inst/extdata/README.md

In artedison/ensRadaptor: Metabolic model creator for ensemble method

explanation of provided data

the latest ens code

./enscode

collected kinetic information for Neurospora crassa

./kin_infor

If the user need to prepare this for other specific organisms, they need parepare a list of km and kcat range and specific value in databases just as all.kine.RData or Neurospora crassa.kine.new.RData. The sublist will be with name of reaction.

the stored measurement files

./measurements

If the user need to prepare this for input, they need to parepare quantification of each compounds as a dataframe in a list. Multiple experiment or replicate can be included as in "exp".

the pathway reaction list

./pathway

The format should be easy to follow and names of reaction, compound, and enzymes should in agreement with the script. The start of each line "Reaction (\d)" isn't read.

template format under ./template_format

This is used by function to format output

spec.metabolite.tab: the default metabolite formatting template under ens.i01

spec.enz.massscal.tab: the enzyme formatting template under ens.i01 with supporting on biomass proportions (all enzyme concentration are proportional with biomass)

reac.rev.mm.tab: the reversible reaction formatting template under ens.i01

reac.irrev.mm.tab: the irreversible reaction formatting template under ens.i01

comb_glycolysis.tab: the combined/simplified reaction for glycolysis ens.i01

addon.comb.meas.tab: the template for formulating combined measurement: the measured signal is a weighted sum of internal and external concentrations

addon.scalenz.tab: the template for formualting biomass proportions for all enzymes

addon.aero.vs.anaero.tab: the template for formualting different reactions under aerobic and anaerobic conditions

data used in tests

./internal_data

artedison/ensRadaptor documentation built on Dec. 8, 2020, 5:31 p.m.