anNET

anNET affords a generalized framework for Network Embedded Thermodynamic (NET) analysis of quantitative metabolomic datasets. Building upon principles of thermodynamics, this method allows for a quality check of measured metabolite concentrations and enables to spot metabolic reactions where active regulation potentially controls metabolic flux.

The applications of anNET are multiple, for example:

• Check thermodynamic consistency
• Estimate unmeasured concentrations
• Resolve concentrations in different compartments
• Find minimum/maximum feasible NADH/NAD ratio or adenylate energy charge
• Infer reaction direction
• Verify reversibility in model
• Spot putative control sites
• Exclude activity of transporters

Requirements

Matlab 6.0 or higher (tested on Windows and Linux)
Matlab Optimization Toolbox 3 (The Mathworks) or Lindo API (Lindo Systems, Inc.)

References

• Kümmel, Panke, and Heinemann, Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol. 2006;2:2006.0034. external pagePubmedcall_made
  
• Zamboni, Kümmel and Heinemann, anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data, BMC Bioinformatics 2008, 9:199. external pageBMCcall_made