Name		Name	Last commit message	Last commit date
Latest commit History 53 Commits
.ipynb_checkpoints		.ipynb_checkpoints
Amino acid metabolism		Amino acid metabolism
Biosynthesis of other secondary metabolites		Biosynthesis of other secondary metabolites
Carbohydrate metabolism		Carbohydrate metabolism
Energy metabolism		Energy metabolism
Lipid metabolism		Lipid metabolism
Metabolism of cofactors and vitamins		Metabolism of cofactors and vitamins
Metabolism of other amino acids		Metabolism of other amino acids
Metabolism of terpenoids and polyketides		Metabolism of terpenoids and polyketides
Nucleotide metabolism		Nucleotide metabolism
Xenobiotics biodegradation and metabolism		Xenobiotics biodegradation and metabolism
__pycache__		__pycache__
clustermapsT		clustermapsT
extracellular_plots		extracellular_plots
filter_plots		filter_plots
pathways_withCompounds		pathways_withCompounds
Chemical structure transformation maps.png		Chemical structure transformation maps.png
ChisholmPro_TOCandDOCdata.2017.04.28.csv		ChisholmPro_TOCandDOCdata.2017.04.28.csv
ChisholmPro_cellSpecific_KEGGexport.2017.07.31_v1.csv		ChisholmPro_cellSpecific_KEGGexport.2017.07.31_v1.csv
Chisholm_Pro_newAcids.2017.04.27.jpg		Chisholm_Pro_newAcids.2017.04.27.jpg
KEGGexpected_2019.05.10.csv		KEGGexpected_2019.05.10.csv
ProKEGG.ipynb		ProKEGG.ipynb
ProKEGG_countCpdsByGroup.ipynb		ProKEGG_countCpdsByGroup.ipynb
Pro_TSQmeasured_cpds.png		Pro_TSQmeasured_cpds.png
Pro_cpds.png		Pro_cpds.png
Pro_pathways.png		Pro_pathways.png
Pro_plotReplicates.ipynb		Pro_plotReplicates.ipynb
Pro_topTen.png		Pro_topTen.png
README.md		README.md
allMeasured.csv		allMeasured.csv
br08901.keg		br08901.keg
colorbar_only.py		colorbar_only.py
compoundList_Amino acid metabolism.csv		compoundList_Amino acid metabolism.csv
compoundList_Biosynthesis of other secondary metabolites.csv		compoundList_Biosynthesis of other secondary metabolites.csv
compoundList_Carbohydrate metabolism.csv		compoundList_Carbohydrate metabolism.csv
compoundList_Chemical structure transformation maps.csv		compoundList_Chemical structure transformation maps.csv
compoundList_Energy metabolism.csv		compoundList_Energy metabolism.csv
compoundList_Glycan biosynthesis and metabolism.csv		compoundList_Glycan biosynthesis and metabolism.csv
compoundList_Lipid metabolism.csv		compoundList_Lipid metabolism.csv
compoundList_Metabolism of cofactors and vitamins.csv		compoundList_Metabolism of cofactors and vitamins.csv
compoundList_Metabolism of other amino acids.csv		compoundList_Metabolism of other amino acids.csv
compoundList_Metabolism of terpenoids and polyketides.csv		compoundList_Metabolism of terpenoids and polyketides.csv
compoundList_Nucleotide metabolism.csv		compoundList_Nucleotide metabolism.csv
compoundList_Xenobiotics biodegradation and metabolism.csv		compoundList_Xenobiotics biodegradation and metabolism.csv
compoundNames.csv		compoundNames.csv
compoundsSBin3_extracellular.jpg		compoundsSBin3_extracellular.jpg
compoundsSBin3_filters.jpg		compoundsSBin3_filters.jpg
dendrogram_vertical.jpg		dendrogram_vertical.jpg
dendrogram_vertical_extracellular.jpg		dendrogram_vertical_extracellular.jpg
figure_extracellular_3m2ob.jpg		figure_extracellular_3m2ob.jpg
figure_extracellular_3m2op.jpg		figure_extracellular_3m2op.jpg
figure_extracellular_4m2op.jpg		figure_extracellular_4m2op.jpg
figure_filter_3m2ob.jpg		figure_filter_3m2ob.jpg
figure_filter_3m2op.jpg		figure_filter_3m2op.jpg
figure_filter_4m2op.jpg		figure_filter_4m2op.jpg
find_metabolites_by_strain.ipynb		find_metabolites_by_strain.ipynb
fxn_plotPathway.py		fxn_plotPathway.py
fxn_plotPathway_v2.py		fxn_plotPathway_v2.py
globalsave.pkl		globalsave.pkl
glutamicAcid.jpg		glutamicAcid.jpg
justAminoAcids_corrected.pdf		justAminoAcids_corrected.pdf
justAminoAcids_extracellular.pdf		justAminoAcids_extracellular.pdf
justAminoAcids_filters.pdf		justAminoAcids_filters.pdf
measured_v_expected_v1.ipynb		measured_v_expected_v1.ipynb
nCompounds_extracellular.jpg		nCompounds_extracellular.jpg
nCompounds_filters.jpg		nCompounds_filters.jpg
next.csv		next.csv
not0801.csv		not0801.csv
optimumLight_AminoAcids_filters.pdf		optimumLight_AminoAcids_filters.pdf
plotByGroup.py		plotByGroup.py
replete_filter_stackedBarPlot.jpg		replete_filter_stackedBarPlot.jpg
shelve.out.bak		shelve.out.bak
shelve.out.dat		shelve.out.dat
shelve.out.dir		shelve.out.dir
stackedBarPlot.jpg		stackedBarPlot.jpg
stackedBarPlot_vertical.jpg		stackedBarPlot_vertical.jpg
stackedBarPlot_vertical_extracellular.jpg		stackedBarPlot_vertical_extracellular.jpg
stackedBarPlot_vertical_replete_filter.jpg		stackedBarPlot_vertical_replete_filter.jpg
~		~

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Pro_mtabs (Kujawinski Lab, WHOI)

This repository holds the code for the following manuscript:
Kujawinski, E. B., R. Braakman, K. Longnecker, J. W. Becker, S. W. Chisholm, K. Dooley, M. C. Kido Soule, G. J. Swarr and K. Halloran (2023). Metabolite diversity among representatives of divergent Prochlorococcus ecotypes. mSystems. DOI: 10.1128/msystems.01261-22 (available here)

The script that was used to find compound information for each Prochlorococcus strain is available here.

11 October 2023
Update to transfer to organization KujawinskiLaboratory. All prior edits as user KujawinskiLaboratory were Krista Longnecker, whose GitHub name is now @redbluewater

17 April 2017 targeted metabolomics data for multiple strains of Prochlorococccus, now integrating pathway maps from KEGG with the compound information.
KLongnecker 4/17/2017

KujawinskiLaboratory/Pro_mtabs

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