Welcome to CBM’s documentation!

Constraint-based reconstruction and analysis (COBRA) methods are a collection of methods to analyze mathematically the metabolitic networks of organisms.

Here, we introduce CBM.jl, a new toolbox that implements a collection of COBRA methods. CBM.jl is written in the Julia

The purpose of CBM.jl is providing the broad range of functionality found in the other COBRA toolboxes, while being easy to use and provividing top of the line performance

We will actively maintain and improve CBM.jl, and in future releases, we plan to add to CBM.jl a strain design toolbox, novel algorithms along with implementing an interface to the libSBML parser to support models expressed in the SBML format

CBM.jl is available at the CBM github page

Contents:

• Getting Started
  • Installation
  • CBM Setup
  • First Run
• IO
  • Loading a model
  • Exporting a model
  • IO Tools
• Simulations
  • Flux Balance Analysis
  • Flux Variability Analysis
  • Find blocked reactions
  • Synthetic Lethal Genes
  • Robustness Analysis
  • Find Dead End Metabolites
  • Find Essential Genes
  • Find Exchange Reactions
  • Find Reactions From Gene
  • Find Reactions From Metabolite
  • Gene Deletion
  • Knockout Genes
  • Knockout Reactions
  • Print Reaction Formula
  • Reaction Info
• Modification
  • Adding a Metabolite
  • Adding a Reaction
  • Change the Objective Reaction
  • Change Reaction Bounds
  • Convert To Irreversible
  • Find Reversible Reactions
  • Convert To Reversible
  • Reduce Model
  • Remove Gene
  • Remove Reaction
• Solvers
  • Supported Solvers
  • Methods
• Julia Tips
  • Packages
  • Function names
  • Function argument signature
  • Getting help
  • Methods