Installation

Mummichog can be installed using pip (pip Installs Packages), the Python package manager:

pip install mummichog

This is OS independent. To read more on pip here <https://pip.pypa.io/en/stable/installing/#installing-with-get-pip-py>.

One can also run mummichog without installing it. Direct python call on a downloaded copy will work. Note: a common error may come up in earlier versions as

AttributeError: 'NoveView' object has no attribute 'sort'

This is caused by an incompatible update in networkx-2.0 library. It can be fixed by specifying

sudo pip install networkx==1.10

Usage

Input data are a tab-delimited file with the first 4 columns in this order:

mz      rtime   p-value t-score
186.0185697     463     0.000149751400132       3.82
279.1773473     90      0.000399613326314       3.56
344.1330624     124     0.000998323061251       -3.31
215.9641894     132     0.00105418285794        -3.29
177.0323244     77     0.00121065359218        3.25

The command line to run mummichog is like this:

mummichog -f testdata0710.txt -o myoutput

The initial paper on mummichog is described in Li et al. Predicting Network Activity from High Throughput Metabolomics. PLoS Computational Biology (2013); doi:10.1371/journal.pcbi.1003123.. More on project website <http://mummichog.org>.