coelho2013_bioinformatics

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

https://github.com/luispedro/coelho2013_bioinformatics

Science Score: 31.0%

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Repository

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

Basic Info

Host: GitHub
Owner: luispedro
Language: Python
Default Branch: master
Homepage:
Size: 120 KB

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Created almost 13 years ago · Last pushed almost 11 years ago

Metadata Files

Readme Citation

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 `__]

Owner

Name: Luis Pedro Coelho
Login: luispedro
Kind: user
Location: Luxembourg & Shanghai
Company: Fudan University

Website: https://luispedro.org
Twitter: luispedrocoelho
Repositories: 204
Profile: https://github.com/luispedro

Citation (CITATION.rst)

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 <http://dx.doi.org/10.1093/bioinformatics/btt392>`__]
    

BibTeX Format
-------------

::


    @article{Coelho08072013,
    author = {Coelho, Luis Pedro and Kangas, Joshua D. and Naik, Armaghan W.
        and Osuna-Highley, Elvira and Glory-Afshar, Estelle and Fuhrman, Margaret
        and Simha, Ramanuja and Berget, Peter B. and Jarvik, Jonathan W. and
        Murphy, Robert F.},
    title = {Determining the subcellular location of new proteins from
        microscope images using local features},

    year = {2013},
    doi = {10.1093/bioinformatics/btt392},
    URL = {http://bioinformatics.oxfordjournals.org/content/early/2013/07/07/bioinformatics.btt392.abstract},
    eprint = {http://bioinformatics.oxfordjournals.org/content/early/2013/07/07/bioinformatics.btt392.full.pdf+html},
    journal = {Bioinformatics}
    }

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