Mummichog

Mummichog is a free Python program for analyzing data from high throughput, untargeted metabolomics. It leverages the organization of metabolic networks to predict functional activity directly from feature tables, bypassing metabolite identification. Thus, high-quality hypotheses can be quickly generated from a LC-MS data table.

Download and use mummichog. Now via standard Python package index.

OS independent install (version 1): pip install mummichog1

Or mummichog 2 (beta test): pip install mummichog

Run it in command line: mummichog -f myData -o myResult

More to click "Software".

Example publications that were supported by using mummichog

Li et al. (2017) Metabolic Phenotypes of Response to Vaccination in Humans. Cell 169(5): p862-877.

Huan, Tao, et al. "Systems biology guided by XCMS Online metabolomics." Nature methods 14.5 (2017): 461.

Xu et al. "Autophagy is essential for effector CD8+ T cell survival and memory formation." Nature immunology 15.12 (2014): 1152-1161.

More to click "Publications".

Jupyter notebooks for data analysis in metabolomics and systems biology

Jupyter notebooks are to data people like lab notebooks to bench scientists. They keep code and result in the same web browser. It's increasinlgy popular for data analysis and collaboration. We continue posting notebooks as tutorials and for record keeping.

More to click "Notebooks".

News

Shuzhao Li lab has moved to The Jackson Laboratory for Genomic Medicine. And we are hiring!
Springer book "Computational Methods and Data Analysis for Metabolomics" is out! At Springer; On Amazon
Integrating metabolomics and exposomics (HiCoNet)
Integrating metabolomics, transcriptomics and microbiome in seasonal influenza vaccination Hagan et al, 2019. Cell, 178(6), pp.1313
Web version is now testing at here.
Mummichog 2 is now on GitHub. Now Python 3 compatible.
MetaboAnalyst 4 has implemented Mummichog 2.
A common error, "AttributeError: 'NodeView' object has no attribute 'sort’", is caused by Networkx 2.x, which is not backward compatible. This can be fixed by installing Networkx 1.x via pip in your terminal, "sudo pip install networkx==1.10".
Mummichog 2 test version is available at Pypi.
Mummichog version 1.0.10 is available at Pypi.
Mummichog helped decipher metabolic phenotypes in human vaccination - Li et al. (2017) at Cell 169(5): p862-877. Also see commentary "Orthogonal Data Integration to Define Immunometabolic-Phenotypes" at Cell Systems.