- Adding biological constraints to a flux balance model (constrainingModels)
- Computation and analysis of microbe-microbe metabolic interactions (microbeMicrobeInteractions)
- Computation and analysis of rescued lethal gene deletions in a host-microbe model (hostMicrobeInteractions)
- Constraint-based modelling concepts (COBRAconcepts)
- Convert a reconstruction into a flux balance analysis model (recon2FBAmodel)
- Create a generic subnetwork from Recon3D (createSubnetworkRecon)
- Create an overview table with model properties (modelProperties)
- Creating a Model (modelCreation)
- E.coli Core Model for Beginners (ecoliCoreModel - PART 1)
- E.coli Core Model for Beginners (ecoliCoreModel - PART 2)
- E.coli Core Model for Beginners (ecoliCoreModel - PART 3)
- Example use of functions listed in the standard operating procedure for metabolic reconstruction (reconstructionSO)
- FastGapFill tutorial (fastGapFill)
- Find leakage and siphon modes in a reconstruction (leakSiphonModes)
- Generation and manipulation of reconstructions with rBioNet (rBioNet)
- How to use modelBorgifier (modelBorgifier)
- Model manipulation (modelManipulation)
- Numerical properties of a reconstruction (numCharact)
- Testing basic properties of a metabolic model (modelSanityChecks)
- Testing chemical and biochemical fidelity (fidelityTesting)
- Test physiologically relevant ATP yields from different carbon sources for a metabolic model (modelATPYield)