Location	Comment
ProteinDegradationTest.m (6)	degradationRate = [0.001 0.01 0.1]; % !Find a reasonable value
txtl_prom_plambda.m (89)	%! make all these reactions conditional on specie availability
txtl_prom_ptet.m (89)	%! make all these reactions conditional on specie availability
txtl_prom_ptet.m (90)	%! has this todo been accomplished? Vipul 2/10/13
txtl_protein_betaGal.m (111)	%! include enzyme concentraction
txtl_prom_ptrc2.m (78)	%! replace these values with correct values
txtl_prom_ptrc2.m (162)	%! make all these reactions conditional on specie availability
txtl_prom_ptet2.m (4)	%! Header needs to be updated (RMM didn't write this file; 29 Sep 2012)
txtl_prom_ptet2.m (5)	%! This file is not properly named; promoter is ptet, not ptet2 ??
txtl_prom_ptet2.m (48)	%! replace these values with correct values
txtl_prom_ptet2.m (77)	%! Looks like lacI is used instead of tetR??? (RMM, 29 Sep 2012)
txtl_prom_ptet2.m (78)	%! I don't see the dimer binding; just the monomer??? (RMM, 29 Sep 2012)
txtl_buffer.m (2)	%! add documentation
txtl_extract.m (2)	%! add documentation
txtl_add_dna.m (325)	% !add error checking for numerical values for the lengths.
txtl_setup_default_basepair_length.m (42)	%! 12/08/12 zoltuz - later on deafaultBasePairs should come from
txtl_setup_default_basepair_length.m (43)	%the config files - that's way tube is provided
txtl_plot.m (86)	%! further refinement of str spliting
txtl_plot.m (103)	%! skip already added proteins and mRNAs to avoid duplicates
txtl_plot.m (347)	%! handle only color expressions
findspecies.m (16)	%! zoltuz 1/10/12 cellfun for speed up: find(cellfun(@(x)
findspecies.m (29)	% !zoltuz 1/10/12 intersect for speed up
txtl_gfp_lookuptable.m (3)	%! zoltuz 1/15/13 make this function configurable (lab independent)
txtl_runsim.m (69)	%! zoltuz 2/4/13 review this part
txtl_adddna.m (321)	% !add error checking for numerical values for the lengths.
txtl_utr_rbs.m (55)	%! 12/8/12 zoltuz - find out why we need the RiboBound here!