulation results is again what > you will > >>>>> need to do. You already have some SED-ML files there, so it would > mostly be > >>>>> adding some more sophisticated ones. > >>>>> > >>>> > >>>> I think that since we need to cater to a broader community than SBML, > >>>> the SED-ML test suite should be independent from the SBML test suite, > >>>> but it would be fine to be using the same framework if that can be > >>>> easily adapted and used in such a manner. I have an inking that > >>>> discussing this in the past with SBML developers that this might not > >>>> be such a straightforward task... > >>>> > >>>>>> It seems like it would be really helpful to have a > >>>>>> collectively-agreed-on test suite that put SED-ML through its > paces, to make > >>>>>> sure everyone agreed that the same file meant the same thing to > everyone. > >>>>>> At least, I assume that this doesn't already exist and I missed it? > >>>>>> > >>>> > >>>> No, nothing like that exists in a general sense. I know a few tools > >>>> that probably have their own internal tests, but nothing commonly used > >>>> by more than one tool. > >>>> > >>>>>> Assuming it doesn't, two questions: if I started putting such a > thing > >>>>>> together, would making it have the same format as the SBML Test > Suite work > >>>>>> for everyone--directory-demarked sets of files with input files, > expected > >>>>>> output files, and a setup file that listed with 'tags' what > different > >>>>>> aspects of SED-ML were being tested in each? Is that overkill, not > enough, > >>>>>> just right? > >>>> > >>>> I think that makes sense, and if you, Lucian, are willing and able to > >>>> set something like that up then it would be a great resource for the > >>>> community. As long as it is something that is easy to maintain and add > >>>> to over time, then I'd imagine once the initial hurdle of setting it > >>>> up is achieved, then we should be able to keep improving it with > >>>> future releases of the specification. > >>>> > >>>>>> Secondly, if you have files you're using that you'd be willing to > send > >>>>>> in/deposit/point me to somewhere, that'd be great! > >>>> > >>>> Something like a github repo where we could submit pull requests to > >>>> bring in more tests or corrections to existing tests would seem to be > >>>> a good way to get the community contributing tests. Would provide a > >>>> good forum to discuss the "correctness" of specific tests as well :) > >>>> > >>>> > >>>> Cheers, > >>>> David. > >>>> > >>> > >>>>> > ------------------------------------------------------------------------------ > >>>> Go from Idea to Many App Stores Faster with Intel(R) XDK > >>>> Give your users amazing mobile app experiences with Intel(R) XDK. > >>>> Use one codebase in this all-in-one HTML5 development environment. > >>>> Design, debug & build mobile apps & 2D/3D high-impact games for > multiple > >>>> OSs. > >>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > >>>> _______________________________________________ > >>>> SED-ML-discuss mailing list > >>>> SED...@li... > >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > >>> > >>> > >>> > >>> > ------------------------------------------------------------------------------ > >>> Go from Idea to Many App Stores Faster with Intel(R) XDK > >>> Give your users amazing mobile app experiences with Intel(R) XDK. > >>> Use one codebase in this all-in-one HTML5 development environment. > >>> Design, debug & build mobile apps & 2D/3D high-impact games for > multiple > >>> OSs. > >>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > >>> _______________________________________________ > >>> SED-ML-discuss mailing list > >>> SED...@li... > >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > >> > >> > >> > ------------------------------------------------------------------------------ > >> Go from Idea to Many App Stores Faster with Intel(R) XDK > >> Give your users amazing mobile app experiences with Intel(R) XDK. > >> Use one codebase in this all-in-one HTML5 development environment. > >> Design, debug & build mobile apps & 2D/3D high-impact games for multiple > >> OSs. > >> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > >> _______________________________________________ > >> SED-ML-discuss mailing list > >> SED...@li... > >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > >> > > > > > > > > > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple > OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > |
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From: Lucian S. <luc...@gm...> - 2015-12-03 16:44:41
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The *tests* should be modeling language agnostic, but the SED-ML files cannot, as you say, actually do that. At the very least, the 'model' elements have to point to a different file, and more complicatedly, the XPath expressions are almost certainly going to be different. What I did in the example I put together was to make two SEDML files; one for SBML and one for CellML. If someone wants to add another language to the tests, we could probably do that, too. -Lucian On Thu, Dec 3, 2015 at 7:46 AM, Chris J. Myers <my...@ec...> wrote: > I agree that it should be modeling language agnostic, but I’m curious how > possible that is. Is it possible for one SED-ML file to tell you how to > simulate either a SBML or CellML version of the same model? I suspect that > this may be tricky, since referencing objects in the two files is likely > quite different. It would be great though if this were possible. Perhaps, > it should at least be easy to do in the scripting languages. > > Chris > > On Dec 2, 2015, at 5:15 PM, Lucian Smith <luc...@gm...> > wrote: > > I agree that we can model the suite after the SBML test suite, but it > should both be its own thing, and have CellML models in it, too. In fact, I > think that each directory/test should basically be modeling-language > agnostic--the point is to test SED-ML, not the modeling. > > I put together a bare-bones repository with a single test in it on github > so we can have an actual thing to talk about: > > https://github.com/luciansmith/sedml-test-suite/ > > If anyone wants access to it, I'll gladly add them to the 'collaborators' > list, which I think should work? Github and I don't get along all that > well ;-) > > I modeled everything off of the SBML test suite, with some changes: I now > have an 'info' file instead of the '.m' file in the SBML test suite, which > was an artifact of how the tests used to be created. There's no longer a > 'settings' file, since everything there in the SBML test suite is here > covered by SED-ML itself. > > All suggestions welcome! > > -Lucian > > > On Dec 2, 2015 12:54 AM, "Alan Garny" <ala...@in...> wrote: > >> +1 regarding David’s suggestion of a GitHub repository for a SED-ML test >> suite and a test suite that is not SBML centric. And, as much as possible, >> I would be happy to contribute to it when it comes to CellML. >> >> >> >> Alan >> >> On 02/12/2015, 03:07, "David Nickerson" <dav...@gm...> >> wrote: >> >> >> To make this effective, I think it would be nice to integrate with the >> SBML Test Suite, since comparing simulation results is again what you will >> need to do. You already have some SED-ML files there, so it would mostly >> be adding some more sophisticated ones. >> >> >> > >> >I think that since we need to cater to a broader community than SBML, >> >the SED-ML test suite should be independent from the SBML test suite, >> >but it would be fine to be using the same framework if that can be >> >easily adapted and used in such a manner. I have an inking that >> >discussing this in the past with SBML developers that this might not >> >be such a straightforward task... >> > >> >>> It seems like it would be really helpful to have a >> collectively-agreed-on test suite that put SED-ML through its paces, to >> make sure everyone agreed that the same file meant the same thing to >> everyone. At least, I assume that this doesn't already exist and I missed >> it? >> >>> >> > >> >No, nothing like that exists in a general sense. I know a few tools >> >that probably have their own internal tests, but nothing commonly used >> >by more than one tool. >> > >> >>> Assuming it doesn't, two questions: if I started putting such a >> thing together, would making it have the same format as the SBML Test Suite >> work for everyone--directory-demarked sets of files with input files, >> expected output files, and a setup file that listed with 'tags' what >> different aspects of SED-ML were being tested in each? Is that overkill, >> not enough, just right? >> > >> >I think that makes sense, and if you, Lucian, are willing and able to >> >set something like that up then it would be a great resource for the >> >community. As long as it is something that is easy to maintain and add >> >to over time, then I'd imagine once the initial hurdle of setting it >> >up is achieved, then we should be able to keep improving it with >> >future releases of the specification. >> > >> >>> Secondly, if you have files you're using that you'd be willing to >> send in/deposit/point me to somewhere, that'd be great! >> > >> >Something like a github repo where we could submit pull requests to >> >bring in more tests or corrections to existing tests would seem to be >> >a good way to get the community contributing tests. Would provide a >> >good forum to discuss the "correctness" of specific tests as well :) >> > >> > >> >Cheers, >> >David. >> > >> >> >------------------------------------------------------------------------------ >> >Go from Idea to Many App Stores Faster with Intel(R) XDK >> >Give your users amazing mobile app experiences with Intel(R) XDK. >> >Use one codebase in this all-in-one HTML5 development environment. >> >Design, debug & build mobile apps & 2D/3D high-impact games for multiple >> OSs. >> >http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 >> >_______________________________________________ >> >SED-ML-discuss mailing list >> >SED...@li... >> >https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> >> ------------------------------------------------------------------------------ >> Go from Idea to Many App Stores Faster with Intel(R) XDK >> Give your users amazing mobile app experiences with Intel(R) XDK. >> Use one codebase in this all-in-one HTML5 development environment. >> Design, debug & build mobile apps & 2D/3D high-impact games for multiple >> OSs. >> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple > OSs. > > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140_______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple > OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > |
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From: Chris J. M. <my...@ec...> - 2015-12-03 15:47:30
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I agree that it should be modeling language agnostic, but I’m curious how possible that is. Is it possible for one SED-ML file to tell you how to simulate either a SBML or CellML version of the same model? I suspect that this may be tricky, since referencing objects in the two files is likely quite different. It would be great though if this were possible. Perhaps, it should at least be easy to do in the scripting languages. Chris > On Dec 2, 2015, at 5:15 PM, Lucian Smith <luc...@gm...> wrote: > > I agree that we can model the suite after the SBML test suite, but it should both be its own thing, and have CellML models in it, too. In fact, I think that each directory/test should basically be modeling-language agnostic--the point is to test SED-ML, not the modeling. > > I put together a bare-bones repository with a single test in it on github so we can have an actual thing to talk about: > > https://github.com/luciansmith/sedml-test-suite/ <https://github.com/luciansmith/sedml-test-suite/> > If anyone wants access to it, I'll gladly add them to the 'collaborators' list, which I think should work? Github and I don't get along all that well ;-) > > I modeled everything off of the SBML test suite, with some changes: I now have an 'info' file instead of the '.m' file in the SBML test suite, which was an artifact of how the tests used to be created. There's no longer a 'settings' file, since everything there in the SBML test suite is here covered by SED-ML itself. > > All suggestions welcome! > > -Lucian > > > > On Dec 2, 2015 12:54 AM, "Alan Garny" <ala...@in... <mailto:ala...@in...>> wrote: > > +1 regarding David’s suggestion of a GitHub repository for a SED-ML test suite and a test suite that is not SBML centric. And, as much as possible, I would be happy to contribute to it when it comes to CellML. > > > > Alan > > On 02/12/2015, 03:07, "David Nickerson" <dav...@gm... <mailto:dav...@gm...>> wrote: > > >> To make this effective, I think it would be nice to integrate with the SBML Test Suite, since comparing simulation results is again what you will need to do. You already have some SED-ML files there, so it would mostly be adding some more sophisticated ones. > >> > > > >I think that since we need to cater to a broader community than SBML, > >the SED-ML test suite should be independent from the SBML test suite, > >but it would be fine to be using the same framework if that can be > >easily adapted and used in such a manner. I have an inking that > >discussing this in the past with SBML developers that this might not > >be such a straightforward task... > > > >>> It seems like it would be really helpful to have a collectively-agreed-on test suite that put SED-ML through its paces, to make sure everyone agreed that the same file meant the same thing to everyone. At least, I assume that this doesn't already exist and I missed it? > >>> > > > >No, nothing like that exists in a general sense. I know a few tools > >that probably have their own internal tests, but nothing commonly used > >by more than one tool. > > > >>> Assuming it doesn't, two questions: if I started putting such a thing together, would making it have the same format as the SBML Test Suite work for everyone--directory-demarked sets of files with input files, expected output files, and a setup file that listed with 'tags' what different aspects of SED-ML were being tested in each? Is that overkill, not enough, just right? > > > >I think that makes sense, and if you, Lucian, are willing and able to > >set something like that up then it would be a great resource for the > >community. As long as it is something that is easy to maintain and add > >to over time, then I'd imagine once the initial hurdle of setting it > >up is achieved, then we should be able to keep improving it with > >future releases of the specification. > > > >>> Secondly, if you have files you're using that you'd be willing to send in/deposit/point me to somewhere, that'd be great! > > > >Something like a github repo where we could submit pull requests to > >bring in more tests or corrections to existing tests would seem to be > >a good way to get the community contributing tests. Would provide a > >good forum to discuss the "correctness" of specific tests as well :) > > > > > >Cheers, > >David. > > > >------------------------------------------------------------------------------ > >Go from Idea to Many App Stores Faster with Intel(R) XDK > >Give your users amazing mobile app experiences with Intel(R) XDK. > >Use one codebase in this all-in-one HTML5 development environment. > >Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > >http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 <http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140> > >_______________________________________________ > >SED-ML-discuss mailing list > >SED...@li... <mailto:SED...@li...> > >https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> > > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 <http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140> > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... <mailto:SED...@li...> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140_______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: Frank B. <fbe...@ca...> - 2015-12-03 08:55:10
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Great … there is a web service that you could use to convert the files to if that would work: http://sysbioapps.dyndns.org/SED-ML_Web_Tools/Services/SedMLService.asmx if you need anything else please let me know. thanks Frank > On Dec 3, 2015, at 9:48 AM, Lucian Smith <luc...@gm...> wrote: > > At first, I thought you were talking about including SED-ML at all, which was amusing, but you actually mean the 'SED-ML Script' language, which is sort of 'the XML with the <>'s filed off', right? Sure, if that would be helpful, I'm happy to include them, especially if there's a translator out there that could make it automatic. As noted, the phraSED is only there in the text descriptions, anyway. > > -Lucian > > On Dec 3, 2015 12:15 AM, "Frank Bergmann" <fbe...@ca...> wrote: > Indeed I would love to see some SED-ML Scripts there, especially since we know that there might be concepts not yet in phraSED. > > Cheers > Frank > > > On Dec 3, 2015, at 1:31 AM, David Nickerson <dav...@gm...> wrote: > > > > Thanks Lucian - that is a great start. Now we just need to fill that > > contributions folder up :) > > > > I think it is fine to include Antimony or phraSED-ML in the > > description (or any other domain specific simple text format people > > use). > > > > > > Cheers, > > David. > > > > On Thu, Dec 3, 2015 at 1:15 PM, Lucian Smith <luc...@gm...> wrote: > >> I agree that we can model the suite after the SBML test suite, but it should > >> both be its own thing, and have CellML models in it, too. In fact, I think > >> that each directory/test should basically be modeling-language agnostic--the > >> point is to test SED-ML, not the modeling. > >> > >> I put together a bare-bones repository with a single test in it on github so > >> we can have an actual thing to talk about: > >> > >> https://github.com/luciansmith/sedml-test-suite/ > >> > >> If anyone wants access to it, I'll gladly add them to the 'collaborators' > >> list, which I think should work? Github and I don't get along all that well > >> ;-) > >> > >> I modeled everything off of the SBML test suite, with some changes: I now > >> have an 'info' file instead of the '.m' file in the SBML test suite, which > >> was an artifact of how the tests used to be created. There's no longer a > >> 'settings' file, since everything there in the SBML test suite is here > >> covered by SED-ML itself. > >> > >> All suggestions welcome! > >> > >> -Lucian > >> > >> > >> On Dec 2, 2015 12:54 AM, "Alan Garny" <ala...@in...> wrote: > >>> > >>> +1 regarding David’s suggestion of a GitHub repository for a SED-ML test > >>> suite and a test suite that is not SBML centric. And, as much as possible, I > >>> would be happy to contribute to it when it comes to CellML. > >>> > >>> > >>> > >>> Alan > >>> > >>> On 02/12/2015, 03:07, "David Nickerson" <dav...@gm...> wrote: > >>> > >>>>> To make this effective, I think it would be nice to integrate with the > >>>>> SBML Test Suite, since comparing simulation results is again what you will > >>>>> need to do. You already have some SED-ML files there, so it would mostly be > >>>>> adding some more sophisticated ones. > >>>>> > >>>> > >>>> I think that since we need to cater to a broader community than SBML, > >>>> the SED-ML test suite should be independent from the SBML test suite, > >>>> but it would be fine to be using the same framework if that can be > >>>> easily adapted and used in such a manner. I have an inking that > >>>> discussing this in the past with SBML developers that this might not > >>>> be such a straightforward task... > >>>> > >>>>>> It seems like it would be really helpful to have a > >>>>>> collectively-agreed-on test suite that put SED-ML through its paces, to make > >>>>>> sure everyone agreed that the same file meant the same thing to everyone. > >>>>>> At least, I assume that this doesn't already exist and I missed it? > >>>>>> > >>>> > >>>> No, nothing like that exists in a general sense. I know a few tools > >>>> that probably have their own internal tests, but nothing commonly used > >>>> by more than one tool. > >>>> > >>>>>> Assuming it doesn't, two questions: if I started putting such a thing > >>>>>> together, would making it have the same format as the SBML Test Suite work > >>>>>> for everyone--directory-demarked sets of files with input files, expected > >>>>>> output files, and a setup file that listed with 'tags' what different > >>>>>> aspects of SED-ML were being tested in each? Is that overkill, not enough, > >>>>>> just right? > >>>> > >>>> I think that makes sense, and if you, Lucian, are willing and able to > >>>> set something like that up then it would be a great resource for the > >>>> community. As long as it is something that is easy to maintain and add > >>>> to over time, then I'd imagine once the initial hurdle of setting it > >>>> up is achieved, then we should be able to keep improving it with > >>>> future releases of the specification. > >>>> > >>>>>> Secondly, if you have files you're using that you'd be willing to send > >>>>>> in/deposit/point me to somewhere, that'd be great! > >>>> > >>>> Something like a github repo where we could submit pull requests to > >>>> bring in more tests or corrections to existing tests would seem to be > >>>> a good way to get the community contributing tests. Would provide a > >>>> good forum to discuss the "correctness" of specific tests as well :) > >>>> > >>>> > >>>> Cheers, > >>>> David. > >>>> > >>> > >>>>> ------------------------------------------------------------------------------ > >>>> Go from Idea to Many App Stores Faster with Intel(R) XDK > >>>> Give your users amazing mobile app experiences with Intel(R) XDK. > >>>> Use one codebase in this all-in-one HTML5 development environment. > >>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple > >>>> OSs. > >>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > >>>> _______________________________________________ > >>>> SED-ML-discuss mailing list > >>>> SED...@li... > >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > >>> > >>> > >>> > >>> ------------------------------------------------------------------------------ > >>> Go from Idea to Many App Stores Faster with Intel(R) XDK > >>> Give your users amazing mobile app experiences with Intel(R) XDK. > >>> Use one codebase in this all-in-one HTML5 development environment. > >>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple > >>> OSs. > >>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > >>> _______________________________________________ > >>> SED-ML-discuss mailing list > >>> SED...@li... > >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > >> > >> > >> ------------------------------------------------------------------------------ > >> Go from Idea to Many App Stores Faster with Intel(R) XDK > >> Give your users amazing mobile app experiences with Intel(R) XDK. > >> Use one codebase in this all-in-one HTML5 development environment. > >> Design, debug & build mobile apps & 2D/3D high-impact games for multiple > >> OSs. > >> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > >> _______________________________________________ > >> SED-ML-discuss mailing list > >> SED...@li... > >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > >> > > > > > > > > -- > > > > > > David Nickerson > > about.me/david.nickerson > > > > ------------------------------------------------------------------------------ > > Go from Idea to Many App Stores Faster with Intel(R) XDK > > Give your users amazing mobile app experiences with Intel(R) XDK. > > Use one codebase in this all-in-one HTML5 development environment. > > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > > _______________________________________________ > > SED-ML-discuss mailing list > > SED...@li... > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140 > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > ------------------------------------------------------------------------------ > Go from Idea to Many App Stores Faster with Intel(R) XDK > Give your users amazing mobile app experiences with Intel(R) XDK. > Use one codebase in this all-in-one HTML5 development environment. > Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140_______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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