Table 1 |
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Feature comparison of several tools for metabolic network analysis. |
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Other tools |
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|
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OptFlux |
CellNetAnalyzer |
COBRA |
SBRT |
|
|
|
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File formats/standards |
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|
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- SBML |
• |
• |
• |
• |
|
|
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- Metatool format |
• |
• |
||
|
|
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- Flat files |
• |
• |
• |
• |
|
|
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Phenotype simulation |
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|
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- FBA: wild type, environmental conditions, gene deletion mutants |
• |
• |
• |
• |
|
|
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- Dynamic FBA |
• |
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|
|
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- ROOM |
• |
|||
|
|
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- MOMA |
• |
(1) |
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|
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- MFA basic methods |
• |
• |
||
|
|
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- Gene-reaction associations |
• |
• |
||
|
|
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- Regulatory network simulation |
(2) |
• |
||
|
|
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Strain optimization |
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|
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- OptKnock algorithm |
• |
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|
|
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- Metaheuristics: OptGene |
• |
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|
|
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Metabolic Network Analysis |
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|
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- Elementary Flux Modes |
• |
• |
||
|
|
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- Minimal cut sets |
• |
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|
|
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- Flux Variability Analysis (FVA) |
• |
• |
• |
• |
|
|
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- Topological network analysis |
(2) |
• |
(3) |
|
|
|
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Visualization |
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|
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- Built-in visualization |
• |
• |
||
|
|
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- Interaction with CellDesigner |
• |
|||
|
|
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- Interaction with Cytoscape |
• |
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|
|
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Other features |
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|
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- Graphical user interface |
• |
• |
||
|
|
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- Does not depend on commercial software |
• |
• |
||
|
|
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- User documentation |
• |
• |
• |
• |
|
|
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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. |
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Rocha et al. BMC Systems Biology 2010 4:45 doi:10.1186/1752-0509-4-45 |
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