Code relating to the 2020 eLife paper:
Cytotoxic T Cells Swarm by Homotypic Chemokine Signaling.
Jorge Luis Galeano Niño, Sophie V. Pageon, Szun S. Tay, Feyza Colakoglu, Daryan Kempe, Jack Hywood, Jessica K. Mazalo, James Cremasco, Matt A. Govendir, Laura F. Dagley, Kenneth Hsu, Simone Rizzetto, Jerzy Zieba, Gregory Rice, Victoria Prior, Geraldine O'Neill, Richard J. Williams, David R. Nisbet, Belinda Kramer, Andrew I. Webb, Fabio Luciani, Mark N. Read, and Maté Biro
eLife (2020) 9:e56554. doi: 10.7554/eLife.56554 https://elifesciences.org/articles/56554
Please cite this paper upon use of any code contained within this repository. We make it available under the GPL v3 licence.
Three modules are included for:
- calculating swarming index (
swarming_metric) - performing agent-based simulations (
motilisim) - extracting summary statistics of motile T cell populations (
motility_analysis)
The swarming metric methodology was lead by Jack Hywood.
The simulation code and motility analysis portions are extensions from code initially developed by Mark N Read in:
MN Read, J Bailey, J Timmis and T Chtanova. (2016). Leukocyte Motility Models Assessed through Simulation and Multi-Objective Optimization-Based Model Selection. PLOS Computational Biology 12(9):e1005082.