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A tutorial on modelling growth and cell division aiming to introduce changes to deterministic and stochastic models of molecular reaction and regulation models that are needed as well as models for growth and cell divisions.

A wiki with instructions on how to do stuff. This includes instructions on how to deal with jupyter notebooks in git.

An ad-hoc Julia library for biological modelling.

An interactive resource for learning systems biology without needing much background in mathematics or programming.

A Julia package for reproducible management of model parameter sets.

A library of loss functions for use in optimisations.

A small library of functions to supply a common API for different ways of simulating a model in DifferentialEquations.jl.

Provide types and management for storing parameters with metadata for filtering and reproducibility.

File IO for parameters belonging to some DifferentialEquations.jl model.

Investigating the R1-R4 feedbacks and nuclear shuttling for the onset of cell division. This project is led by Weibing Yang and myself .

A general library for using Organism with python

Vertex based topologies for creating realistic spatial tissue models which play nice with DifferentialEquations.jl.

Files needed to run models for Bou Daher et al (2018) 'Anisotropic growth is achieved through the additive mechanical effect of material anisotropy and elastic asymmetry' eLife

Code for simulations of individual Microtubules in 3D and constrained by a meshed description of a cell membrane.

Source for differential pressure and force sensors control and acquisition.

Script to extract the 3D orientation in 3D confocal images of filaments in single cells (TIFF, CZI format).