Concentration gradient

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Luke Wheeler

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Jun 18, 2020, 11:50:39 AM6/18/20
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Hello, 

I was wondering if it is possible to encode a spatial concentration gradient within a compartment in the antimony language? I am hoping to create a spatially-resolved model that can be simulated with Tellurium. 

Thanks,

Luke 

Lucian Smith

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Jun 18, 2020, 12:19:48 PM6/18/20
to Luke Wheeler, The SBML L3 Spatial Processes and Geometries package discussion list, tellurium-discuss
Neither antimony nor Tellurium support spatial modeling at present, unfortunately.  The tools I know of that support spatial modeling include:

* VCell (though it's a little out of date)
* XitoSBML
* CellOrganizer
* CellBlender/MCell

You might get a better response from the sbml-spatial list, at sbml-s...@lists.sourceforge.net

-Lucian

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Luke Wheeler

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Jun 18, 2020, 1:19:07 PM6/18/20
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Thanks for the information! It's a simple enough model that I want to build right now that it might be the most efficient to just write it from scratch, especially since I need to wrap it inside another piece of code. One of the things I like so much about Tellurium/Antimony is how easy it is to use inside of a custom model (I'm modeling evolution of metabolic pathways). However, I will keep those other tools in mind for the future. 

-Luke


On Thursday, June 18, 2020 at 10:19:48 AM UTC-6, Lucian Smith wrote:
Neither antimony nor Tellurium support spatial modeling at present, unfortunately.  The tools I know of that support spatial modeling include:

* VCell (though it's a little out of date)
* XitoSBML
* CellOrganizer
* CellBlender/MCell

You might get a better response from the sbml-spatial list, at sbml-s...@lists.sourceforge.net

-Lucian

On Thu, Jun 18, 2020 at 8:50 AM Luke Wheeler <lwhe...@gmail.com> wrote:
Hello, 

I was wondering if it is possible to encode a spatial concentration gradient within a compartment in the antimony language? I am hoping to create a spatially-resolved model that can be simulated with Tellurium. 

Thanks,

Luke 

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Herbert M Sauro

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Jun 18, 2020, 1:20:04 PM6/18/20
to Lucian Smith, Luke Wheeler, The SBML L3 Spatial Processes and Geometries package discussion list, tellurium-discuss
You could fake a spatial model by creating a series of connected compartments or species but it would be tedious to construct, although one could write some software that would build it for you. I've done this before to simulate simple one diffusion.

Herbert



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Herbert Sauro, Professor
University of Washington, Bioengineering

Luke Wheeler

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Jun 18, 2020, 1:20:43 PM6/18/20
to Herbert M Sauro, Lucian Smith, The SBML L3 Spatial Processes and Geometries package discussion list, tellurium-discuss
Okay, thanks for that suggestion. That might be a way I can hack it. Cheers!

Luke 

Herbert M Sauro

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Jun 18, 2020, 3:24:12 PM6/18/20
to Luke Wheeler, tellurium-discuss
Sounds like an interesting project. Do you have any published papers on it yet?

Herbert


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Luke Wheeler

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Jun 18, 2020, 3:31:11 PM6/18/20
to Herbert M Sauro, tellurium-discuss
Thanks! No publications yet on this specific project, but I have been using Tellurium in my work to model the evolution of the Anthocyanin pigment pathway in plants. See here: https://academic.oup.com/icb/article/59/3/585/5497801?guestAccessKey=6d4d5dc9-52b6-4a41-8789-0e90597a0816. Currently finishing up a second paper on a more detailed set of simulations in this same pathway. Thanks for creating such a useful tool! 

Luke 
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