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Start a presentation notebook #10

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Bertinus opened this issue Oct 20, 2022 · 6 comments
Open

Start a presentation notebook #10

Bertinus opened this issue Oct 20, 2022 · 6 comments
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@Bertinus Bertinus self-assigned this Oct 20, 2022
@Bertinus Bertinus changed the title Make a presentation notebook Start a presentation notebook Oct 20, 2022
@Bertinus Bertinus removed their assignment Oct 31, 2022
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Bertinus commented Oct 31, 2022 •
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Start when the "backbone" of the codebase is more stable

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Have an example to show that we can simulate concentrations inside several cellular compartments.

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Bertinus commented Nov 22, 2022 •
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We will probably need several notebooks

  • Quick start/Overview (CellPop, sets, basic intervention, covid intervention, simulate different types of trajectories, simulation of experimental noise)
  • Use cases / Benchmarks
  • Training and example on a small sample of the Replogle dataset (small sample of genes) + UMAP visualization of trajectories.
  • Databases and visualization of InteractionData. Also show that some network motifs can lead to cycles/differentiation.
  • Advanced: define your own equations (several cellular compartments, chromatine accessibility...), mutations
  • Advanced: implement communication between cells.
  • Advanced: Scaling (notebook on the cluster directly)

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Regarding cell-cell communication:

Take inspiration from https://www.biorxiv.org/content/10.1101/2022.10.15.512320v1.full.pdf

The CellPop object would contain some kind of adjacency matrix between individual cells, as well as their coordinates. Neighbouring cells would exchange information and influence each other's states.

@Bertinus Bertinus self-assigned this Nov 24, 2022
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@josephdviviano FYI

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Check this https://www.nature.com/articles/s41586-022-05688-9

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