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Murphy Lab - Software - MBoC 2015 - Cell and Nuclear Shape Models

The software and intermediate results used for the following paper can be downloaded below:

G. R. Johnson, T. E. Buck, D. P. Sullivan, G. K. Rohde, and R. F. Murphy (2015) Joint modeling of cell and nuclear shape variation. Molecular Biology of the Cell 26: 4046-4056. http://dx.doi.org/10.1091/mbc.E15-06-0370


This source code is released under GNU LGPL v2.1.


Source Code

Primary Data

Intermediate Results

These files can be used to regenerate the tables and figures in the paper.

Recreating results

To recreate the results from the article (i.e. the figures and tables),
Download and expand the source code to the desired directory.

wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_source_code.tgz
tar -xzf MBoC_Shape_source_code.tgz
Either download and expand the primary data into the same root directory. wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_hela_images.tgz
wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_h1299_images.tgz
wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_mcf7_images.tgz
for FILE in *images*.tgz; do tar -xvf "$FILE"; done

Or download and expand the intermediate results into the same root directory.

wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_h1299_intermediate_results.tgz
wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_hela_intermediate_results.tgz
wget -nc http://murphylab.web.cmu.edu/software/2015_MBoC_Cell_And_Nuclear_Shape/MBoC_Shape_mcf7_intermediate_results.tgz
for FILE in *results*.tgz; do tar -xvf "$FILE"; done

Go into the code directory and run the code

cd code
>> masterscript

Note that the masterscript will check for the presence of the intermediate results files and if they are present it will skip processing of the corresponding primary data. If neither the primary data nor the intermediate results are present for a given cell line, the masterscript will warn about the missing data but will process data for other cell lines if present. Thus the results for just one cell line can be reproduced by downloading either primary data or intermediate results for that cell line.

System requirements

This package has been tested using Matlab 2014a in CentOS.

Last Updated: 07 Mar 2016

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