sbml-spatial Mailing List for Systems Biology Markup Language (SBML)

For SME, you’d just go to:

https://github.com/spatial-model-editor/spatial-model-editor

and open one of the example models (File\open example models), they are all encoded in SBML L3 spatial. You can also just do file\open any other SBML L3 spatial model.

Caveats: SME is meant for 2d models, with the given feature sets we support.

Cheers
Frank

From: Lucian Smith <luc...@gm...>
Sent: Monday, July 25, 2022 7:28 PM
To: The SBML L3 Spatial Processes and Geometries package discussion list <sbm...@li...>; Jim Schaff <sc...@uc...>; Moraru, Ion <mo...@uc...>; Matthias König <kon...@go...>; Bartholomew Jardine <ba...@uw...>; Prof. Dr. Akira Funahashi <fu...@bi...>
Subject: [sbml-spatial] How to get spatial models to load?

Matthias's main question for the sbml-spatial community is:  how does one run a spatial simulator and load a spatial model?

There's a repository of models at:

https://github.com/sbmlteam/sbml-spatial-models

Can everyone with a simulator reply and explain how to run your simulator and load a spatial model; perhaps one from the repository?

-Lucian

Matthias's main question for the sbml-spatial community is:  how does one
run a spatial simulator and load a spatial model?

There's a repository of models at:

https://github.com/sbmlteam/sbml-spatial-models

Can everyone with a simulator reply and explain how to run your simulator
and load a spatial model; perhaps one from the repository?

-Lucian

>

Hey, everyone!  Matthias (as an SBML editor) has provided a lot of feedback
from his read through the spatial spec, available here:

https://docs.google.com/document/d/1ys_meGuiPZcSpe250XH5AnnsOcul_IPMryVpmXgtiQg/edit#

I've translated the issues that deal with the spec to github issues:

https://github.com/sbmlteam/sbml-specifications/labels/L3%20Package%3A%20spatial

and welcome everyone's comments there (or you can just reply here and I'll
copy them over).

I'll make a separate thread for the 'how do I get the simulators to run?'
question.

-Lucian

Thanks for the replies!  I've copied everyone's responses to

https://github.com/sbmlteam/sbml-specifications/issues/385

As far as I can tell, VCell supports spatial but not Robin conditions, and
JSim supports Robin conditions but not spatial.

In that case, I think it's probably best to drop the Robin conditions from
the spec for now, and add them in in the future if/when they get more
support from SBML-spatial-aware simulators.

Feel free to comment either here or on github.

-Lucian

On Sat, Jul 23, 2022 at 10:55 AM Schaff,Jim <sc...@uc...> wrote:

> Hi All,
>
>
> VCell does not support robin boundary conditions in our standard
> production solvers, we did use them a bit in one of our prototype moving
> boundary codes (there we referred to them as "mixed" boundary condition
> type).
>
>
> VCell does have support for
>
>    - ​Dirichlet (only at coordinate min/max boundaries​)
>    - Neumann (scalar flux normal to surface - at min/max boundaries and
>    internal surfaces)
>    - Periodic (only at coordinate min/max boundaries)​
>
> VCell does not have plans to offer Robin/Mixed boundary conditions in the
> near future.
>
>
> Best regards,
>
> Jim.
>
>
>
> ------------------------------
> *From:* Bartholomew Jardine <ba...@uw...>
> *Sent:* Friday, July 22, 2022 6:45 PM
> *To:* The SBML L3 Spatial Processes and Geometries package discussion list
> *Cc:* Schaff,Jim; Moraru,Ion
> *Subject:* Re: [sbml-spatial] Anyone implement support for the 'Robin'
> boundary conditions?
>
> *** Attention: This is an external email. Use caution responding, opening
> attachments or clicking on links. ***
> We, JSim users, used this when dealing 1D flow through a capillary. It
> specifies the boundary condition for the left hand side (input).
> A simple ex below:
>
> when(x=x.min) {(-F*L/V)*(C-Cin)+D*C:x = 0;}    //  Robin Inflow boundary condition
>
>  C:x means partial derivative with respect to x (partial dC/dx)
>
> Excerpt taken from this simple model:
>
> realDomain t sec; t.min=0; t.max=10.0; t.delta=0.01;  //Time domain
>
> real L = 0.1 cm;                                     //Spatial domain
> real Ngrid=31; // steps for spatial integrator
> realDomain x cm; x.min=0.0; x.max=L; x.ct=Ngrid;
>
> real C(x,t) mM;           // Concentration variable
> extern real Cin(t) mM;    // Inflowing Concentration from Function Generator
> real Cout(t) mM;          // Outflowing Concentration
> extern real C0(x) mM;     // Initial distribution of Material
> real D= 0.00001 cm^2/sec; // Diffusion coefficient
> real F=1 ml/(g*min);      // Flow (milliliters/(gram of  tissue)/minute)
> real V=0.05 ml/g;          // Volume (milliters/(gram of tissue))
>
> when(t=t.min) {C= if(x=x.min) Cin else C0;} // Initial distribution assigned to Concentration
>                                             // variable
> when(x=x.min) {(-F*L/V)*(C-Cin)+D*C:x = 0;}    //  Inflow boundary condition  <--- Robin condition
> when(x=x.max) {C:x=0; Cout=C;}
>
> C:t=-F*L/V*C:x + D*C:x:x ;             // Partial differential equation describing system
>
>
>
> -Bart Jardine
>
> Research Engineer, 206-685-2006
> Dept. of Bioengineering, University of Washington
>
>
> On Fri, Jul 22, 2022 at 3:24 PM Lucian Smith <luc...@gm...>
> wrote:
>
>> Hi, everyone!  One bit of feedback from the SBML editors was that the
>> Robin boundary condition seemed a bit obscure, and wanted to make sure it
>> had some support.  IIRC, it was added at least partially at the behest of
>> the JSim team, but JSim is no longer under active development (since the
>> passing of Dr. Bassingthwaighte) and never got sbml-spatial support in the
>> first place.  Did VCell or anyone else implement support for it, or has it
>> been orphaned at this point?
>>
>> -Lucian Smith
>> _______________________________________________
>> sbml-spatial mailing list
>> sbm...@li...
>> https://lists.sourceforge.net/lists/listinfo/sbml-spatial
>> <https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/sbml-spatial__;!!Cn_UX_p3!nqNOei-ZNKYJZPK89_k2vFKOWIjfsnd2V9nvWSxYAQ7XDDpIILOCtVzQ6n-efzGmWxl5bzFx620CXQ$>
>>
> _______________________________________________
> sbml-spatial mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-spatial
>

Hi All,


VCell does not support robin boundary conditions in our standard production solvers, we did use them a bit in one of our prototype moving boundary codes (there we referred to them as "mixed" boundary condition type).


VCell does have support for

  *   ?Dirichlet (only at coordinate min/max boundaries?)
  *   Neumann (scalar flux normal to surface - at min/max boundaries and internal surfaces)
  *   Periodic (only at coordinate min/max boundaries)?

VCell does not have plans to offer Robin/Mixed boundary conditions in the near future.


Best regards,

Jim.



________________________________
From: Bartholomew Jardine <ba...@uw...>
Sent: Friday, July 22, 2022 6:45 PM
To: The SBML L3 Spatial Processes and Geometries package discussion list
Cc: Schaff,Jim; Moraru,Ion
Subject: Re: [sbml-spatial] Anyone implement support for the 'Robin' boundary conditions?

*** Attention: This is an external email. Use caution responding, opening attachments or clicking on links. ***
We, JSim users, used this when dealing 1D flow through a capillary. It specifies the boundary condition for the left hand side (input).
A simple ex below:


when(x=x.min) {(-F*L/V)*(C-Cin)+D*C:x = 0;}    //  Robin Inflow boundary condition

 C:x means partial derivative with respect to x (partial dC/dx)

Excerpt taken from this simple model:



realDomain t sec; t.min=0; t.max=10.0; t.delta=0.01;  //Time domain

real L = 0.1 cm;                                     //Spatial domain
real Ngrid=31; // steps for spatial integrator
realDomain x cm; x.min=0.0; x.max=L; x.ct=Ngrid;

real C(x,t) mM;           // Concentration variable
extern real Cin(t) mM;    // Inflowing Concentration from Function Generator
real Cout(t) mM;          // Outflowing Concentration
extern real C0(x) mM;     // Initial distribution of Material
real D= 0.00001 cm^2/sec; // Diffusion coefficient
real F=1 ml/(g*min);      // Flow (milliliters/(gram of  tissue)/minute)
real V=0.05 ml/g;          // Volume (milliters/(gram of tissue))

when(t=t.min) {C= if(x=x.min) Cin else C0;} // Initial distribution assigned to Concentration
                                            // variable
when(x=x.min) {(-F*L/V)*(C-Cin)+D*C:x = 0;}    //  Inflow boundary condition  <--- Robin condition
when(x=x.max) {C:x=0; Cout=C;}

C:t=-F*L/V*C:x + D*C:x:x ;             // Partial differential equation describing system


-Bart Jardine

Research Engineer, 206-685-2006<tel:206-685-2006>
Dept. of Bioengineering, University of Washington


On Fri, Jul 22, 2022 at 3:24 PM Lucian Smith <luc...@gm...<mailto:luc...@gm...>> wrote:
Hi, everyone!  One bit of feedback from the SBML editors was that the Robin boundary condition seemed a bit obscure, and wanted to make sure it had some support.  IIRC, it was added at least partially at the behest of the JSim team, but JSim is no longer under active development (since the passing of Dr. Bassingthwaighte) and never got sbml-spatial support in the first place.  Did VCell or anyone else implement support for it, or has it been orphaned at this point?

-Lucian Smith
_______________________________________________
sbml-spatial mailing list
sbm...@li...<mailto:sbm...@li...>
https://lists.sourceforge.net/lists/listinfo/sbml-spatial<https://urldefense.com/v3/__https://lists.sourceforge.net/lists/listinfo/sbml-spatial__;!!Cn_UX_p3!nqNOei-ZNKYJZPK89_k2vFKOWIjfsnd2V9nvWSxYAQ7XDDpIILOCtVzQ6n-efzGmWxl5bzFx620CXQ$>

We, JSim users, used this when dealing 1D flow through a capillary. It
specifies the boundary condition for the left hand side (input).
A simple ex below:

when(x=x.min) {(-F*L/V)*(C-Cin)+D*C:x = 0;}    //  Robin Inflow
boundary condition

 C:x means partial derivative with respect to x (partial dC/dx)

Excerpt taken from this simple model:

realDomain t sec; t.min=0; t.max=10.0; t.delta=0.01;  //Time domain

real L = 0.1 cm;                                     //Spatial domain
real Ngrid=31; // steps for spatial integrator
realDomain x cm; x.min=0.0; x.max=L; x.ct=Ngrid;

real C(x,t) mM;           // Concentration variable
extern real Cin(t) mM;    // Inflowing Concentration from Function Generator
real Cout(t) mM;          // Outflowing Concentration
extern real C0(x) mM;     // Initial distribution of Material
real D= 0.00001 cm^2/sec; // Diffusion coefficient
real F=1 ml/(g*min);      // Flow (milliliters/(gram of  tissue)/minute)
real V=0.05 ml/g;          // Volume (milliters/(gram of tissue))

when(t=t.min) {C= if(x=x.min) Cin else C0;} // Initial distribution
assigned to Concentration
                                            // variable
when(x=x.min) {(-F*L/V)*(C-Cin)+D*C:x = 0;}    //  Inflow boundary
condition  <--- Robin condition
when(x=x.max) {C:x=0; Cout=C;}

C:t=-F*L/V*C:x + D*C:x:x ;             // Partial differential
equation describing system



-Bart Jardine

Research Engineer, 206-685-2006
Dept. of Bioengineering, University of Washington


On Fri, Jul 22, 2022 at 3:24 PM Lucian Smith <luc...@gm...>
wrote:

> Hi, everyone!  One bit of feedback from the SBML editors was that the
> Robin boundary condition seemed a bit obscure, and wanted to make sure it
> had some support.  IIRC, it was added at least partially at the behest of
> the JSim team, but JSim is no longer under active development (since the
> passing of Dr. Bassingthwaighte) and never got sbml-spatial support in the
> first place.  Did VCell or anyone else implement support for it, or has it
> been orphaned at this point?
>
> -Lucian Smith
> _______________________________________________
> sbml-spatial mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-spatial
>

Hi, everyone!  One bit of feedback from the SBML editors was that the Robin
boundary condition seemed a bit obscure, and wanted to make sure it had
some support.  IIRC, it was added at least partially at the behest of the
JSim team, but JSim is no longer under active development (since the
passing of Dr. Bassingthwaighte) and never got sbml-spatial support in the
first place.  Did VCell or anyone else implement support for it, or has it
been orphaned at this point?

-Lucian Smith

Version 0.98 of the spatial specification is now available at

https://github.com/sbmlteam/sbml-specifications/blob/develop/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.98.pdf

It addresses a handful of issues spotted by Jim Schaff (welcome back, Jim!)

I've filed all the issue he raised as github issues, which you can see at:

https://github.com/sbmlteam/sbml-specifications/labels/L3%20Package%3A%20spatial

but to summarize:
* Some elements could have lower dimensionality than mentioned in the text.
* VCell actually does use 'difference', so that's back in.
* Clarifications added for initial conditions and 'boundary conditions'.

That's all the we-should-change-this-bit feedback we've gotten since asking
the SBML editors to look at it (and it was subsequently posted to
sbml-discuss), so I'm going to assume for now that this will be the version
we'll publish in JIB.  But if anyone has any other comments/suggestions,
now's the time to speak up!  It would be particularly satisfying to have
the last draft version be version 0.99 ;-)

-Lucian Smith