In house Organisms:

Current News:

  • E. coli, H. pylori, S. aureus, S. cerevisiae, and H. sapiens may now be exported and browsed at the BiGG database. Note: In a few reconstructions, author specified sinks are not present. Please see reconstruction publication for details.
  • SBML (Systems Biology Markup Language,, level 2 version 1) versions of the in silico reconstructions are now available on each organism page. The script to generate these reconstructions is here.


Flux Balance Analysis

Extreme Pathway Analysis

SBML generator - SimPheny output specific

  • (A perl program that converts SimPheny output to SBML level 2, version 1)

Core E. coli Model

  • The core E. coli model and accompanying files.

Supplemental Data

Other material



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In Silico Lab:  858-822-1144

Wet Lab:  858-246-1625

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