Bio Model Analyzer is a biological modelling tool that illustrates signalling pathways and determines cellular stabilization. The tool represents a merging of perspectives from systems biology, formal methods, human computer interaction and design. At one level, Bio Model Analyzer is a sketching tool that enables users to draw out a biological system of interest (e.g. a genetic regulatory network) by dragging and dropping cells, their contents (DNA, proteins, etc.), extracellular components and relationships onto a simple canvas.
Python code for statistically analysing patterns of somatic evolutionary selection in genes or proteins.
A preprint is available:
Hall, Michael WJ, et al. "Investigating structure function relationships in the NOTCH family through large-scale somatic DNA sequencing studies." bioRxiv (2020).
It has also been used in Fowler, Joanna C., et al. "Selection of oncogenic mutant clones in normal human skin varies with body site." Cancer discovery 11.2 (2021): 340-361.
Clone competition simulations
Python code to run various simulations of mutant clonal competition. It can run Moran, 2D Moran, Wright-Fisher, 2D Wright-Fisher and (non-competitive) branching processes.
The code has been used in:
Fowler, Joanna C., et al. "Selection of oncogenic mutant clones in normal human skin varies with body site." Cancer discovery 11.2 (2021): 340-361.
Abby, Emilie, et al. "Notch1 mutation drives clonal expansion in normal esophageal epithelium but impairs tumor growth." bioRxiv (2021).
Michael WJ, Philip H. Jones, and Benjamin A. Hall. "Relating evolutionary selection and mutant clonal dynamics in normal epithelia." Journal of the Royal Society Interface 16.156 (2019): 20190230.
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