sbml-spatial — The SBML L3 Spatial Processes package discussion list

Re: [sbml-spatial] Draft abstract for JIB

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

Great!

Another issue:  here's my list of everyone's ORCIDs:

Schaff, James:  https://orcid.org/0000-0003-3286-7736
Lakshminarayanam, Anu: https://orcid.org/0000-0001-9383-4212
Murphy, Robert: https://orcid.org/0000-0003-0358-901X
Bergmann, Frank:  https://orcid.org/0000-0001-5553-4702
Funahashi, Akira:  https://orcid.org/0000-0003-0605-239X
Sullivan, Devin:  https://orcid.org/0000-0001-6176-108X

Most of them are self-evidently you all, but Jim and Anu's pages are both
blank (at least to the public).  Can you two confirm that those links are
actually you?

-Lucian


On Wed, Oct 26, 2022 at 6:53 AM Robert Murphy <mu...@an...> wrote:

> Adding Devin at his gmail address
> =======================
> Robert F. Murphy, Ph.D.
> Ray and Stephanie Lane Professor of Computational Biology Emeritus
> School of Computer Science
> Carnegie Mellon University
> email: mu...@cm... <mu...@cm...>
> AIMBE Fellow, IEEE Fellow
>
>
> On Oct 26, 2022, at 9:42 AM, Robert Murphy <mu...@an...> wrote:
>
> I agree.  Looks good.
>
> Best,
>
> Bob
> =======================
> Robert F. Murphy, Ph.D.
> Ray and Stephanie Lane Professor of Computational Biology Emeritus
> School of Computer Science
> Carnegie Mellon University
> email: mu...@cm... <mu...@cm...>
> AIMBE Fellow, IEEE Fellow
>
>
> On Oct 26, 2022, at 5:26 AM, Bergmann, Dr. Frank <
> fra...@bi...> wrote:
>
> Hello Lucian,
>
> I think that is all that is needed, and works for me.
>
> Thank you
> Frank
>
> *From:* Lucian Smith <luc...@gm...>
> *Sent:* Tuesday, October 25, 2022 10:06 PM
> *To:* The SBML L3 Spatial Processes and Geometries package discussion
> list <sbm...@li...>; Bergmann, Dr. Frank <
> fra...@bi...>; Jim Schaff <sc...@uc...>;
> Anuradha Iyer <al...@gm...>; de...@kt...; Robert Murphy <
> mu...@an...>
> *Subject:* Draft abstract for JIB
>
> With the SBML Spatial spec finalized (yay!) we can publish it in the
> forthcoming special edition of JIB.  Here's a draft abstract for it (in
> LaTeX):  any suggestions?
>
> "While many biological processes can be modeled by abstracting away the
> space in which those processes occur, some modeling (particularly at the
> cellular level) requires space itself to be modeled, with processes
> happening not in well-mixed compartments, but spatially-defined
> compartments.  The \emph{SBML Level~3 Core} specification does not include
> an explicit mechanism to encode geometries and spatial processes in a
> model, but it does provide a mechanism for SBML \emph{packages} to extend
> the Core specification and add additional syntactic constructs. The SBML
> \emph{Spatial Processes} package for SBML Level~3 adds the necessary
> features to allow models to encode geometries and other spatial information
> about the elements and processes it describes."
>
>
>
>

Re: [sbml-spatial] Draft abstract for JIB

[Robert M. <mu...@an...>]

I agree.  Looks good.

Best,

Bob
=======================
Robert F. Murphy, Ph.D.
Ray and Stephanie Lane Professor of Computational Biology Emeritus
School of Computer Science
Carnegie Mellon University
email: mu...@cm...
AIMBE Fellow, IEEE Fellow


> On Oct 26, 2022, at 5:26 AM, Bergmann, Dr. Frank <fra...@bi...> wrote:
> 
> Hello Lucian, 
>  
> I think that is all that is needed, and works for me. 
>  
> Thank you
> Frank
>  
> From: Lucian Smith <luc...@gm...> 
> Sent: Tuesday, October 25, 2022 10:06 PM
> To: The SBML L3 Spatial Processes and Geometries package discussion list <sbm...@li...>; Bergmann, Dr. Frank <fra...@bi...>; Jim Schaff <sc...@uc...>; Anuradha Iyer <al...@gm...>; de...@kt...; Robert Murphy <mu...@an...>
> Subject: Draft abstract for JIB
>  
> With the SBML Spatial spec finalized (yay!) we can publish it in the forthcoming special edition of JIB.  Here's a draft abstract for it (in LaTeX):  any suggestions?
>  
> "While many biological processes can be modeled by abstracting away the space in which those processes occur, some modeling (particularly at the cellular level) requires space itself to be modeled, with processes happening not in well-mixed compartments, but spatially-defined compartments.  The \emph{SBML Level~3 Core} specification does not include an explicit mechanism to encode geometries and spatial processes in a model, but it does provide a mechanism for SBML \emph{packages} to extend the Core specification and add additional syntactic constructs. The SBML \emph{Spatial Processes} package for SBML Level~3 adds the necessary features to allow models to encode geometries and other spatial information about the elements and processes it describes."

Re: [sbml-spatial] Draft abstract for JIB

[Anuradha I. <al...@gm...>]

The abstract looks good. Thanks for taking care of this, Lucian!

On Wed, Oct 26, 2022 at 9:53 AM Robert Murphy <mu...@an...> wrote:

> Adding Devin at his gmail address
> =======================
> Robert F. Murphy, Ph.D.
> Ray and Stephanie Lane Professor of Computational Biology Emeritus
> School of Computer Science
> Carnegie Mellon University
> email: mu...@cm... <mu...@cm...>
> AIMBE Fellow, IEEE Fellow
>
>
> On Oct 26, 2022, at 9:42 AM, Robert Murphy <mu...@an...> wrote:
>
> I agree.  Looks good.
>
> Best,
>
> Bob
> =======================
> Robert F. Murphy, Ph.D.
> Ray and Stephanie Lane Professor of Computational Biology Emeritus
> School of Computer Science
> Carnegie Mellon University
> email: mu...@cm... <mu...@cm...>
> AIMBE Fellow, IEEE Fellow
>
>
> On Oct 26, 2022, at 5:26 AM, Bergmann, Dr. Frank <
> fra...@bi...> wrote:
>
> Hello Lucian,
>
> I think that is all that is needed, and works for me.
>
> Thank you
> Frank
>
> *From:* Lucian Smith <luc...@gm...>
> *Sent:* Tuesday, October 25, 2022 10:06 PM
> *To:* The SBML L3 Spatial Processes and Geometries package discussion
> list <sbm...@li...>; Bergmann, Dr. Frank <
> fra...@bi...>; Jim Schaff <sc...@uc...>;
> Anuradha Iyer <al...@gm...>; de...@kt...; Robert Murphy <
> mu...@an...>
> *Subject:* Draft abstract for JIB
>
> With the SBML Spatial spec finalized (yay!) we can publish it in the
> forthcoming special edition of JIB.  Here's a draft abstract for it (in
> LaTeX):  any suggestions?
>
> "While many biological processes can be modeled by abstracting away the
> space in which those processes occur, some modeling (particularly at the
> cellular level) requires space itself to be modeled, with processes
> happening not in well-mixed compartments, but spatially-defined
> compartments.  The \emph{SBML Level~3 Core} specification does not include
> an explicit mechanism to encode geometries and spatial processes in a
> model, but it does provide a mechanism for SBML \emph{packages} to extend
> the Core specification and add additional syntactic constructs. The SBML
> \emph{Spatial Processes} package for SBML Level~3 adds the necessary
> features to allow models to encode geometries and other spatial information
> about the elements and processes it describes."
>
>
>
>

Re: [sbml-spatial] Draft abstract for JIB

[Robert M. <mu...@an...>]

Adding Devin at his gmail address
=======================
Robert F. Murphy, Ph.D.
Ray and Stephanie Lane Professor of Computational Biology Emeritus
School of Computer Science
Carnegie Mellon University
email: mu...@cm...
AIMBE Fellow, IEEE Fellow


> On Oct 26, 2022, at 9:42 AM, Robert Murphy <mu...@an...> wrote:
> 
> I agree.  Looks good.
> 
> Best,
> 
> Bob
> =======================
> Robert F. Murphy, Ph.D.
> Ray and Stephanie Lane Professor of Computational Biology Emeritus
> School of Computer Science
> Carnegie Mellon University
> email: mu...@cm... <mailto:mu...@cm...>
> AIMBE Fellow, IEEE Fellow
> 
> 
>> On Oct 26, 2022, at 5:26 AM, Bergmann, Dr. Frank <fra...@bi... <mailto:fra...@bi...>> wrote:
>> 
>> Hello Lucian, 
>>  
>> I think that is all that is needed, and works for me. 
>>  
>> Thank you
>> Frank
>>  
>> From: Lucian Smith <luc...@gm... <mailto:luc...@gm...>> 
>> Sent: Tuesday, October 25, 2022 10:06 PM
>> To: The SBML L3 Spatial Processes and Geometries package discussion list <sbm...@li... <mailto:sbm...@li...>>; Bergmann, Dr. Frank <fra...@bi... <mailto:fra...@bi...>>; Jim Schaff <sc...@uc... <mailto:sc...@uc...>>; Anuradha Iyer <al...@gm... <mailto:al...@gm...>>; de...@kt... <mailto:de...@kt...>; Robert Murphy <mu...@an... <mailto:mu...@an...>>
>> Subject: Draft abstract for JIB
>>  
>> With the SBML Spatial spec finalized (yay!) we can publish it in the forthcoming special edition of JIB.  Here's a draft abstract for it (in LaTeX):  any suggestions?
>>  
>> "While many biological processes can be modeled by abstracting away the space in which those processes occur, some modeling (particularly at the cellular level) requires space itself to be modeled, with processes happening not in well-mixed compartments, but spatially-defined compartments.  The \emph{SBML Level~3 Core} specification does not include an explicit mechanism to encode geometries and spatial processes in a model, but it does provide a mechanism for SBML \emph{packages} to extend the Core specification and add additional syntactic constructs. The SBML \emph{Spatial Processes} package for SBML Level~3 adds the necessary features to allow models to encode geometries and other spatial information about the elements and processes it describes."
> 

Re: [sbml-spatial] Draft abstract for JIB

[Akira F. <fu...@bi...>]

Hi Lucian,

Thank you so much for preparing the manuscript.
The abstract is perfectly fine.

Best,
-- 
Akira

Re: [sbml-spatial] Draft abstract for JIB

[Bergmann, D. F. <fra...@bi...>]

Hello Lucian,

I think that is all that is needed, and works for me.

Thank you
Frank

From: Lucian Smith <luc...@gm...>
Sent: Tuesday, October 25, 2022 10:06 PM
To: The SBML L3 Spatial Processes and Geometries package discussion list <sbm...@li...>; Bergmann, Dr. Frank <fra...@bi...>; Jim Schaff <sc...@uc...>; Anuradha Iyer <al...@gm...>; de...@kt...; Robert Murphy <mu...@an...>
Subject: Draft abstract for JIB

With the SBML Spatial spec finalized (yay!) we can publish it in the forthcoming special edition of JIB.  Here's a draft abstract for it (in LaTeX):  any suggestions?

"While many biological processes can be modeled by abstracting away the space in which those processes occur, some modeling (particularly at the cellular level) requires space itself to be modeled, with processes happening not in well-mixed compartments, but spatially-defined compartments.  The \emph{SBML Level~3 Core} specification does not include an explicit mechanism to encode geometries and spatial processes in a model, but it does provide a mechanism for SBML \emph{packages} to extend the Core specification and add additional syntactic constructs. The SBML \emph{Spatial Processes} package for SBML Level~3 adds the necessary features to allow models to encode geometries and other spatial information about the elements and processes it describes."

[sbml-spatial] Draft abstract for JIB

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

With the SBML Spatial spec finalized (yay!) we can publish it in the
forthcoming special edition of JIB.  Here's a draft abstract for it (in
LaTeX):  any suggestions?

"While many biological processes can be modeled by abstracting away the
space in which those processes occur, some modeling (particularly at the
cellular level) requires space itself to be modeled, with processes
happening not in well-mixed compartments, but spatially-defined
compartments.  The \emph{SBML Level~3 Core} specification does not include
an explicit mechanism to encode geometries and spatial processes in a
model, but it does provide a mechanism for SBML \emph{packages} to extend
the Core specification and add additional syntactic constructs. The SBML
\emph{Spatial Processes} package for SBML Level~3 adds the necessary
features to allow models to encode geometries and other spatial information
about the elements and processes it describes."

Re: [sbml-spatial] What does isotropic mean in 2D?

[Bergmann, D. F. <fra...@bi...>]

You can certainly add more validation rules to make it clearer.


  *   You’d use isotropic if you wanted to have the same one in all directions (works for 1d-3d)
  *   You’d use anisotropic to define it just along one direction. If just one is defined, it would work for 1d. The typical usecase would be to define 2 for the 2 coordinate components in 2d, or 3 in 3d. (Note: by defining the same coefficient along the 2 coordinate components in 2d using anisotropic, would actually make it isotropic!)
  *   Tensor makes no sense for 1d. However, it would be the same to define one tensor for 2d, instead of 2 anisotropic ones.

Hope that helps,
Best
Frank

From: Lucian Smith <luc...@gm...>
Sent: Monday, August 8, 2022 7:19 PM
To: The SBML L3 Spatial Processes and Geometries package discussion list <sbm...@li...>
Subject: [sbml-spatial] What does isotropic mean in 2D?

One final issue remains from Matthias's read-through of the spatial spec, namely:

"p15L4ff The description in 3.10.2 applies for 3D geometries; probably not true for 2D and 1D geometries. There is probably some additional clarification required."

The section in question is:

"The required type attribute of DiffusionCoefficient is of type DiffusionKind and indicates whether the diffusion coefficient is “isotropic” (i.e. applies equally in all dimensions/directions), “anisotropic” (i.e. applies only for a single coordinate), or “tensor” (i.e. applies only for a particular pair of coordinates). Coefficients of type “isotropic” may not have any coordinateReference attributes defined, since diffusion is defined for all axes."

So:  What does it mean to say that diffusion is isotropic, anisotropic, or tensor in 2D geometries?  In 1D geometries?  Do we restrict some/all from applying in 2D or 1D entirely?

I'm happy to make up something, but I figure it's probably better if anyone with some experience here chimes in.

-Lucian

[sbml-spatial] What does isotropic mean in 2D?

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

One final issue remains from Matthias's read-through of the spatial spec,
namely:

"p15L4ff The description in 3.10.2 applies for 3D geometries; probably not
true for 2D and 1D geometries. There is probably some additional
clarification required."

The section in question is:

"The required type attribute of DiffusionCoefficient is of type
DiffusionKind and indicates whether the diffusion coefficient is
“isotropic” (i.e. applies equally in all dimensions/directions),
“anisotropic” (i.e. applies only for a single coordinate), or “tensor”
(i.e. applies only for a particular pair of coordinates). Coefficients of
type “isotropic” may not have any coordinateReference attributes defined,
since diffusion is defined for all axes."

So:  What does it mean to say that diffusion is isotropic, anisotropic, or
tensor in 2D geometries?  In 1D geometries?  Do we restrict some/all from
applying in 2D or 1D entirely?

I'm happy to make up something, but I figure it's probably better if anyone
with some experience here chimes in.

-Lucian

Re: [sbml-spatial] How to get spatial models to load?

[Matthias K. <kon...@go...>]

Hi all,
I could try/test the SME by Frank so far and this looks great.
Could the other tool developers provide some instructions how to run/test
spatial models in the respective tools?

I am trying the examples from
https://github.com/sbmlteam/sbml-spatial-models

Best Matthias

On Mon, Jul 25, 2022 at 7:28 PM Lucian Smith <luc...@gm...>
wrote:

> 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 König, PhD.
Junior Group Leader Systems Medicine of the Liver Lab
Humboldt-Universität zu Berlin,
Institute of Biology, Institute for Theoretical Biology
Philippstraße 13, Haus 20, 10115 Berlin
Tel: +49 30 2093 98435
https://livermetabolism.com
kon...@go...
https://twitter.com/konigmatt
https://github.com/matthiaskoenig

Re: [sbml-spatial] How to get spatial models to load?

[Bergmann, D. F. <fra...@bi...>]

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

[sbml-spatial] How to get spatial models to load?

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

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

>

[sbml-spatial] Matthias's comments on the SBML Spatial specification

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

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

Re: [sbml-spatial] Anyone implement support for the 'Robin' boundary conditions?

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

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
>

Re: [sbml-spatial] Anyone implement support for the 'Robin' boundary conditions?

[Schaff,Jim <sc...@uc...>]

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
_______________________________________________
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Re: [sbml-spatial] Anyone implement support for the 'Robin' boundary conditions?

[Bartholomew J. <ba...@uw...>]

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
>

[sbml-spatial] Anyone implement support for the 'Robin' boundary conditions?

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

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] New version!

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

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

Re: [sbml-spatial] Letter to the SBML Editors, author list, grant support

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

OK, replies are still trickling in about authorship and grants, but the
salient features are all there, and we can work out the authors and grants
separately for the JIB submission anyway.  I'm going ahead and sending the
letter and spec to the SBML Editors today!  Thanks everyone; this was a
long road, and everyone's contributions at various points along it were
critical.

-Lucian

On Fri, Apr 29, 2022 at 12:57 AM Bergmann, Dr. Frank <
fra...@bi...> wrote:

> That looks fine to me as is.
>
>
>
> Thank  you
>
> Frank
>
>
>
> *From:* Lucian Smith <luc...@gm...>
> *Sent:* Friday, April 29, 2022 2:11 AM
> *To:* The SBML L3 Spatial Processes and Geometries package discussion
> list <sbm...@li...>
> *Subject:* [sbml-spatial] Letter to the SBML Editors, author list, grant
> support
>
>
>
> OK!  The first draft of a letter to the SBML Editors is up at:
>
>
>
>
> https://docs.google.com/document/d/1oFK46XrgeUzgVkzqcMc7AZJtYpN6zMVSpf5BkEqmiXc/edit
>
>
>
> All comments welcome!
>
>
>
> Also, we should make sure the author list is final, and collect a list of
> grants that helped support it.  If you're not on the author list and think
> you should be, or if you know someone who you think should be there, or if
> you have Opinions about the order of the author list, please let us know!
> And if you know of a grant that helped support the creation of this spec,
> let us know that, too.
>
>
>
> Thank you all!
>
>
>
> -Lucian Smith
> _______________________________________________
> sbml-spatial mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-spatial
>

Re: [sbml-spatial] Letter to the SBML Editors, author list, grant support

[Bergmann, D. F. <fra...@bi...>]

That looks fine to me as is.

Thank  you
Frank

From: Lucian Smith <luc...@gm...>
Sent: Friday, April 29, 2022 2:11 AM
To: The SBML L3 Spatial Processes and Geometries package discussion list <sbm...@li...>
Subject: [sbml-spatial] Letter to the SBML Editors, author list, grant support

OK!  The first draft of a letter to the SBML Editors is up at:

https://docs.google.com/document/d/1oFK46XrgeUzgVkzqcMc7AZJtYpN6zMVSpf5BkEqmiXc/edit

All comments welcome!

Also, we should make sure the author list is final, and collect a list of grants that helped support it.  If you're not on the author list and think you should be, or if you know someone who you think should be there, or if you have Opinions about the order of the author list, please let us know!  And if you know of a grant that helped support the creation of this spec, let us know that, too.

Thank you all!

-Lucian Smith

Re: [sbml-spatial] Spec version 0.96!

[Michael H. <mh...@li...>]

Very exciting!

MH

On 27 Apr 2022, at 21:56, Lucian Smith wrote:

> So, I managed to actually edit the spec today!  Going over our notes 
> from
> last time
>
> https://docs.google.com/document/d/1l7gEmnFe0lPFZWBBj-98KOxW6kTjyECo0PIx8zCCEJ0/edit
>
> it looks like all we needed to do was confirm that neither 
> quadrilateral
> meshes nor relative complements were used in any of our software, and 
> to
> take them out of the spec.  So, that's now done, and I can draft a 
> letter
> to the SBML editors.  We should be able to publish in JIB this year!
>
> Any comments welcome:
>
> https://github.com/sbmlteam/sbml-specifications/blob/release/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.96.pdf
>
> I'll work on the letter to the editors tomorrow, and will welcome 
> comments
> on that.then.  Thanks everyone!
>
> -Lucian
> _______________________________________________
> sbml-spatial mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-spatial

[sbml-spatial] Letter to the SBML Editors, author list, grant support

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

OK!  The first draft of a letter to the SBML Editors is up at:

https://docs.google.com/document/d/1oFK46XrgeUzgVkzqcMc7AZJtYpN6zMVSpf5BkEqmiXc/edit

All comments welcome!

Also, we should make sure the author list is final, and collect a list of
grants that helped support it.  If you're not on the author list and think
you should be, or if you know someone who you think should be there, or if
you have Opinions about the order of the author list, please let us know!
And if you know of a grant that helped support the creation of this spec,
let us know that, too.

Thank you all!

-Lucian Smith

[sbml-spatial] Spec version 0.96!

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

So, I managed to actually edit the spec today!  Going over our notes from
last time

https://docs.google.com/document/d/1l7gEmnFe0lPFZWBBj-98KOxW6kTjyECo0PIx8zCCEJ0/edit

it looks like all we needed to do was confirm that neither quadrilateral
meshes nor relative complements were used in any of our software, and to
take them out of the spec.  So, that's now done, and I can draft a letter
to the SBML editors.  We should be able to publish in JIB this year!

Any comments welcome:

https://github.com/sbmlteam/sbml-specifications/blob/release/sbml-level-3/version-1/spatial/specification/spatial-v1-sbml-l3v1-rel0.96.pdf

I'll work on the letter to the editors tomorrow, and will welcome comments
on that.then.  Thanks everyone!

-Lucian

[sbml-spatial] Finalize spec!

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

Hey, everyone!  I'm using HARMONY to finalize the spatial spec, since I
always seem to not have time after the meetings to actually work on it.  If
anyone wants to join some live spec editing (riveting, I know), feel free
to join me:  it should be on the HARMONY schedule for tomorrow at 10-12
Eastern (7-9 Pacific).

-Lucian

Re: [sbml-spatial] Spatial Breakout at COMBINE 2021

[Frank T. B. <fra...@bi...>]

Thank you all, that was a brief and productive meeting! Below you will find the document we discussed for all to see. 

@dan: one question was whether VCell supported quadrilateral ParametericObjects, or whether those should be removed from the specification. The other feature to potentially remove was the relative complement on CSGs. We would produce a final version of the specification without those if VCell wouldn't support them at this time. 

Again, thank you so much. 

Cheers
Frank

Here the document we discussed: 
https://docs.google.com/document/d/1l7gEmnFe0lPFZWBBj-98KOxW6kTjyECo0PIx8zCCEJ0/edit

> -----Original Message-----
> From: Frank T. Bergmann <fra...@bi...>
> Sent: Friday, October 8, 2021 3:51 PM
> To: The SBML L3 Spatial Processes and Geometries package discussion list
> <sbm...@li...>
> Subject: [sbml-spatial] Spatial Breakout at COMBINE 2021
> 
> Dear all,
> 
> To break the silence in this list, I have signed us up for a time slot at COMBINE
> 2021. We can meet:
>       Wednesday, October 13 * 16:00 - 17:00 (CEST)
> 
> In the session, I would be hoping that we could just like last year:
> 
> *	exchange some examples between software tools,
> *	find if there are any last issues to be addressed,
> *	and prepare to move the package for acceptance.
> 
> If you have registered for COMBINE, you can access the zoom link shortly
> before the event here:
> 	https://combine2021.sched.com/event/nYHV/sbml-level-3-package-for-
> spatial-processes-next-steps
> 
> (should you have been unable to register for COMBINE you could still do so, but
> I can also send you the zoom link directly).
> 
> Hope to talk to you next week,
> Thanks
> Frank
> 
> 
> _______________________________________________
> sbml-spatial mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-spatial