Biowulf High Performance Computing at the NIH
AMON on Helix
Quick Links

AMON (Annotation of Metabolite Origins via Networks) is an open-source bioinformatics application that can be used to
(1) annotate which compounds in the metabolome could have been produced by bacteria present or the host;
(2) evaluate the pathway enrichment of host verses microbial metabolites, and
(3) to visualize which compounds may have been produced by host versus microbial enzymes in KEGG pathway maps.


Important Notes

Interactive job

This application can only be run on Helix, and not on Biowulf.

[user@biowulf]$ ssh Helix 
[user@helix]$ APPS=/usr/local/apps 
[user@helix]$ export PATH=$APPS/AMON/1.0.0/bin:$PATH 
[user@helix]$ export LD_LIBRARY_PATH=$APPS/AMON/1.0.0/lib:$LD_LIBRARY_PATH 
[user@helix]$ export PYTHONPATH=$APPS/AMON/1.0.0/lib/pythin3.6/site-packages:$PYTHONPATH 
[user@helix]$ export AMON_DATA=$APPS/AMON/1.0.0/sample_data 
Copy sample data to the current folder:
[user@helix]$ cp $AMON_DATA/* .
Run the AMON application on the sample data:
[user@helix]$ -i ko_list.txt -o test
Review the results stored in the output folder test:
[user@helix]$ ls test
AMON_log.txt            gene_set_1_compound_pathway_enrichment.tsv  origin_table.tsv
enrichment_heatmap.png  kegg_mapper.tsv
[user@helix]$  head test/kegg_mapper.tsv
C02631  blue
K13489  blue
C03287  blue
K00926  blue
C20423  blue
K08224  blue
K00800  blue
K00162  blue
K01505  blue
[user@helix]$ head -n 10 test/gene_set_1_compound_pathway_enrichment.tsv
        pathway size    overlap probability     adjusted probability
Purine metabolism       95      70      1.5357411062115152e-24  3.2404137341062968e-22
Methane metabolism      86      63      4.696075577134766e-22   4.954359733877178e-20
Aminoacyl-tRNA biosynthesis     52      44      1.0032329802784207e-20  7.05607196129156e-19
Folate biosynthesis     57      45      1.1333844794425998e-18  5.978603129059714e-17
Pentose phosphate pathway       35      32      3.680767932496869e-18   1.5532840675136786e-16
Lipopolysaccharide biosynthesis 54      42      4.0149350164351284e-17  1.4119188141130203e-15
Glycolysis / Gluconeogenesis    31      28      7.816512870575171e-16   2.3561203081305158e-14
Central carbon metabolism in cancer     37      31      4.8353494377765e-15     1.2753234142135519e-13
Phosphotransferase system (PTS) 57      41      1.266083970361715e-14   2.968263530514687e-13
Visualize the output heat map:
[user@helix]$ test/enrichment_heatmap.png

End the interactive session:
[user@helix ~]$ exit
[user@biowulf ~]$