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

Hello everyone!
My project, "Development of a system that generates spatial SBML models
using deep learning" under Google Summer of Code 2020, is now complete. As
a result, I have been able to generate a few hundred spatial SBML models,
which can contribute to the development of the SBML Version 3 spatial
package. I am enclosing the link to a sample folder containing 20
microscopic cellular images, corresponding ground truth images and, spatial
SBML models generated via this project.

https://drive.google.com/drive/folders/1z83_pUTlI7eYKL9J9iV-EV6lLAEqC7pG?usp=sharing

Kindly inform me whether these are suitable as test models for the spatial
package; I would be glad to contribute many more such models.

Cheers!
Medha Bhattacharya.

On Tue, May 12, 2020 at 4:05 PM MEDHA BHATTACHARYA <me1...@gm...>
wrote:

> Hello everyone!
>
> I am Medha Bhattacharya, a second-year undergraduate student pursuing a
> Bachelor of Technology (Computer Science and Engineering) at Indira Gandhi
> Delhi Technical University for Women, India. I am glad to inform you all of
> my selection in the Google Summer of Code 2020 program with National
> Resource for Network Biology.
>
> Project title: Development of a system that generates spatial SBML models
> using deep learning.
>
> (Issue: https://github.com/nrnb/GoogleSummerOfCode/issues/140)
>
> This project aims at creating and implementing a software tool that
> automatically generates various spatial SBML models via XitoSBML by
> comprehensively segmenting microscopic images of cells using deep learning.
> Consequently, my project will create a large number of spatial SBML models.
> Furthermore, as XitoSBML uses JSBML to write spatial SBML models, it will
> be used throughout.
>
> Since the development of the SBML Version 3 spatial package is currently
> under progress, a large number of test models are required. These can be
> provided as deliverables via this project to the SBML repository.
> Additionally, the provision of several spatial SBML models will enable
> testing the compatibility of software tools that deal with spatial SBML
> models.
>
> The link to my blog-post:  https://gsoc2020mb.blogspot.com/
>
> I am hoping to be able to contribute towards the development of the SBML
> spatial package this summer!
>
> Cheers!
>
> Medha
>