sed-ml-discuss — Migrating to google groups: https://groups.google.com/d/forum/sed-ml-discuss

[SED-ML-discuss] A couple of questions regarding simulation algorithms

[Alan G. <ala...@in...>]

Hi,

 

>From the SED-ML L1V2 specifications, it would seem that a simulation can
have only one algorithm (section 2.4.3). However, what if I need to specify
two algorithms? Indeed, some DAE models may require solving a system of
non-linear algebraic equations, in which case we might want to be able to
use two solvers such as IDA
<http://computation.llnl.gov/casc/sundials/description/description.html#desc
r_ida>  and KINSOL
<http://computation.llnl.gov/casc/sundials/description/description.html#desc
r_kinsol>  from the SUNDIALS library. I guess that for now, I could specify
IDA as the simulation algorithm and refer to KINSOL in an annotation in the
SED-ML simulation object?

 

Another question I have is about algorithm parameters that don't have a
corresponding KiSAO id. For example, for CVODE
<http://computation.llnl.gov/casc/sundials/description/description.html#desc
r_cvode> , I have seen KiSAO ids for CVODE itself, as well as for the
maximum step size, the maximum number of steps, relative tolerance and
absolute tolerance, but not for the type of integration method (i.e. BDF or
Adams-Moulton) and a few other parameters that can be set in CVODE. I
understand that it's more of a KiSAO question, but until those KiSAO ids
become available, what would be the best way to 'set' those parameters in a
SED-ML file? Once again, I am thinking of referring to them in various
annotations in the SED-ML algorithm object, but is that the recommended
approach?

 

I am not happy with that approach since it will effectively render my SED-ML
file unusable by others, but I can't think of any other way at this stage.

 

Cheers, Alan.

Re: [SED-ML-discuss] SED-ML-discuss Digest, Vol 47, Issue 2

[Pedro M. <ped...@ma...>]

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
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>     or, via email, send a message with subject or body 'help' to
>     sed...@li...
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>
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>
>     When replying, please edit your Subject line so it is more specific
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>
>
>     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
>
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>     ------------------------------
>
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>     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.

Re: [SED-ML-discuss] SED-ML-discuss Digest, Vol 47, Issue 2

[Frank B. <fbe...@ca...>]

I would be fine with that … considering that in L1V2 we already have the range constructs, It would be fine to have a general timecourse, that has a range as child element that defines the points the timecourse will hit, those could be a uniformrange, in which case it would be just like the uniformtimecourse we have right now, or it could be a vector range, in which you define the points you want to hit precisely, or a functional range, where some function would define which time points should be hit. I think that goes well with the other elements of SED-ML. 

Examples: 

// uniform timecourse
<timecourse id=‘foo’>
<uniformRange start="0.0” end =“10.0” numberOfPoints=“100” type=“linear” />
</timecourse>

// vector range: hitting points 3, 6, 9, 10
<timecourse id=“foo1”>
<vectorRange>
    <value>3</value>
    <value>6</value>
    <value>9</value>
    <value>10</value>
</vectorRange>
</timecourse>

Cheers
Frank


> On Aug 21, 2015, at 6:09 PM, Herbert Sauro <uw....@gm...> 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...> wrote:
> Send SED-ML-discuss mailing list submissions to
>         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...
> 
> You can reach the person managing the list at
>         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...>
> Subject: Re: [SED-ML-discuss] COMBINE 2015
> To: "sed...@li..."
>         <sed...@li...>
> Message-ID:
>         <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...]
> Sent: Monday, August 10, 2015 11:34 AM
> To: 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...]
> Sent: Saturday, July 25, 2015 9:25 AM
> To: 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...>
> Subject: [SED-ML-discuss] Fwd: [sbml-discuss] COMBINE 2015: Reminders
> To: sed...@li...
> Message-ID:
>         <CAD...@ma...>
> Content-Type: text/plain; charset=UTF-8
> 
> ---------- Forwarded message ----------
> From: Chris J. Myers <my...@ec...>
> Date: Fri, Aug 21, 2015 at 7:28 AM
> Subject: [sbml-discuss] COMBINE 2015: Reminders
> To: com...@go..., sbm...@go...,
> sed...@li..., "sbo...@go...
> Developers" <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 $109/night (including breakfast)
> at the University of Utah Guest House.  After that deadline, we cannot
> guarantee availability of these rooms.  Instructions for making your
> reservations are on the COMBINE website:
> 
> http://co.mbine.org/events/COMBINE_2015
> 
> 3) October 1st - registration deadline.  Even though this deadline is
> still a little ways off, please consider registering as soon as
> possible to help us have an accurate count of participants.
> 
> https://umarket.utah.edu/um2/elecandcompcombine/productlist.php?storecookie=1
> 
> 4) Finally, there are still funds available to support registration
> fees for students, postdoctoral researchers, and other junior
> researchers, as well as, participants from underrepresented groups
> working on systems and synthetic biology standards.  There are also
> still funds available for travel and lodging support for US-based
> students, postdocs, and participants from underrepresented groups.
> Please apply for these here:
> 
> https://docs.google.com/forms/d/111ICZyQDLgZ3DUnc-bYnlVYPbtrGvzygDLdA20Pzta8/viewform
> 
> Look forward to welcoming you to Salt Lake City in October.
> 
> Chris Myers
> 
> --
> You received this message because you are subscribed to the Google
> Groups "sbml-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to sbm...@go....
> To post to this group, send email to sbm...@go....
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/sbml-discuss/0A2882E7-497E-4482-B775-CC2112686C0C%40ece.utah.edu.
> For more options, visit https://groups.google.com/d/optout.
> 
> 
> --
> 
> 
> David Nickerson
> about.me/david.nickerson
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Fri, 21 Aug 2015 15:40:42 +0200
> From: "Alan Garny" <ala...@in...>
> Subject: [SED-ML-discuss] Create a 'uniform' time course simulation
> To: <sed...@li...>
> Message-ID: <00a001d0dc16$f9768630$ec639290$@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...>
> Subject: Re: [SED-ML-discuss] Create a 'uniform' time course
>         simulation
> To: sed...@li...
> Message-ID: <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...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> -------------- next part --------------
> An HTML attachment was scrubbed...
> 
> ------------------------------
> 
> ------------------------------------------------------------------------------
> 
> 
> ------------------------------
> 
> _______________________________________________
> SED-ML-discuss mailing list
> 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

Re: [SED-ML-discuss] SED-ML-discuss Digest, Vol 47, Issue 2

[Alan G. <ala...@in...>]

Hi Herbert,

 

Unless I am missing something, there are currently three types of simulations: UniformTimeCourse, OneStep and SteadyState. So, at the moment, Jonathan’s suggestion seems to be the only way to do what I am after. Yet, I thought it was an overkill, so I decided to implement my ‘warning solution’ instead, but it really goes against the idea of using something like SED-ML. So, now, I am working on implementing Jonathan’s suggestion (unless a simulation is a truly uniform time course, in which case I use UniformTimeCourse) and although I don’t ‘like’ it, at least it makes my use of SED-ML meaningful.

 

Regarding a non-uniform option that requires a list, I am not sure it would be the way to go. Such a list could easily end up with thousands of items, which would just be ‘crazy’. Personally, I would really favour being able to specify a ‘uniform’ time course using a point interval. Sure, the last interval may not be equal to the point interval (as is the case in my example), but at least it would do the job (and it is, to me, the approach closest to what experimentalists do by specifying a sampling rate to retrieve their experimental data).

 

Alan

 

From: Herbert Sauro [mailto:uw....@gm...] 
Sent: 21 August 2015 18:09
To: sed...@li...
Subject: Re: [SED-ML-discuss] SED-ML-discuss Digest, Vol 47, Issue 2

 

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.

 

Re: [SED-ML-discuss] SED-ML-discuss Digest, Vol 47, Issue 2

[Herbert S. <uw....@gm...>]

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...> wrote:

> Send SED-ML-discuss mailing list submissions to
>         sed...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> 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...>
> Subject: Re: [SED-ML-discuss] COMBINE 2015
> To: "sed...@li..."
>         <sed...@li...>
> Message-ID:
>         <
> 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...]
> Sent: Monday, August 10, 2015 11:34 AM
> To: 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...]
> Sent: Saturday, July 25, 2015 9:25 AM
> To: 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...>
> Subject: [SED-ML-discuss] Fwd: [sbml-discuss] COMBINE 2015: Reminders
> To: sed...@li...
> Message-ID:
>         <
> CAD...@ma...>
> Content-Type: text/plain; charset=UTF-8
>
> ---------- Forwarded message ----------
> From: Chris J. Myers <my...@ec...>
> Date: Fri, Aug 21, 2015 at 7:28 AM
> Subject: [sbml-discuss] COMBINE 2015: Reminders
> To: com...@go..., sbm...@go...,
> sed...@li..., "sbo...@go...
> Developers" <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 $109/night (including breakfast)
> at the University of Utah Guest House.  After that deadline, we cannot
> guarantee availability of these rooms.  Instructions for making your
> reservations are on the COMBINE website:
>
> http://co.mbine.org/events/COMBINE_2015
>
> 3) October 1st - registration deadline.  Even though this deadline is
> still a little ways off, please consider registering as soon as
> possible to help us have an accurate count of participants.
>
>
> https://umarket.utah.edu/um2/elecandcompcombine/productlist.php?storecookie=1
>
> 4) Finally, there are still funds available to support registration
> fees for students, postdoctoral researchers, and other junior
> researchers, as well as, participants from underrepresented groups
> working on systems and synthetic biology standards.  There are also
> still funds available for travel and lodging support for US-based
> students, postdocs, and participants from underrepresented groups.
> Please apply for these here:
>
>
> https://docs.google.com/forms/d/111ICZyQDLgZ3DUnc-bYnlVYPbtrGvzygDLdA20Pzta8/viewform
>
> Look forward to welcoming you to Salt Lake City in October.
>
> Chris Myers
>
> --
> You received this message because you are subscribed to the Google
> Groups "sbml-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to sbm...@go....
> To post to this group, send email to sbm...@go....
> To view this discussion on the web visit
>
> https://groups.google.com/d/msgid/sbml-discuss/0A2882E7-497E-4482-B775-CC2112686C0C%40ece.utah.edu
> .
> For more options, visit https://groups.google.com/d/optout.
>
>
> --
>
>
> David Nickerson
> about.me/david.nickerson
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 21 Aug 2015 15:40:42 +0200
> From: "Alan Garny" <ala...@in...>
> Subject: [SED-ML-discuss] Create a 'uniform' time course simulation
> To: <sed...@li...>
> Message-ID: <00a001d0dc16$f9768630$ec639290$@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...>
> Subject: Re: [SED-ML-discuss] Create a 'uniform' time course
>         simulation
> To: sed...@li...
> Message-ID: <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...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
>
> ------------------------------------------------------------------------------
>
>
> ------------------------------
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> End of SED-ML-discuss Digest, Vol 47, Issue 2
> *********************************************
>

Re: [SED-ML-discuss] Create a 'uniform' time course simulation

[Alan G. <ala...@in...>]

Thanks Jonathan. I can indeed see that working in SED-ML, but I agree that
it's not particularly pretty. As a starting point, I think I am going to
stick to a uniformTimeCourse and warn the user if it's not truly uniform.

 

Alan

 

From: Jonathan Cooper [mailto:jon...@cs...] 
Sent: 21 August 2015 16:58
To: sed...@li...
Subject: Re: [SED-ML-discuss] Create a 'uniform' time course simulation

 

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...
https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

 

Re: [SED-ML-discuss] Create a 'uniform' time course simulation

[Jonathan C. <jon...@cs...>]

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...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] Create a 'uniform' time course simulation

[Alan G. <ala...@in...>]

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] Fwd: [sbml-discuss] COMBINE 2015: Reminders

[David N. <dav...@gm...>]

---------- Forwarded message ----------
From: Chris J. Myers <my...@ec...>
Date: Fri, Aug 21, 2015 at 7:28 AM
Subject: [sbml-discuss] COMBINE 2015: Reminders
To: com...@go..., sbm...@go...,
sed...@li..., "sbo...@go...
Developers" <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

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-- 


David Nickerson
about.me/david.nickerson

Re: [SED-ML-discuss] COMBINE 2015

[Sharon C. <Sha...@as...>]

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...]
Sent: Monday, August 10, 2015 11:34 AM
To: 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...]
Sent: Saturday, July 25, 2015 9:25 AM
To: 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

Re: [SED-ML-discuss] COMBINE 2015

[Sharon C. <Sha...@as...>]

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...]
Sent: Saturday, July 25, 2015 9:25 AM
To: 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

[SED-ML-discuss] Various thoughts

[Lucian S. <luc...@gm...>]

Not sure if my last email actually went through or not, what with
sourceforge's recent miseries.  At any rate, I have finally have a basic
implementation of everything in SED-ML, and I have a few observations and
questions:

* I don't think that the data generators have enough places to store
information to actually pull out particular data for some setups:  tasks
can reference multiple tasks, which can reference multiple tasks, which can
each reference a model--perhaps the exact same model for each.  I'll try to
mock up an example of this to illustrate it, but basically, just using
'taskReference' and 'modelReference' (even if used together) is not enough
to uniquely identify all the potential variables.  I'm not sure how to fix
this; this seems like a fundamental issue with how SED-ML files are put
together.

* I still don't know what purpose functional ranges serve.  Frank claimed
they could be used to 'run a repeated task until some condition is met in
the model', but there are no examples that I could find of this, nor can I
see how this could work.

* The 'dataSet' element has way too many identifiers.  All it really needs
is the 'dataReference' attribute, which is a string, and could therefore be
used as a 'label' by anything that needed it.  The 'label' attribute is
already redundant with the optional 'name' attribute, anyway.  And then
there's its required 'id' attribute.  Why is it required?  Literally
nothing in SED-ML can reference it, as far as I can tell--does it serve
some other purpose I haven't seen?

In addition, the 'label' attribute is inconsistent with the plots, none of
which have a label, and which presumably use the NDataReference attributes
if they needed one (or perhaps the 'name' attributes of the referenced data
generators).  I would drop the 'label' attribute entirely, or at least make
it optional, and also make the 'id' attribute optional.

* It doesn't seem to be possible to reference multiple ranges in a single
computation in a repeated task.  I think it would make things much simpler
if the ranges simply behaved the same as variables and parameters, namely,
that their IDs were always defined locally for the MathML of repeated
tasks, letting you drop the 'range' attribute for the 'setValue' element.

-Lucian

[SED-ML-discuss] COMBINE 2015

[Chris J. M. <my...@ec...>]

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 <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

Re: [SED-ML-discuss] Question about tasks

[Lucian S. <luc...@gm...>]

Tried to send this while sourceforge was down; re-sending...

I have a question about repeated tasks that repeat multiple tasks.
Say I have this:

   <listOfTasks>
     <task id="task1" modelReference="mod1" simulationReference="sim1"/>
     <task id="task2" modelReference="mod1" simulationReference="sim2"/>
     <repeatedTask id="task3" range="vector_for_S1">
       <listOfRanges>
         <vectorRange id="vector_for_S1">
           <value> 0 </value>
           <value> 1 </value>
           <value> 5 </value>
         </vectorRange>
       </listOfRanges>
       <listOfChanges>
         <setValue range="vector_for_S1" modelReference="mod1"
target="/sbml:sbml/sbml:model/descendant::*[@id='S1']">
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <ci> vector_for_S1 </ci>
           </math>
         </setValue>
       </listOfChanges>
       <listOfSubTasks>
         <subTask order="0" task="task1"/>
         <subTask order="1" task="task2"/>
       </listOfSubTasks>
     </repeatedTask>
   </listOfTasks>

 Note that the 'setValue' element only says that we are to set S1 in
model mod1, but doesn't have a taskReference.  Since both task1 and
task2 use the same model, I can think of two options here.  One, the
above construct is illegal, since it is underdefined.  Two, the above
construct is legal, and the change is made to mod1 for *both* task1
and task2.  I suppose another possibility is that the change applies
to the first task in the list that has the given model, but that seems
relatively fraught, and would rather that not be the case ;-)

 The spec merely says, "A variable element must contain a
taskReference if it occurs inside a listOfVariables inside a
dataGenerator element. A variable element must contain a
modelReference if it occurs inside a listOfVariables inside a
computeChange element. A variable element appearing within a
functionalRange or setValue element must contain a modelReference if
and only if it references a model variable."

 This would seem to indicate that a 'setValue' element should *never*
use a 'taskReference' attribute, which also seems wrong, since
otherwise, how could you ever compute a change for a value in a model
for one task, but not change that value for the same model in the
other task?

 Any opinions or experience?

 -Lucian

[SED-ML-discuss] Multiple ranges in a single computation?

[Lucian S. <luc...@gm...>]

Since there's only one 'range' attribute, it looks to me like you can only
refer to a single range in any given computation.  Is that the case, or is
there some other workaround that could be done?

-Lucian

Re: [SED-ML-discuss] Functional ranges

[Lucian S. <luc...@gm...>]

I don't suppose anyone's tried to create a repeated task that runs until a
condition in the model is met?  Is there an example?  It still seems to me
that the necessary mechanics are missing.

-Lucian

On Thu, Jun 18, 2015 at 12:20 PM, Lucian Smith <luc...@gm...>
wrote:

> On Thu, Jun 18, 2015 at 12:05 PM, Frank Bergmann <fbe...@ca...>
> wrote:
>
>> One example would be running a repeated task until some condition is met
>> in your model. For that you will not be able to produce a vectorRange or
>> uniformRange beforehand, as you don’t know how many steps it would take.
>
>
> Aha!  OK, that would indeed be helpful.  However, I can't figure out how
> you would do that, since the math of a functionalRange returns a scalar.
> How can it adjust its size?  How could a program tell it was adjusting its
> size?  Is there an example somewhere?
>
> -Lucian
>

Re: [SED-ML-discuss] including experimental data points in a SED-ML archive

[Nicolas Le N. <n.l...@gm...>]

Dear Johann,

The advised format to encode simulation results is the Numerical Markup Language:

https://github.com/numl/numl

This can be used for storing results or data used for parameter estimations.

Note that the SED-ML archive has been superseded by the COMBINE archive:

http://co.mbine.org/standards/omex
http://www.biomedcentral.com/1471-2105/15/369

Best regards

On 24/06/15 15:45, Johann Eicher wrote:
> Hi all,
>
> I am one of the developers of the online model simulator JWS Online
> (jjj.bio.vu.nl). We have incorporated a feature which allows users to
> upload and download SED-ML archives of time-course plots. We would like
> to include experimental data points in the archive for inclusion in the
> plots. Is this possible? If so, could you suggest how?
>
> For an example of a typical time simulation using JWS Online, you can
> follow this link, and click on the 'Time evolution' tab:
>
> http://jjj.bio.vu.nl/models/teusink/simulate/
>
> The SED-ML button in the top-righthand corner will generate a SED-ML
> archive of the plot.
>
> Thanks for your help!
>


-- 
Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
Tel: +441223496433, Mob:+447833147074, twitter:@lenovere, Skype:n.lenovere
n.l...@gm..., http://orcid.org/0000-0002-6309-7327
http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/

[SED-ML-discuss] including experimental data points in a SED-ML archive

[Johann E. <joh...@gm...>]

Hi all,

I am one of the developers of the online model simulator JWS Online
(jjj.bio.vu.nl). We have incorporated a feature which allows users to
upload and download SED-ML archives of time-course plots. We would like
to include experimental data points in the archive for inclusion in the
plots. Is this possible? If so, could you suggest how?

For an example of a typical time simulation using JWS Online, you can
follow this link, and click on the 'Time evolution' tab:

http://jjj.bio.vu.nl/models/teusink/simulate/

The SED-ML button in the top-righthand corner will generate a SED-ML
archive of the plot.

Thanks for your help!

-- 
Johann Eicher
Postdoctoral Research Fellow
Triple-J Group for Molecular Cell Physiology
Stellenbosch University

Re: [SED-ML-discuss] Another setValue question

[Frank B. <fbe...@ca...>]

> That'd be great, but that's not what the spec says at the moment--sounds like it needs to be updated.  SetValue inherits from ComputeChange, and 'target' for ComputeChange is required.  SetValue could perhaps change that rule, but does not explicitly do so at the moment in the spec.  Not that there are any validation rules, of course.
> 

the spec tries to say just that in paragraph 3 of 2.4.6.4 … it just cannot be captured in the Schema 

Frank

> -Lucian
> 
> On Sat, Jun 20, 2015 at 12:43 AM, Frank Bergmann <fbe...@ca...> wrote:
> >
> > symbol refers currently just about to time only for SBML, as there is no xpath expression that could be written there. we talked about other symbols, referring to other implicit qualities of the model, but that never made it into the spec. So yes, that is there to facilitate the use case of changing time …
> >
> > So, what do you do about the required 'target' attribute?
> >
> 
> As far as i recall, you have to have one of them … either symbol … or target …
> 
> Frank
> 
> > -Lucian
> > ------------------------------------------------------------------------------
> > _______________________________________________
> > 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

Re: [SED-ML-discuss] Another setValue question

[Lucian S. <luc...@gm...>]

That'd be great, but that's not what the spec says at the moment--sounds
like it needs to be updated.  SetValue inherits from ComputeChange, and
'target' for ComputeChange is required.  SetValue could perhaps change that
rule, but does not explicitly do so at the moment in the spec.  Not that
there are any validation rules, of course.

This also means that 'setValue' can change the value of time, but
computeChange cannot.

-Lucian

On Sat, Jun 20, 2015 at 12:43 AM, Frank Bergmann <fbe...@ca...>
wrote:

> >
> > symbol refers currently just about to time only for SBML, as there is no
> xpath expression that could be written there. we talked about other
> symbols, referring to other implicit qualities of the model, but that never
> made it into the spec. So yes, that is there to facilitate the use case of
> changing time …
> >
> > So, what do you do about the required 'target' attribute?
> >
>
> As far as i recall, you have to have one of them … either symbol … or
> target …
>
> Frank
>
> > -Lucian
> >
> ------------------------------------------------------------------------------
> > _______________________________________________
> > 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
>

Re: [SED-ML-discuss] Another setValue question

[Frank B. <fbe...@ca...>]

> 
> symbol refers currently just about to time only for SBML, as there is no xpath expression that could be written there. we talked about other symbols, referring to other implicit qualities of the model, but that never made it into the spec. So yes, that is there to facilitate the use case of changing time …
> 
> So, what do you do about the required 'target' attribute?
> 

As far as i recall, you have to have one of them … either symbol … or target … 

Frank

> -Lucian
> ------------------------------------------------------------------------------
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Another setValue question

[Lucian S. <luc...@gm...>]

On Thu, Jun 18, 2015 at 10:48 PM, Frank Bergmann <fbe...@ca...>
wrote:

>
> > On Jun 18, 2015, at 11:54 PM, Lucian Smith <luc...@gm...>
> wrote:
> >
> > The 'setValue' class inherits from 'computeChange'.  'computeChange' has
> a required 'target' attribute; to which it adds a required 'modelReference'
> and optional 'range' and 'symbol'.
> >
> > I'm not sure what 'symbol' is supposed to do.  The docs only say:
> >
> > "The value to be changed is identified via the combination of the
> attributes modelReference and either symbol or target, in order to select
> an implicit or explicit variable within the referenced model."
> >
> > Which implies that 'symbol' means an 'implicit' variable within the
> referenced model, but I have no idea what an implicit variable within the
> referenced model might be.
> >
>
> symbol refers currently just about to time only for SBML, as there is no
> xpath expression that could be written there. we talked about other
> symbols, referring to other implicit qualities of the model, but that never
> made it into the spec. So yes, that is there to facilitate the use case of
> changing time …
>

So, what do you do about the required 'target' attribute?

-Lucian

Re: [SED-ML-discuss] Another setValue question

[Frank B. <fbe...@ca...>]

> On Jun 18, 2015, at 11:54 PM, Lucian Smith <luc...@gm...> wrote:
> 
> The 'setValue' class inherits from 'computeChange'.  'computeChange' has a required 'target' attribute; to which it adds a required 'modelReference' and optional 'range' and 'symbol'.
> 
> I'm not sure what 'symbol' is supposed to do.  The docs only say:
> 
> "The value to be changed is identified via the combination of the attributes modelReference and either symbol or target, in order to select an implicit or explicit variable within the referenced model."
> 
> Which implies that 'symbol' means an 'implicit' variable within the referenced model, but I have no idea what an implicit variable within the referenced model might be.
> 

symbol refers currently just about to time only for SBML, as there is no xpath expression that could be written there. we talked about other symbols, referring to other implicit qualities of the model, but that never made it into the spec. So yes, that is there to facilitate the use case of changing time …

Frank

> However, the 'target' attribute is still required, right?  But it's ignored if there's a 'symbol' attribute?  None of the examples ever use 'symbol' in any context for a 'setValue' attribute--the only time it's ever used in an example is in the Variable class to set time.  Is it used to set a local Variable element to a new value?  Can it be used to set 'time' to a new value?  Is that even legal?
> 
> -Lucian
> ------------------------------------------------------------------------------
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] Another setValue question

[Lucian S. <luc...@gm...>]

The 'setValue' class inherits from 'computeChange'.  'computeChange' has a
required 'target' attribute; to which it adds a required 'modelReference'
and optional 'range' and 'symbol'.

I'm not sure what 'symbol' is supposed to do.  The docs only say:

"The value to be changed is identified via the combination of the
attributes modelReference and either symbol or target, in order to select
an implicit or explicit variable within the referenced model."

Which implies that 'symbol' means an 'implicit' variable within the
referenced model, but I have no idea what an implicit variable within the
referenced model might be.

However, the 'target' attribute is still required, right?  But it's ignored
if there's a 'symbol' attribute?  None of the examples ever use 'symbol' in
any context for a 'setValue' attribute--the only time it's ever used in an
example is in the Variable class to set time.  Is it used to set a local
Variable element to a new value?  Can it be used to set 'time' to a new
value?  Is that even legal?

-Lucian

Re: [SED-ML-discuss] Functional ranges

[Lucian S. <luc...@gm...>]

On Thu, Jun 18, 2015 at 12:05 PM, Frank Bergmann <fbe...@ca...>
wrote:

> One example would be running a repeated task until some condition is met
> in your model. For that you will not be able to produce a vectorRange or
> uniformRange beforehand, as you don’t know how many steps it would take.


Aha!  OK, that would indeed be helpful.  However, I can't figure out how
you would do that, since the math of a functionalRange returns a scalar.
How can it adjust its size?  How could a program tell it was adjusting its
size?  Is there an example somewhere?

-Lucian