Start a presentation notebook

[Bertinus]

Start when the "backbone" of the codebase is more stable

[Bertinus]

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

[Bertinus]

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)

[Bertinus]

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]

@josephdviviano FYI

[Bertinus]

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