ModelSEED/ModelSEED — pull request #160 by mdejongh (2012-11-18 03:15:56+00:00)
Title: Cytoseed nov17

Initial commit of code to print a file that Cytoseed can read (using version under development). Here are the steps needed to get the model ready for Cytoseed. Note that "set_abstract_fatty_acids.pl" and "scott.pl" only need to be run once after the biochemistry and then the mapping is imported. This should be done once and for all in the distrubted biochemistry and mapping.

ms import biochemistry main --verbose
perl set_abstract_fatty_acids.pl biochemistry/mdejongh/main
ms import mapping map --biochemistry main -v
perl scott.pl mapping/mdejongh/map biochemistry/mdejongh/main
ms import annotation 83333.1 ecoli --mapping map -v
ms genome buildmodel annotation/mdejongh/ecoli Seed83333.1 -v
model gapfill Seed83333.1 -v
model managesol Seed83333.1 -v --solution "GF0.0"
model runfba -o Seed83333.1 > fba.out
model runfba -o --fva Seed83333.1 > fba.out