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 Balance Analysis: Alternate optimal solutions
- Flux Balance Analysis (FBA) and its variants
- Flux Variability analysis (FVA)
- genetic Minimal Cut Sets - gMCS
- Proton shuttle testing with sparse flux balance analysis
- Quadruple precision Flux Balance Analysis
- Reaction essentiality across multiple models
- Relaxed Flux Balance Analysis: Recon 3
- Relaxed Flux Balance Analysis: Toy model
- Robust Metabolic Transformation Analysis - rMTA
- Sensitivity of a flux balance analysis solution with respect to input data
- 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 of E. coli core
- Uniform sampling a genome-scale model
- Variational Kinetics
- Varying Parameters analysis
- ICON-GEMs
- Benchmark solvers for solving whole body metabolic models
- Numerical properties of a whole body metabolic model
Base ¶
Base ¶
- Contribute to the COBRA Toolbox with MATLAB.devTools
- Engaging with The COBRA Toolbox community
- Initialise and verify The COBRA Toolbox
- Introduction to MATLAB
- Input and output of reconstructions and models
- Primer on Flux Balance Analysis and its applications
- Primer on Non-FBA based COBRA methods
- Verify the COBRA Toolbox
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
- Refinement of genome-scale reconstructions through the DEMETER pipeline
- 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
Visualization ¶
Visualization ¶
- createMetIntrcNetwork: Metabolite-Metabolite network function for COBRA
- Introduction to Cell Designer
- Metabolic visualisation in ReconMap (Minerva)
- Paint4Net: visualisation toolbox for COBRA
- SAMMI Interactive Network Visualization Tool
- Visualisation and map manipulation in Cell Designer (PART 1)
- Visualisation and map manipulation in Cell Designer (PART 2)
- Visualize Elementary Flux Modes from E. coli model
- Visualize Elementary Flux Modes from Human model