[donovanr]

Yes, this. A lot of work in this field is missing from that timeline. Just circa 2010-2020, Les Loew's VCell 3D PDE approaches, Faeder et al.'s BioNetGen / ODE work, Luthey-Schulten Shulten's grid based cell models, the Pittsburgh supercomputing center's 3D monte-carlo MCell, the image-based deep learning models at the Allen Institute for Cell Science...

It's nice to see the idea of virtual cells make a comeback now, though the meaning seems to have shifted to transciptomics-based transformer / gpu-powered models (which have issues[0]), it's a fun field / problem, but I think it will make better progress if we take advantage of all the varied computational work that has come before.

[0] Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all https://arxiv.org/abs/2410.13956

[udara]

oh that's interesting, I didn't come across these the way I was looking at it! thank you for informing us, I will read up on these and add it to the timeline!