Reproducible code archive for http://dx.doi.org/10.1093/bioinformatics/btt392
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doitall.sh

README.rst

Source code for paper Determining the subcellular location of new proteins from microscope images using local features by Coelho et al. in Bioinformatics

This repository is for reproduction of the results in the paper. If you want to apply the methods to your data, check out the tutorial on doing so. It is a step by step manual on applying the methods to your data.

Dependencies

sudo apt-get install python python-pip python-virtualenv
sudo apt-get install dvipng

Instructions

  1. For the Human Protein Atas data, please download from http://murphylab.web.cmu.edu/software/2012_PLoS_ONE_Reannotation/

    Edit the file sources/hpa.py to point to where you downloaded all the data.

  2. Get the randtag data from http://murphylab.web.cmu.edu/software/2013_Bioinformatics_LocalFeatures/ or from Data Dryad

  3. The remaining data should be automatically downloaded when you run:

    doitall.sh
    

This will also run the computation.

If you want to take advantage of multiple processors, edit the file doitall.sh and set the NR_CPUS variable. Note that the whole computation (i) takes a very long time (days) on a single core and (ii) is designed to take full advantage of multiples cores.

Citation

For referring to this work, please cite:

Determining the subcellular location of new proteins from microscope images using local features by Luis Pedro Coelho, Joshua D. Kangas, Armaghan Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B. Berget, Jonathan W. Jarvik, and Robert F. Murphy (2013). Bioinformatics, [DOI]