Tutorials ¶
Analysis ¶
Analysis ¶
- Flux Balance Analysis
- Flux Balance Analysis
- Flux Balance Analysis (FBA) and its variants
- Flux Variability analysis (FVA)
- ICON-GEMs
- Flux Balance Analysis: Alternate optimal solutions
- Flux Balance Analysis: Alternate optimal solutions
- Atomically resolve a metabolic reconstruction
- Atomically resolve a metabolic reconstruction
- Benchmark solvers for solving whole body metabolic models
- Browse Networks in the Matlab Command Window Using surfNet
- Initialisation of conserved moiety tutorials
- Analyse properties of conserved moieties
- Build Atom Transition Multigraph
- Identify Conserved Moieties
- Visualise conserved moieties in dopaminergic neuronal metabolism
- Entropic flux balance analysis
- Reaction essentiality across multiple models
- genetic Minimal Cut Sets - gMCS
- Flux Balance Analysis
- Computation and analysis of rescued lethal gene deletions in a host-microbe model
- Computation and analysis of microbe-microbe metabolic interactions
- Creation, interrogation, and analysis of personalized microbiota models from the AGORA models through metagenomic data integration
- Determining MinSpan vectors of COBRA model
- Numerical properties of a reconstruction
- Numerical properties of a whole body metabolic model
- Nutrition Algorithm Walkthrough
- A step-by-step guide to parsimoneous enzyme usage Flux Balance Analysis - pFBA
- Quadruple precision Flux Balance Analysis
- Robust Metabolic Transformation Analysis - rMTA
- Relaxed Flux Balance Analysis: Recon 3
- Relaxed Flux Balance Analysis: Toy model
- Varying Parameters analysis
- Sensitivity of a flux balance analysis solution with respect to input data
- 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
- Proton shuttle testing with sparse flux balance analysis
- Sparse Linear Optimisation
- Analyze Steady-State Community COBRA Models
- A step-by-step guide to parsimoneous enzyme usage Flux Balance Analysis - pFBA
- Analyze Steady-State Community COBRA Models
- A step-by-step guide to parsimoneous enzyme usage Flux Balance Analysis - pFBA
- Analyze Steady-State Community COBRA Models
- Uniform sampling of E. coli core
- Uniform sampling of E. coli core via Constrained Riemannian Hamiltonain Monte Carlo (CRHMC)
- Uniform sampling a genome-scale model
- Variational Kinetics
- Analyse combinedModel, input to component contribution
- Apply updated component contribution method to Recon3D and analyse solution
- Subset of a model that admits a thermodynamically consistent flux
- Thermodynamically constrain a metabolic model
- Thermodynamically constrain Recon3D
- Thermodynamically constrain a metabolic model
Base ¶
Base ¶
- Input and output of reconstructions and models
- Contribute to the COBRA Toolbox with MATLAB.devTools
- Engaging with The COBRA Toolbox community
- Initialise the COBRA Toolbox
- Initialise and verify The COBRA Toolbox
- (tbc) Introduction to the COBRA Toolbox
- Introduction to MATLAB
- Practical on Flux Balance Analysis and its applications
- Primer on Flux Balance Analysis and its applications
- Primer on Non-FBA based COBRA methods
- Verify the COBRA Toolbox
Data integration ¶
Data integration ¶
- Extraction of context-specific models via XomicsToModel
- Extraction of context-specific models
- Fit a COBRA model to an experimental flux vector
- MetaboAnnotator: An efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions
- Metabotools tutorial I
- Metabotools tutorial II - Integration of quantitative metabolomic data
- Extract a thermodynamically consistent subnetwork from a given model
- Extract a thermodynamically consistent subnetwork from a given model
- unsteady-state Flux Balance Analysis (uFBA)
Design ¶
Reconstruction ¶
Reconstruction ¶
- Constraint-based modelling concepts
- Adding more complex constraints on a model
- Adding biological constraints to a flux balance model
- Create a generic subnetwork from Recon 3D
- Refinement of genome-scale reconstructions through the DEMETER pipeline
- E.coli Core Model for Beginners (PART 1)
- E.coli Core Model for Beginners (PART 2)
- E.coli Core Model for Beginners (PART 3)
- FastGapFill tutorial
- Testing chemical and biochemical fidelity
- Find leakage and siphon modes in a reconstruction
- Test physiologically relevant ATP yields from different carbon sources for a metabolic model
- How to use modelBorgifier
- Creating a Model
- Model manipulation
- Create an overview table with model properties
- Testing basic properties of a metabolic model (aka sanity checks)
- Generation and manipulation of reconstructions with rBioNet
- Convert a reconstruction into a flux balance analysis model
- Convert a reconstruction into a flux balance analysis model
- Example use of functions listed in the Standard operating procedure for metabolic reconstruction.
Visualization ¶
Visualization ¶
- Visualize Elementary Flux Modes from E. coli model
- Visualize Elementary Flux Modes from Human model
- SAMMI Interactive Network Visualization Tool
- Introduction to Cell Designer
- createMetIntrcNetwork: Metabolite-Metabolite network function for COBRA
- Visualisation and map manipulation in Cell Designer (PART 1)
- Visualisation and map manipulation in Cell Designer (PART 2)
- Extraction of a submap from a Cell Designer map (PART 3)
- Paint4Net: visualisation toolbox for COBRA
- Metabolic visualisation of Recon3Map with Minerva