PSAMM documentation

Contents:

• Overview
  • Citing PSAMM
  • Software license
• 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
  • Dependencies
  • Cplex
  • Gurobi
  • GLPK
  • QSopt_ex
  • LP Solver Compatibility
  • LP Solver Global Options
• Model file format
  • Biomass
  • Extracellular Compartment
  • Default Compartment
  • Compartments
  • Compounds
  • Reactions
  • Exchange compounds
  • Reaction flux limits
  • Model Definition
• 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
  • Test suite
  • Adding new tests
  • Documentation tests
• FAQ
• PSAMM API
  • psamm.balancecheck – check balance of charge and formula
  • psamm.bayesian – Bayesian Matching Functions
  • psamm.bayesian_util – Bayesian Matching Utility Functions
  • psamm.command – Command line interface
  • psamm.database – Reaction database
  • psamm.datasource.context – File system contexts
  • psamm.datasource.entry – Model entry representations
  • psamm.datasource.kegg – KEGG data parser
  • psamm.datasource.modelseed – ModelSEED data parser
  • psamm.datasource.native – Native data format parser
  • psamm.datasource.reaction – Parser for reactions
  • psamm.datasource.sbml – SBML model parser
  • psamm.expression.affine – Affine expressions
  • psamm.expression.boolean – Boolean expressions
  • psamm.fastcore – Fastcore (approximate consistent subset)
  • psamm.fastgapfill – FastGapFill algorithm
  • psamm.fluxanalysis – Constraint-based reaction flux analysis
  • psamm.fluxcoupling – Flux coupling analysis
  • psamm.formula – Chemical compound formula
  • psamm.gapfill – GapFind/GapFill
  • psamm.gapfilling – Gap-filling functions
  • psamm.graph – Graph Related Functions
  • psamm.importer – Import Functions
  • psamm.lpsolver.cplex – CPLEX LP solver
  • psamm.lpsolver.generic – Generic linear programming solver
  • psamm.lpsolver.glpk – GLPK LP solver
  • psamm.lpsolver.gurobi – Gurobi LP solver
  • psamm.lpsolver.lp – Linear programming problems
  • psamm.lpsolver.qsoptex – QSopt_ex LP solver
  • psamm.manual_curation – Model Mapping Curation
  • psamm.mapmaker – Mapmaker Functions
  • psamm.massconsistency – Mass consistency check
  • psamm.metabolicmodel – Metabolic model representation
  • psamm.moma – Minimization of metabolic adjustments
  • psamm.randomsparse – Find a random minimal network of model reactions
  • psamm.reaction – Reaction equations and compounds
  • psamm.translate_id – ID Translation Functions
  • psamm.util – Internal utilities
• References

Indices and tables

• Index
• Module Index
• Search Page