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New model GSoC2026 - #24
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… mappings in some BioDynamo versions
…ic a cylindrical capsule
…python draft file to analyse the csv
…oth the basal necrosis probability and the factor
… cup both with and without aging factor. fitting oxygen_saturation_for_proliferation
…ndaries z and generalization of CART cell spwan
… parameters. Add new parameters to initialize substances in restricted areas. New tumoral and cart cell volumes
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New hyperparameter from add glucose gradient
salva24
marked this pull request as ready for review
September 30, 2026 10:22
salva24
marked this pull request as draft
October 1, 2026 15:25
…s for result analysis and radius analysis
salva24
marked this pull request as ready for review
October 3, 2026 18:52
vgvassilev
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Oct 4, 2026
vgvassilev
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Oct 6, 2026
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Can we ask claude to draw this with mermaid for github?
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I just tried a few attempts but honestly I do not like the results as much as the diagram I've done myself. Let's discuss it tomorrow
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Yes, it is ugly but I believe it can replay 1:1 yours…
vgvassilev
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Oct 7, 2026
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Please find all other classes marked as "final" and consider dropping it. |
lmluque
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Oct 13, 2026
lmluque
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Oct 22, 2026
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Thanks, Salva and Hari, for addressing the comments and implementing the fixes!
I think the remaining points could be tracked as separate GitHub Issues rather than holding up this PR. In particular:
- Documenting the assumptions behind the 2D diffusion approximation.
- Checking the sensitivity of the results to the initial oxygen concentration.
- Investigating whether retaining the unconstrained cell velocity introduces numerical artefacts near the boundaries.
Otherwise, looks good to me! Thanks again for all your work on this! :)
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This PR extends and calibrates CARTopiaX to reproduce the experimental results reported in Ando et al., Evaluating CAR-T Cell Therapy in a Hypoxic 3D Tumor Model (Advanced Healthcare Materials, 2019).
The implemented changes improve the biological realism of the simulation by reproducing the experimental setup and the observed CAR T-cell behavior under hypoxic conditions. This demonstrates CARTopiaX as a flexible and robust in silico hypothesis-testing framework capable of replicating published studies, accelerating CAR T-cell research, and reducing reliance on costly and time-consuming wet-lab experiments.