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Re: [SED-ML-discuss] SED-ML-discuss Digest, Vol 47, Issue 2
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From: Pedro M. <ped...@ma...> - 2015-08-24 07:48:55
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I agree that it should be possible to define a series of arbitrary time points. Actually, it is quite common to encounter this in parameter estimation, so it is definitely needed. Pedro On 08/21/2015 05:09 PM, Herbert Sauro wrote: > Is there a non-uniform option? If not maybe we should have one, then you > could specify a list. Also it might be useful to add an interval based > distriubtion in addition to the number of points but no sure if thay > will help since your intevals are non-uniform, ie last interval is 1, > all others are 3. > > > Herbert > > On Fri, Aug 21, 2015 at 7:57 AM, > <sed...@li... > <mailto:sed...@li...>> wrote: > > Send SED-ML-discuss mailing list submissions to > sed...@li... > <mailto:sed...@li...> > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > or, via email, send a message with subject or body 'help' to > sed...@li... > <mailto:sed...@li...> > > You can reach the person managing the list at > sed...@li... > <mailto:sed...@li...> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of SED-ML-discuss digest..." > > > Today's Topics: > > 1. Re: COMBINE 2015 (Sharon Crook) > 2. Fwd: [sbml-discuss] COMBINE 2015: Reminders (David Nickerson) > 3. Create a 'uniform' time course simulation (Alan Garny) > 4. Re: Create a 'uniform' time course simulation (Jonathan Cooper) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 10 Aug 2015 18:38:12 +0000 > From: Sharon Crook <Sha...@as... <mailto:Sha...@as...>> > Subject: Re: [SED-ML-discuss] COMBINE 2015 > To: "sed...@li... > <mailto:sed...@li...>" > <sed...@li... > <mailto:sed...@li...>> > Message-ID: > > <679...@ex... > <mailto:679...@ex...>> > Content-Type: text/plain; charset="iso-8859-1" > > SORRY EVERYONE. Obviously replied to the wrong email. But see you > there!!! > > Sharon Crook > Associate Professor of Mathematics, Statistics and Life Sciences > Arizona State University > Vice President, Organization for Computational Neuroscience > http://math.la.asu.edu/~crook > http://neuroml.org > ________________________________ > From: Sharon Crook [Sha...@as... <mailto:Sha...@as...>] > Sent: Monday, August 10, 2015 11:34 AM > To: sed...@li... > <mailto:sed...@li...> > Subject: Re: [SED-ML-discuss] COMBINE 2015 > > Hi Chris, > > How should I proceed with registration. You had indicated that you > would cover registration and lodging if I cover flight and the rest > (unless you received a NSF grant). I'm still fine with this but > didn't know how to register or reserve room if I don't pay. Let me know. > > I will plan to arrive late on October 11 and stay October 12, 13, > 14. Will have to fly back to AZ on the 14th. > > Best, > Sharon > > Sharon Crook > Associate Professor of Mathematics, Statistics and Life Sciences > Arizona State University > Vice President, Organization for Computational Neuroscience > http://math.la.asu.edu/~crook > http://neuroml.org > ________________________________ > From: Chris J. Myers [my...@ec... <mailto:my...@ec...>] > Sent: Saturday, July 25, 2015 9:25 AM > To: sed...@li... > <mailto:sed...@li...> > Subject: [SED-ML-discuss] COMBINE 2015 > > Dear SED-ML developers, > > Registration is now open for COMBINE 2015 which will be held at the > University of Utah in Salt Lake City from October 12 to 16: > > http://co.mbine.org/events/COMBINE_2015 > > In addition to the presentations on various COMBINE standards such > as SED-ML, there will be breakout sessions every afternoon to > discuss future directions for each standard. Therefore, we would > like to have a good representation from all COMBINE communities present. > > Please complete the registration as soon as possible and certainly > before October 1st, so we have an accurate head count for the > catering. While there is a registration fee of US$250 to cover > breaks, lunches, and a banquet, we have received funds from NSF to > cover the registration fees for students, postdoctoral researchers, > other junior researchers, as well as, participants from > underrepresented groups working on systems and synthetic biology > standards. We have also received funds from NSF to provide partial > travel support and lodging (based on double occupancy) for US-based > students, postdoctoral scholars, and participants from > underrepresented groups. If you are eligible for either of these > awards, please fill out the application for these funds before > registering. Funds will be distributed as applications are received > until exhausted, so please submit your application as soon as possible. > > I would also like to point out that lodging is available at US$109 > per night at the University of Utah Guest House. Our room block is > limited in size, and it expires on September 14th, so please book > your rooms as soon as possible. > > Finally, abstract submission is also now open. To be considered for > a presentation slot, you must submit your abstract before September 1st. > > Thank you and we look forward to welcoming you to Salt Lake City in > October. > > Chris Myers > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 2 > Date: Fri, 21 Aug 2015 14:31:15 +1200 > From: David Nickerson <dav...@gm... > <mailto:dav...@gm...>> > Subject: [SED-ML-discuss] Fwd: [sbml-discuss] COMBINE 2015: Reminders > To: sed...@li... > <mailto:sed...@li...> > Message-ID: > > <CAD...@ma... > <mailto:CADizRjirdEqNeEoCFLKVeKnZpsKkdOnKgVt%2Bq...@ma...>> > Content-Type: text/plain; charset=UTF-8 > > ---------- Forwarded message ---------- > From: Chris J. Myers <my...@ec... <mailto:my...@ec...>> > Date: Fri, Aug 21, 2015 at 7:28 AM > Subject: [sbml-discuss] COMBINE 2015: Reminders > To: com...@go... > <mailto:com...@go...>, > sbm...@go... <mailto:sbm...@go...>, > sed...@li... > <mailto:sed...@li...>, > "sbo...@go... <mailto:sbo...@go...> > Developers" <sbo...@go... > <mailto:sbo...@go...>> > > > Hi All, > > I wanted to remind you of some important upcoming dates for COMBINE > 2015. > > 1) September 1st - abstract deadline. We would like to have a wide > variety of contributed talks. If you have some work that you would > like to share with the COMBINE community, please consider submitting > an abstract. > > https://docs.google.com/forms/d/1LRBoHsut-fI813KZcbj6mSjZu7a9kreCCICXb_ZUApo/viewform > > 2) September 14th - hotel reservation deadline. We have a block of > rooms allocated for a reduced rate of $109/night (including breakfast) > at the University of Utah Guest House. After that deadline, we cannot > guarantee availability of these rooms. Instructions for making your > reservations are on the COMBINE website: > > http://co.mbine.org/events/COMBINE_2015 > > 3) October 1st - registration deadline. Even though this deadline is > still a little ways off, please consider registering as soon as > possible to help us have an accurate count of participants. > > https://umarket.utah.edu/um2/elecandcompcombine/productlist.php?storecookie=1 > > 4) Finally, there are still funds available to support registration > fees for students, postdoctoral researchers, and other junior > researchers, as well as, participants from underrepresented groups > working on systems and synthetic biology standards. There are also > still funds available for travel and lodging support for US-based > students, postdocs, and participants from underrepresented groups. > Please apply for these here: > > https://docs.google.com/forms/d/111ICZyQDLgZ3DUnc-bYnlVYPbtrGvzygDLdA20Pzta8/viewform > > Look forward to welcoming you to Salt Lake City in October. > > Chris Myers > > -- > You received this message because you are subscribed to the Google > Groups "sbml-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send > an email to sbm...@go... > <mailto:sbml-discuss%2Bu...@go...>. > To post to this group, send email to sbm...@go... > <mailto:sbm...@go...>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sbml-discuss/0A2882E7-497E-4482-B775-CC2112686C0C%40ece.utah.edu. > For more options, visit https://groups.google.com/d/optout. > > > -- > > > David Nickerson > about.me/david.nickerson <http://about.me/david.nickerson> > > > > ------------------------------ > > Message: 3 > Date: Fri, 21 Aug 2015 15:40:42 +0200 > From: "Alan Garny" <ala...@in... <mailto:ala...@in...>> > Subject: [SED-ML-discuss] Create a 'uniform' time course simulation > To: <sed...@li... > <mailto:sed...@li...>> > Message-ID: <00a001d0dc16$f9768630$ec639290$@inria.fr <http://inria.fr>> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > > > I am trying to create a SED-ML document with a 'uniform' time course > simulation. Among other things, I understand that I must set a number of > points, but this is causing me problems in some cases. > > > > For example, say that I want a simulation with an initial time and > output > start time of 0 time unit, and an output end time of 10 time units. > Now, say > that I want data points to be generated every 3 time units, i.e. at time > units 0, 3, 6, 9 and 10 (hence 'uniform' in quotes). > > If my understanding of section 2.4.3.3.4 of the SED-ML specifications is > correct, I would need to instruct SED-ML that I want 4 points. It's > all fine > when it comes to writing my SED-ML document, but when it comes to > reading it > and executing it, I would suspect SED-ML capable software to > generate data > points at time units 0, 2.5, 5, 7.5 and 10, which is not what I want. > > > > I understand that the current specifications agree with the idea of a > uniform time course, but what if I still want to do the above? Can it be > done in SED-ML and if so how? > > > > FWIW, the reason I like to specify a point interval rather than a > number of > points is that I can then change my output start/end time without > having to > recalculate the number of points I would need in order to keep my > 'original' > point interval. > > > > Cheers, Alan. > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 4 > Date: Fri, 21 Aug 2015 15:57:46 +0100 > From: Jonathan Cooper <jon...@cs... > <mailto:jon...@cs...>> > Subject: Re: [SED-ML-discuss] Create a 'uniform' time course > simulation > To: sed...@li... > <mailto:sed...@li...> > Message-ID: <55D...@cs... > <mailto:55D...@cs...>> > Content-Type: text/plain; charset="windows-1252" > > Hi Alan, > > I think you could express it in L1V2 using a repeatedTask (that doesn't > actually repeat) containing 2 subTasks - the first a running a > uniformTimeCourse for the truly uniform part and the second a oneStep to > get you to the final end time. But that's not particularly pretty! > > Best wishes, > Jonathan > > On 21/08/2015 14:40, Alan Garny wrote: > > > > Hi, > > > > I am trying to create a SED-ML document with a ?uniform? time course > > simulation. Among other things, I understand that I must set a number > > of points, but this is causing me problems in some cases. > > > > For example, say that I want a simulation with an initial time and > > output start time of 0 time unit, and an output end time of 10 time > > units. Now, say that I want data points to be generated every 3 time > > units, i.e. at time units 0, 3, 6, 9 and 10 (hence ?uniform? in > quotes). > > > > If my understanding of section 2.4.3.3.4 of the SED-ML specifications > > is correct, I would need to instruct SED-ML that I want 4 points. > It?s > > all fine when it comes to writing my SED-ML document, but when it > > comes to reading it and executing it, I would suspect SED-ML capable > > software to generate data points at time units 0, 2.5, 5, 7.5 and 10, > > which is not what I want. > > > > I understand that the current specifications agree with the idea of a > > uniform time course, but what if I still want to do the above? Can it > > be done in SED-ML and if so how? > > > > FWIW, the reason I like to specify a point interval rather than a > > number of points is that I can then change my output start/end time > > without having to recalculate the number of points I would need in > > order to keep my ?original? point interval. > > > > Cheers, Alan. > > > > > > > > > ------------------------------------------------------------------------------ > > > > > > _______________________________________________ > > SED-ML-discuss mailing list > > SED...@li... > <mailto:SED...@li...> > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > > > ------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > <mailto:SED...@li...> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > End of SED-ML-discuss Digest, Vol 47, Issue 2 > ********************************************* > > > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > -- Pedro Mendes Professor of Computational Systems Biology http://www.comp-sys-bio.org School of Computer Science Manchester Centre for Integrative Systems Biology University of Manchester Manchester Institute of Biotechnology 131 Princess Street Manchester, M1 7DN, U.K. |
