Inferring cell dynamics in multi-cellular systems with incomplete data

Bachelor thesis Benjamin Frey

This thesis was conducted using the FitMultiCell package using Approximate Bayesian Computation on a HPC cluster from Heidelberg University. The workflow included FitMultiCell, Python and batch scripts and took advantage of the slurm manager on the cluster.

Cluster internal submission scripts are not included in this repository, only analysis scripts for the .feather files.

Additionally, key results datasets as well as the thesis are included.

Key method:

https://fitmulticell.gitlab.io/

Pre-print of results:

Inferring cell motility in complex environments with incomplete tracking data Nils Bundgaard, Christoph Harmel, Andrea Imle, Samy Sid Ahmed, Benjamin Frey, Jörn Starruß, Oliver T. Fackler, Frederik Graw bioRxiv 2022.02.10.479738; doi: https://doi.org/10.1101/2022.02.10.479738