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Table 1 Feature comparison of several tools for metabolic network analysis.

From: OptFlux: an open-source software platform for in silico metabolic engineering

   Other tools
  OptFlux CellNetAnalyzer COBRA SBRT
File formats/standards     
- SBML
- Metatool format   
- Flat files
Phenotype simulation     
- FBA: wild type, environmental conditions, gene deletion mutants
- Dynamic FBA    
- ROOM    
- MOMA   (1)  
- MFA basic methods   
- Gene-reaction associations   
- Regulatory network simulation (2)   
Strain optimization     
- OptKnock algorithm    
- Metaheuristics: OptGene    
Metabolic Network Analysis     
- Elementary Flux Modes   
- Minimal cut sets    
- Flux Variability Analysis (FVA)
- Topological network analysis (2)   (3)
Visualization     
- Built-in visualization   
- Interaction with CellDesigner    
- Interaction with Cytoscape    
Other features     
- Graphical user interface   
- Does not depend on commercial software   
- User documentation
  1. Notes
  2. (1) Implementation based on linear programming formulation (linear MOMA)
  3. (2) Plug-ins under development
  4. (3) Includes some basic graph analysis methods
  5. The table provides a comparison of the main features of OptFlux with the major alternatives in metabolic network analysis. Features have divided into six groups: file formats and standards, phenotype simulation, strain optimization, network analysis, visualization and other features.