Start a presentation notebook

Bertinus commented 2 years ago

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

Bertinus commented 1 year ago

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

Bertinus commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

@josephdviviano FYI

Bertinus commented 1 year ago

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

Bertinus / FLeCS

Start a presentation notebook #10