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Murphy Lab - Software - PLoS CB 2015 - Punctate Proteins

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

G. R. Johnson, J. Li, A. Shariff, G.K.Rohde, and R.F. Murphy (2015) Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of their Relation to Microtubules. PLoS Computational Biology 11:e1004614.

License

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

Downloads

The data and code are contained in the following files.

Source Code

PLoS_CB_PP_source_code.tgz [47 MB]

Primary Data

The original image files were provided courtesy of Dr. Emma Lundberg, Dr. Mathias Uhlen and the Human Protein Atlas project, http://proteinatlas.org. They can be requested by contacting Dr. Lundberg.

Intermediate Results

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

PLoS_CB_PP_intermediate_results.tgz [477 GB]

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_PLoS_CB_Punctate_Proteins/PLoS_CB_PP_source_code.tgz tar -xzf PLoS_CB_PP_source_code.tgz

Download and expand the intermediate results into the same root directory

wget -nc http://murphylab.web.cmu.edu/software/2015_PLoS_CB_Punctate_Proteins/PLoS_CB_PP_intermediate_results.tgz tar -xzf PLoS_CB_PP_intermediate_results.tgz

Go into the code directory and run the code

cd code matlab >> masterscript

Note that the masterscript will check for the presence of the intermediate results files and if they are not present it will process the primary images. Doing all calculations from the primary data will take approximately one week, depending on number of cores available.

System requirements

MATLAB

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

Last Updated: 07 Dec 2015