CellSim3D

Welcome to the CellSim3D repository. CellSim3D is a software package to simulate the mechanistic aspects of cell division in three dimensions. The code is written in C/C++ and CUDA.

References:

If you use the code, please cite the following papers:

The 3D model is based on the 2D model introduced in

A new model for cell division and migration with spontaneous topology changes, A. Mkrtchyan, J.A. Åström and M. Karttunen, Soft Matter 10, 4332-4339 (2014). [http://dx.doi.org/10.1039/C4SM00489B]

3D model:

CellSim3D: GPU Accelerated Software for Simulations of Cellular Growth and Division in Three Dimensions, Pranav Madhikar, Jan Åström, Jan Westerholm, Mikko Karttunen, Computer Physics Communications 232, 206-213 (2018).[https://doi.org/10.1016/j.cpc.2018.05.024]

Compilation

CellSim3D can be compiled easily with the packaged makefile. First change the -arch variable to correspond to the compute capability of your GPU.

For example: -arch=sm_52 for a GPU of compute capability of 5.2

Then:

mkdir bin
make -j12 CellDiv to compile the simulator.

The simulator can be found in the bin directory

Simulator Source Code Description (note: subject to change):

GPUBounce.cu

This file contains the entry point for the simulator code. This is where the GPU is selected and memory is allocated. Simulation parameters are read from the input json file.

All GPU functions (force calculation, integration, cell division) is controlled from here.

propagate.cu

This file contains GPU kernel code that is used for force calculations and integration.

centermass.cu

This file only contains a single GPU kernel that calculate the centers of mass of individual cells. This is needed for the calculation of cell volumes and the cell division algorithm

BondKernels.cu

This file calculates the equilibrium bond lengths of bonded nodes in a cell. For now, this code is not very crucial since this bond length does not change over the course of a simulation. It will be used in later releases more extensively.

postscriptinit.cu

This file contains some legacy code that is no longer used. It also contains the implementation of the cell division algorithm.

propagatebound.cu

Code here is used to calculate the bounding boxes around cells, which are then used during neighbor list generation. Neighbor list generation itself is also carried out here.

PressureKernels.cu

Cell internal pressure is managed with the code here.

IntegrationKernels.cu and AdaptiveTimeKernels.cu

Code here is not currently used.

Analysis Scripts (In the scripts/ directory):

The scripts directory contains various analysis scripts. Their functionality can be explored by running

  python3 script.py --help

The most important ones are:

celldiv.py

This is the interface to the binary format of the trajectory. It can be used to read the trajectory into numpy arrays.

render.py

This is the rendering engine used to visualize the simulations. It produces images which can be made into movies. Requires Blender 2.7 or higher. Uses the scene set in CellDiv.blend

Learn more by running

  blender -b CellDiv.blend -P scripts/render.py -- --help