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Re: [SED-ML-discuss] Fwd: [kisao:feature-requests] #31 Number of Runs
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From: Herbert S. <uw....@gm...> - 2017-07-18 17:26:50
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Thanks for that, very useful, seems there is no clear consensus at the moment. from my point of view I'd need to do some implementations to see how the different possibilities pan out. We could probably do some test in August. I assume there is sufficient post processing semantics to compute means and sds? Also I assume the kiaso terms are rich enough to specify the stochastic simulation alogorithm. As far as I am aware, to compute the mean and sd, the simulation points need to be on a grid. In sedml where does this happen, on the Kisao term? Herbert On Tue, Jul 18, 2017 at 10:13 AM David Nickerson <dav...@gm...> wrote: > Just to provide the link to the github issue where there has been some > discussion relevant to this thread: > https://github.com/SED-ML/sed-ml/issues/22. > > > On 19 July 2017 at 05:08, Herbert Sauro <uw....@gm...> wrote: > > Chris can you give your arguments for needing a kiaso term for the > number of > > runs? I can't decide whether the size of the ensemble is part of the > > algorithm or not. Usually it's not. > > > > Unfortunately this wasn't discussed at harmony. There should be a wider > > discussion on how to deal with ensemble runs for stochastic systems since > > many of use will be affected. True, we already have repeated tasks but I > > can't remember the arguments against using that for stochastic multiple > > runs. > > > > Herbert > > > > On Tue, Jul 18, 2017 at 1:23 AM Nicolas Le Novere <n.l...@gm...> > > wrote: > >> > >> Hi Chris, > >> > >> Last I heard, Anna was kind enough to update KiSAO when a new request > >> came. > >> > >> What I am unclear about is where in KiSAO, would you like to put this? > The > >> number of run looks like a SED-ML attribute rather than a KiSAO term. > >> Actually I thought that this was already covered by the current > structures > >> supporting repeated simulations. > >> > >> On 13/07/17 23:09, Chris Myers wrote: > >> > Who maintains KISAO? I would like to get this added ASAP. It is > >> > critical if we want SED-ML to support stochastic simulation properly. > >> > > >> > Chris > >> > > >> >> Begin forwarded message: > >> >> > >> >> *From: *"Chris Myers" <cc...@us... > >> >> <mailto:cc...@us...>> > >> >> *Subject: **[kisao:feature-requests] #31 Number of Runs* > >> >> *Date: *July 13, 2017 at 4:02:19 PM MDT > >> >> *To: *"Ticket 31" <31...@fe... > >> >> <mailto:31...@fe...>> > >> >> *Reply-To: *"Ticket 31" <31...@fe... > >> >> <mailto:31...@fe...>> > >> >> > >> >> > >> >> > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ > >> >> > >> >> *[feature-requests:#31] > >> >> <https://sourceforge.net/p/kisao/feature-requests/31/> Number of > Runs* > >> >> > >> >> *Status:* open > >> >> *Created:* Thu Jul 13, 2017 10:02 PM UTC by Chris Myers > >> >> *Last Updated:* Thu Jul 13, 2017 10:02 PM UTC > >> >> *Owner:* nobody > >> >> > >> >> This should indicate the number of runs that a simulation should > >> >> perform. It would typically be used to specify the number of runs > for a > >> >> stochastic simulation. > >> >> > >> >> > >> >> > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ > >> >> > >> >> Sent from sourceforge.net <http://sourceforge.net> because you > >> >> indicated interest in > https://sourceforge.net/p/kisao/feature-requests/31/ > >> >> > >> >> To unsubscribe from further messages, please visit > >> >> https://sourceforge.net/auth/subscriptions/ > >> >> > >> > > >> > >> > >> -- > >> Nicolas LE NOVERE, > >> The Babraham Institute, Babraham Campus Cambridge, CB22 3AT > >> Tel: +441223496433 Mob:+447833147074 http://lenoverelab.org > >> orcid.org//0000-0002-6309-7327 Skype:n.lenovere twitter:@lenovere > >> > >> > >> > >> > ------------------------------------------------------------------------------ > >> Check out the vibrant tech community on one of the world's most > >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot > >> _______________________________________________ > >> SED-ML-discuss mailing list > >> SED...@li... > >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > _______________________________________________ > > SED-ML-discuss mailing list > > SED...@li... > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > > -- > > > David Nickerson > about.me/david.nickerson > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > |
