added sybil IO for ecoli
sybil test2
Nothing much, just some test with sybil
function works now
changed and cleaned up ecoli.R
changes in diffbac and config
Working model with sybil, however still (old) negative substrate bug
Fixed negative substrate bug -> was just (again) stupid mistake of setting constraints
Added sybil model structure to data, so work independent of sybilSBML is possible (-;
Some thoughts on oop and first separate implementation
some minor changes.
Interesting observation: when switching from glpk to solver clp the negative substrate bug occurs again.
However, with the rounding of substrate the code works again.
tried to change other functions for sybil.
Changing bacterial movement didnt work,
commented out for now...
oop class model
arena class def
some minor changes (attributes added) in the oop tex file
Merge branch 'master' of https://github.com/euba/BacArena into sybil
Merge branch 'sybil' of https://github.com/euba/BacArena into sybil
del latex tmp stuff
added bac class in oop model
oop defs