[!] NOTICE TO USERS: POPPY now (v0.1.3-alpha) uses the offline Equilibrator-API to obtain thermodynamic data. Please refrain from using older versions to access Equilibrator due to capacity constraints of that server.
Tools for creating and exploring metabolic reaction networks.
poppy_create.py
constructs a network of potential metabolic reactions using
resources supplied by KEGG (http://www.kegg.jp/) and MINE
(http://minedatabase.mcs.anl.gov/).
./poppy_create.py --kegg --enhance --equilibrator_filter --infile examples/E_coli.origins.txt network.pkl
poppy_path.py
performs path-finding, sub-network extraction and enumeration
of putative biosynthetic pathways. Can write HTML reports for pathway
enumeration.
./poppy_path.py -p 4 -d 3 -r 5 --model examples/E_coli.model.tab --bounds examples/E_coli.concentrations.tab --ratios examples/E_coli.ratios.tab --pH 7.6 --c_min 0.0000001 --c_max 0.1 --pathway_html E_coli_pathways network.pkl C00989
./poppy_path.py -p 4 -d 3 -r 5 -S examples/Synechocystis.origins.txt --model examples/Synechocystis.model.tab --bounds examples/Synechocystis.concentrations.tab --ratios examples/Synechocystis.ratios.tab --pH 8.4 --c_min 0.0000001 --c_max 0.1 --pathway_html Synechocystis_pathways network.pkl C00989
poppy_rank.py
ranks identified pathways in terms of thermodynamic
driving forces. Also used for calculating transformed standard reaction Gibbs
free energy changes.
./poppy_rank.py --write_gibbs --pH 7.6 examples/E_coli.model.tab E_coli.model_drgs.tab
./poppy_rank.py --write_gibbs --pH 8.4 examples/Synechocystis.model.tab Synechocystis.model_drgs.tab
mdf.py
performs Max-min Driving Force (MDF; Noor et al., 2014) and Network-Embedded
MDF (NEM) analysis.
./mdf.py --min_conc 0.0000001 --max_conc 0.1 --constraints examples/E_coli.concentrations.tab --ratios examples/E_coli.Lys_opt_ratios.tab --pathway examples/E_coli.Lys_pathway.txt examples/E_coli.model.tab E_coli.model_drgs.tab E_coli_Lys_nem.csv
./mdf.py --min_conc 0.0000001 --max_conc 0.1 --constraints examples/Synechocystis.concentrations.tab --ratios examples/Synechocystis.Lys_opt_ratios.tab --pathway examples/Synechocystis.Lys_pathway.txt examples/Synechocystis.model.tab Synechocystis.model_drgs.tab Synechocystis_Lys_nem.csv
Python ≥ 3.5.1 with:
- SciPy and NumPy (https://www.scipy.org/)
- NetworkX (https://github.com/networkx/networkx)
- RDKit (https://github.com/rdkit/rdkit)
- MINE-API (https://github.com/JamesJeffryes/MINE-API; included as
mineclient3.py
) - tablib
- PuLP
- eQuilibrator-API (https://gitlab.com/elad.noor/equilibrator-api)
R ≥ 3.0 with:
- ggplot2
- RColorBrewer
Johannes Asplund-Samuelsson ([email protected])