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Just a note, for some reason you don't now need the SOCKs proxy from in the
ABI.

> -----Original Message-----
> From: cellml-discussion-bounces at cellml.org
> [mailto:cellml-discussion-bounces at cellml.org] On Behalf Of Randall
> Britten
> Sent: Monday, 19 May 2008 4:59 p.m.
> To: 'CellML Discussion List'
> Cc: 'Kevin Burrage'
> Subject: Re: [cellml-discussion] Representing stochastic models in CellML
>
> Hi
>
> I'd prefer Skype at that time.
>
> I've found the Skype conference calls work fairly well, easiest if one
> person initiates the call, and all others make sure that the initiator
knows
> their skype-name, and that they want to be called to join in. Also, Skype
> from within the ABI works well too, though you'll need IT to explain how
to
> use the SOCKS proxy, or to set it up for you if you have not done it
before.
>
> Regards,
> Randall
>
>> -----Original Message-----
>> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-
>> bounces at cellml.org] On Behalf Of Andrew
>> Sent: Monday, 19 May 2008 4:17 p.m.
>> To: Kevin Burrage
>> Cc: cellml-discussion at cellml.org
>> Subject: Re: [cellml-discussion] Representing stochastic models in
>> CellML
>>
>> Kevin Burrage wrote:
>>> Andrew
>>>
>>> i am at conference early next week and then lectures and meetings
>>> wednesday and thursday - i am free friday 23 at say 8.30am - but how
>>> are we going to do it. I am not sure that i can access the grid room
>>> - can skype work?
>>> BW
>> Hi Kevin,
>>
>> I am happy with 7:30 PM NZST (8:30 AM for you) on Friday the 23rd.
>>
>> I have got Skype working at home (and I have seen it working on the UoA
>> network for other people although not always); we could try running it
>> as a conference call and this might allow more people to participate
>> (but may also be more prone to not working).
>>
>> Perhaps the best thing would be for everyone who is interested, and
>> whether they would be happy with the time, and whether they would
>> rather
>> conference call in or (for people in Auckland) be in the same room at
>> the ABI.
>>
>> Best regards,
>> Andrew
>>
>>> Kevin
>>> -------------------------------------------------
>>> Kevin Burrage
>>> Professor of Computational Systems Biology, COMLAB, University of
>> Oxford
>>> and Professor of Computational Mathematics, IMB, University of
>> Queensland
>>> -------------------------------------------------
>>>
>>>
>>>
>>> On Wed, 14 May 2008 11:58:03 +1200
>>> Andrew Miller <ak.miller at auckland.ac.nz> wrote:
>>> Kevin Burrage wrote:
>>>> Andrew
>>>>
>>>> I have lots of ideas on this - but email not a good way of doing it.
>>>> Am in oxford at the moment but could skype you if you were
>> interested.
>>> Hi Kevin,
>>>
>>> Sorry for the delay in getting back to you about this.
>>>
>>> There seems to be a lot of interest amongst members of
>>> the CellML community in Auckland about hearing your views
>>> on this; one suggestion I heard was to use the BestGRID
>>> rather than Skype so more people could be involved at this
>>> end (although I am not sure how convenient it would be for
>>> you to access the BestGRID facilities in Oxford so the
>>> timezones would work out).
>>>
>>> When would be the most convenient for you? Given that
>>> there are a number of people who have indicated a desire
>>> to be involved in these discussion, and also a few that
>>> are interested in sitting in to listen, I would suggest
>>> making it at earliest next week, to ensure everyone can
>>> get their schedules to fit, and to ensure that software is
>>> working ahead of time. Since you are, I presume, in a
>>> GMT+1 timezone, and we are in GMT+12, the best time would
>>> probably be early in the morning for you / night time for
>>> us, e.g. 7-8 AM Oxford / 6-7 PM NZ, 8-9 AM Oxford / 7-8 PM
>>> NZ , or 9-10 AM Oxford / 8-9 PM NZ.
>>>
>>> Best regards,
>>> Andrew
>>>
>>>> BW
>>>>
>>>> Kevin
>>>> -------------------------------------------------
>>>> Kevin Burrage
>>>> Professor of Computational Systems Biology, COMLAB, University of
>> Oxford
>>>> and Professor of Computational Mathematics, IMB, University of
>>>> Queensland
>>>> -------------------------------------------------
>>>>
>>>>
>>>>
>>>> On Wed, 23 Apr 2008 17:31:26 +1200
>>>> Andrew Miller <ak.miller at auckland.ac.nz> wrote:
>>>> Hi all,
>>>>
>>>> I have spent some time looking into how we might be able
>>>> to represent stochastic models in CellML. This is
>>>> something that would be useful to ensure we have properly
>>>> contemplated for CellML 1.2. I have pasted in the notes I
>>>> wrote on this below.
>>>>
>>>> Please let me know if you have any suggestions, comments,
>>>> or criticisms of the below document. At some point, this
>>>> will obviously need to be transformed into a more robust
>>>> proposal, but for now, I just want to make sure we keep
>>>> the option open to use the CellML 1.2 core to represent
>>>> stochastic models.
>>>>
>>>> Best regards,
>>>> Andrew
>>>>
>>>> -----
>>>>
>>>> Overall goal:
>>>> Describe a framework which can be used in CellML 1.2 to
>>>> represent a
>>>> range of
>>>> different systems which require stochastic differential
>>>> equations to
>>>> describe.
>>>>
>>>> Constraints:
>>>> Do not want to describe the procedure for solving the
>>>> model in core
>>>> CellML,
>>>> only the underlying mathematical / statistical model.
>>>> Want to express the model in such a way that the
>>>> procedure is computable
>>>> from the model.
>>>> Want there to be only one interpretation of the model.
>>>> Want the representation to be abstract enough that it is
>>>> meaningful for a
>>>> number of different fields, and not just chemical
>>>> equations in a well
>>>> stirred vessel.
>>>> Want the representation to work naturally when mixed
>>>> with systems of
>>>> ordinary
>>>> differential equations.
>>>>
>>>> Use cases:
>>>> Chemical reactions under the Chemical Master Equation
>>>> model of Gillespie:
>>>> We need to split these into separate species. This is
>>>> a Poisson process,
>>>> so there are simple ways to represent it.
>>>>
>>>> It is more efficient to represent models using Weiner
>>>> processes when
>>>> this
>>>> there are large enough numbers of molecules to justify
>>>> this but ODEs are
>>>> not being used.
>>>>
>>>> However, Poisson and Weiner processes are both Levy
>>>> Processes, that is,
>>>> they have stationary independent increments, are zero
>>>> at time zero, and
>>>> are cadlag. This is not necessarily a good thing
>>>> because some things we
>>>> want to model might have memory of past events or a
>>>> time dependence.
>>>>
>>>> How we can represent this in CellML:
>>>> For the continuous case, integral equations for the
>>>> increment in terms of
>>>> built in processes like Weiner and Poisson processes (I
>>>> don't believe
>>>> there
>>>> is a clean way to represent increments in MathML).
>>>>
>>>> Implementations will need to identify these and work out
>>>> the
>>>> distribution of
>>>> the time until the next event (good implementations
>>>> might be able to
>>>> perform
>>>> symbolic algebra to work this out, but most
>>>> implementations would probably
>>>> just recognise common cases like Poisson distributions
>>>> with arbitrary
>>>> parameters, and deal with expressions involving a Weiner
>>>> process by
>>>> sampling
>>>> from the increment distribution in each time step),
>>>> which could be put
>>>> into a
>>>> slightly generalised Gibson-Bruck type of framework
>>>> where we store the
>>>> time of
>>>> the next event.
>>>>
>>>> None of this helps for non stationary independent
>>>> processes, however.
>>>>
>>>> How could this be related to the standards:
>>>> It has been proposed that CellML 1.2 have a core
>>>> specification which
>>>> describes
>>>> the basic way of representing the mathematical structure
>>>> in very general
>>>> terms, and secondary specifications be used to narrow
>>>> CellML down to
>>>> specific
>>>> subsets which can be implemented in their entirety by a
>>>> actual software
>>>> packages.
>>>>
>>>> Core CellML 1.2 should be general enough to represent
>>>> concepts like
>>>> probability distributions (MathML allows new operators
>>>> to be defined,
>>>> so we
>>>> could create ones for our base types of stochastic
>>>> process). The ODE IV
>>>> secondary specification would not allow stochastic
>>>> models, while we would
>>>> have another alternative secondary specification which
>>>> extended the ODE IV
>>>> one to allow certain limited types of stochastic model
>>>> (limited to
>>>> types we
>>>> know how to solve).
>>>>
>>>> In terms of interaction with the typing system, in a
>>>> stochastic system we
>>>> have both reals and real-valued random variables. Once
>>>> we have one random
>>>> variable in our system, this will propagate to
>>>> everything else which
>>>> is affected by it, so most of the model will technically
>>>> be a random
>>>> variable.
>>>> However, we want to be able to easily mix stochastic
>>>> models with
>>>> existing ODE
>>>> IV models to create hybrid models, so we don't really
>>>> want the required
>>>> datatype to change just to connect up a random variable
>>>> to a non-random
>>>> variable. For this reason, I don't think it is
>>>> worthwhile to consider a
>>>> random variable of a certain type a different datatype,
>>>> and instead we
>>>> would
>>>> require tools to deduce this information if they require
>>>> it.
>>>>
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• [cellml-discussion] FW: Representing stochastic models in CellML, Mike Cooling, 05/23/2008

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