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

BMC Systems Biology

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

		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	•	•	•	•

Notes
(1) Implementation based on linear programming formulation (linear MOMA)
(2) Plug-ins under development
(3) Includes some basic graph analysis methods
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.

ISSN: 1752-0509