Software

Biophysics

ACAM - Apposed Cortex Adhesion Model

With A. Nestor-Bergmann, G. B. Blanchard, A. G. Fletcher

Each cell cortex in ACAM is represented as an active, continuum morphoelastic rod with resistance to bending and extension. By explicitly considering both cortices along bicellular junctions, the model is able to replicate important cell behaviours that are not captured in many existing models e.g. cell-cell shearing and material flow around cell vertices.

Data processing

DataMerge, a command line tool to interpolate data files of time series... and much more

DataMerge is a linux command line which allows to merge a number of datafiles organised in columns indexed in a one-dimensional way into a single dataset. It can handle files of data tabulated on different grids, by using interpolation methods. E.g., data recorded every 10 seconds and data recorded every 15 seconds can be interpolated into either grid. Interpolation can be linear between adjacent points, or use a least-square approximation on a moving window. It also allows to process columns individually, perform cross-column calculations or change the unit in which quantities are expressed. Several other methods also allow to perform cross-row calculations, such as finite differences or normalisation by an automatically detected entry row.