Skip to content
Supplementary material for the preprint "Identifying density-dependent interactions in collective cell behaviour"
MATLAB C
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
Code
Data
ExperimentalData.xlsx
README.md

README.md

scratchIBM

Supplementary data, and code, for the preprint "Identifying density-dependent interactions in collective cell behaviour" available on bioRxiv

Experimental data

Raw data in the /Data folder corresponds to experiment indices in the main document as follows:

Index Folder
1 8000_E2
2 8000_G2
3 10000_H1
4 10000_H2
5 8000_F2
6 10000_A2
7 12000_H3
8 12000_F3
9 12000_D2

Experimental data is recorded 12 h after seeding. Hence, raw data indicated by filename ending corresponds to the following times:

Filename end Time
"_12h" 0 h
"_30h" 18 h
"_48h" 36 h

For more details, see ExperimentalData.xlsx

Code

Requirements

  • MATLAB R2018a or later
  • MEX and C compiler
  • (optional) Parallel computing toolbox If you do not have this toolbox, you must replace parfor with for in the following files:
    1. ABC_SimulateModel.m
    2. ABC_SMC.m

Installation

Before use, you must compile the MEX code contained in IBM.c using the Install.m script or typing:

mex IBM.c  -R2018a

into the command window.

Examples

Simulating IBM

See Example_IBM.m for an example IBM realisation.

ABC Rejection

  • Parallel computing toolbox highly recommend
  • This function can take a large amount of time to run for Nsamples > 100
    • We have set Nsamples = 100 and alpha = 0.1 for demonstrative purposes

Run Example_ABCRejection.m code (in the main document, we use Nsamples = 100000)

ABC SMC Model Selection

  • Parallel computing toolbox highly recommend
  • This function can take a large amount of time to run for N > 10
    • We have set N = 8 and not used the full sequence of thresholds for demonstrative purposes

Run Example_ABCSMC.m code (in the main document, we use Nsamples = 5000)

You can’t perform that action at this time.