Analysis of optimality in natural and perturbed metabolic networks

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• Supporting Information
  for the manuscript Analysis of optimality in natural and perturbed metabolic networks
  by Daniel Segre' , Dennis Vitkup and George M. Church, Proc. Natl. Acad. Sci. USA (2002), 99(23), 15112-15117 [ PNAS site, PubMed, pdf ]

• Interactive prediction of E. coli mutant phenotypes using Minimization of Metabolic Adjustment

• Downloadable Minimal Perturbation Analysis (MOMA) software:
  • Latest Windows version (tested on Windows 2000): moma_win2000.tar
  • Latest Unix version (Self-contained tar, 2 Mb): moma_Ecoli_linux_Apr2004.tar
  • Latest Unix version (as above, gzipped, 300 Kb): moma_Ecoli_linux_Apr2004.tar.gz
  • Optimization libraries: Object Oriented Quadratic Programming (OOQP), GNU linear programming kit (GLPK)
  • Older MOMA Perl script: mpa_5_17.pl
    Supplementary files: glpsol_dan.c, glpsol_dan.exe
    MOMA software documentation, IBM Quadratic Programming
  • E. coli parameter files (for comparison with Edwards and Palsson) [ S.par , constraintsJ.par , objvector.par ]
  • E. coli parameter files (for comparison with Emmerling et al.) [ S.par , constraintsS.par , objvector.par ]

• MOMA in BioSPICE
  • Harvard's BioSPICE MOMA client and server OAA agents for linux and windows
  • BioSPICE main page

• Links
  • Flux Balance Analysis software (see also FluxAnalyzer )
  • List of E. coli reactions (from Palsson's group)
  • Flux Balance Analysis primers (Palsson's group): [1] [2]
  • Edwards and Palsson, PNAS, 97, 5528-5533 (2000)
  • Badarinarayana et al., Nature Biotech., 19, 1060-1065, 2001
  • Link to data from Badarinarayana et al.
  • Emmerling et al., J. Bacteriology, 184(1), 152-164 (2002)

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Last update: Daniel Segre', February 19, 2004

dsegre [at] genetics.med.harvard.edu