PSAMM documentation¶
Contents:
- Overview
- PSAMM Tutorials
- Installation and Materials
- Importing, Exporting, and working with Models with PSAMM
- Model Curation
- Constraint Based Analysis with PSAMM
- Reactant/Product Pair Prediction and Visualization Using FindPrimaryPairs
- Automated Comparison of Models Using ModelMapping
- Supplementing your model with other data
- Generating Metabolic Models Based On Functional Annotations
- Install
- Model file format
- Command line interface
- Linear programming solver
- Flux balance analysis (
fba
) - Flux variability analysis (
fva
) - Robustness (
robustness
) - Random sparse network (
randomsparse
) - Gene Deletion (
genedelete
) - Flux coupling analysis (
fluxcoupling
) - Stoichiometric consistency check (
masscheck
) - Formula consistency check (
formulacheck
) - Charge consistency check (
chargecheck
) - Flux consistency check (
fluxcheck
) - Reaction duplicates check (
dupcheck
) - Gap check (
gapcheck
) - GapFill (
gapfill
) - FastGapFill (
fastgapfill
) - Predict primary pairs (
primarypairs
) - PSAMM-Vis (
vis
) - SBML Export (
sbmlexport
) - Excel Export (
excelexport
) - Table Export (
tableexport
) - Search (
search
) - PSAMM-SBML-Model
- Console (
console
) - Psammotate (
psammotate
) - GIMME (
gimme
) - TMFA (
tmfa
)
- Development
- FAQ
- PSAMM API
psamm.balancecheck
– check balance of charge and formulapsamm.bayesian
– Bayesian Matching Functionspsamm.bayesian_util
– Bayesian Matching Utility Functionspsamm.command
– Command line interfacepsamm.database
– Reaction databasepsamm.datasource.context
– File system contextspsamm.datasource.entry
– Model entry representationspsamm.datasource.kegg
– KEGG data parserpsamm.datasource.modelseed
– ModelSEED data parserpsamm.datasource.native
– Native data format parserpsamm.datasource.reaction
– Parser for reactionspsamm.datasource.sbml
– SBML model parserpsamm.expression.affine
– Affine expressionspsamm.expression.boolean
– Boolean expressionspsamm.fastcore
– Fastcore (approximate consistent subset)psamm.fastgapfill
– FastGapFill algorithmpsamm.fluxanalysis
– Constraint-based reaction flux analysispsamm.fluxcoupling
– Flux coupling analysispsamm.formula
– Chemical compound formulapsamm.gapfill
– GapFind/GapFillpsamm.gapfilling
– Gap-filling functionspsamm.graph
– Graph Related Functionspsamm.importer
– Import Functionspsamm.lpsolver.cplex
– CPLEX LP solverpsamm.lpsolver.generic
– Generic linear programming solverpsamm.lpsolver.glpk
– GLPK LP solverpsamm.lpsolver.gurobi
– Gurobi LP solverpsamm.lpsolver.lp
– Linear programming problemspsamm.lpsolver.qsoptex
– QSopt_ex LP solverpsamm.manual_curation
– Model Mapping Curationpsamm.mapmaker
– Mapmaker Functionspsamm.massconsistency
– Mass consistency checkpsamm.metabolicmodel
– Metabolic model representationpsamm.moma
– Minimization of metabolic adjustmentspsamm.randomsparse
– Find a random minimal network of model reactionspsamm.reaction
– Reaction equations and compoundspsamm.translate_id
– ID Translation Functionspsamm.util
– Internal utilities
- References