Just a note, for some reason you don't now need the SOCKs proxy from in the ABI.
> -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] 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: [EMAIL PROTECTED] [mailto:cellml-discussion- >> [EMAIL PROTECTED] On Behalf Of Andrew >> Sent: Monday, 19 May 2008 4:17 p.m. >> To: Kevin Burrage >> Cc: cellml-discussion@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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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. >>>> >> _______________________________________________ >> cellml-discussion mailing list >> cellml-discussion@cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > _______________________________________________ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
