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Murphy Lab - Software - Bioinformatics/ISMB 2017 - T Cell Causal Models

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

X. Ruan, C. Wülfing, and R. F. Murphy (2017) Image-based Spatiotemporal Causality Inference for Protein Signaling Networks. Bioinformatics 33:i217-i214. DOI: 10.1093/bioinformatics/btx258


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


Source Code

This file contains all source code, including open source packages listed below.

Primary Data

The primary data are spatiotemporal maps of protein concentration image and can be downloaded here. The source code contains a Matlab script to download all of these files (see instructions below).

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),

  1. Download and expand the source code to the desired directory.

    wget -nc http://murphylab.cbd.cmu.edu/software/2017_TcellCausalModels/Tcell_causality_source_code_v1.0.tgz
    tar -xzf Tcell_causality_source_code_v1.0.tgz
  2. (optional) Download and expand the intermediate result files to the same directory. These files occupy 1.8 GB. Having these files avoids having to do cross validation and permutation tests. This process takes approximately 1000 hours on a single cpu. wget -nc http://murphylab.cbd.cmu.edu/software/2017_TcellCausalModels/Tcell_causality_intermediate_results.tgz
    tar -xzf Tcell_causality_intermediate_results.tgz
  3. 3.Download the primary input data, which are time series data for standardized movies for each cell for each protein and each condition (these files occupy 1.9 GB). If running with intermediate result, this step is optional. wget -nc http://murphylab.cbd.cmu.edu/software/2017_TcellCausalModels/Tcell_time_series_models.tgz
    tar -xzf Tcell_time_series_models.tgz
  4. 4.Run the master script. Note that the script will skip any steps for results that are presented in the intermediate results folder, such as cross validation, permutation tests. The total run time for the script is approximately 1000 hours on a single cpu beginning from the raw images (if intermediate results are not present) or 3 hours beginning from the intermediate results. bash master_script.sh

    System requirements

    • MATLAB
    This package has been tested using Matlab 2015b in CentOS.

    Open source packages used

    • bonf_holm by David Groppe
    • export_fig by Oliver J. Woodford, Yair M. Altman
    • line2arrow by Kelly Kearney
    • maximalCliques by Jeffrey Wildman
    • pmkmp by Matteo Niccoli

Last Updated: 04 Mar 2021

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