Tutorials¶
Analysis¶
Analysis¶
- A step-by-step guide to parsimoneous enzyme usage Flux Balance Analysis - pFBA
- Analyze Steady-State Community COBRA Models
- Atomically resolve a metabolic reconstruction
- Browse Networks in the Matlab Command Window Using surfNet
- Computation and analysis of microbe-microbe metabolic interactions
- Computation and analysis of rescued lethal gene deletions in a host-microbe model
- Creation and simulation of personalized microbiota models through metagenomic data integration
- Determining MinSpan vectors of COBRA model
- Flux Balance Analysis (FBA)
- Flux Variability analysis (FVA)
- genetic Minimal Cut Sets - gMCS
- Proton shuttle testing with sparse flux balance analysis
- Reaction essentiality across multiple models
- Relaxed Flux Balance Analysis: Recon 3
- Relaxed Flux Balance Analysis: Toy model
- Simulation of growth of human gut microbes on different diets
- Sparse Flux Balance Analysis
- Sparse flux balance analysis test for a minimial stoichiometrically balanced cycle involving ATP hydrolysis
- Sparse Linear Optimisation
- Thermodynamically constrain a metabolic model
- Uniform sampling
- Variational Kinetics
- Varying Parameters analysis
Base¶
Data integration¶
Design¶
Reconstruction¶
Reconstruction¶
- Adding biological constraints to a flux balance model
- Adding more complex constraints on a model
- Constraint-based modelling concepts
- Convert a reconstruction into a flux balance analysis model
- Create a generic subnetwork from Recon 3D
- Create an overview table with model properties
- Creating a Model
- E.coli Core Model for Beginners (PART 1)
- E.coli Core Model for Beginners (PART 2)
- E.coli Core Model for Beginners (PART 3)
- Example use of functions listed in the Standard operating procedure for metabolic reconstruction.
- FastGapFill tutorial
- Find leakage and siphon modes in a reconstruction
- Generation and manipulation of reconstructions with rBioNet
- How to use modelBorgifier
- Model manipulation
- Numerical properties of a reconstruction
- Test physiologically relevant ATP yields from different carbon sources for a metabolic model
- Testing basic properties of a metabolic model (aka sanity checks)
- Testing chemical and biochemical fidelity
