Quick Start¶
A basic work-flow with influx_si
is composed of the following steps:
Create a MTF file set (Multiple TSV Files) describing your metabolic reactions and carbon transitions (.netw), experimental data (.miso) label input (.linp), some non mandatory measurements (.mflux, .mmet) and optional files providing initial values for estimated parameters, constraints and so on (.tvar, .cntsr, .opt). Let an example MTF set have a prefix
mynetwork
. The syntax rules for reactions will be more or less obvious to someone working on metabolism biochemistry. So, to go quickly, you can inspire from example filestest/mtf/e_coli.netw
and co. distributed with theinflux_si
software (runinflux_s --copy_test
to bring them to your current directory). You can also consult the help message fromtxt2ftbl -h
for--mtf
option.
Note
NA
values (as “Non Available”) are admitted as measurements values where appropriate. The difference with the situation where measurements are simply omitted from a file is that NA measurements are simulated and are present in the result files*.sim
while absent measurements are not.Note
In case of
influx_i
, label kinetics can be provided in .miso file using non-emptyTime
column. Empty cells inValue
column are equivalent toNA
.
Set your current directory to the directory of
mynetwork.*
and run$ influx_s.py --prefix mynetwork
or
$ influx_i.py --prefix mynetworkdepending on stationary or instationary labeling context. We suppose here that directory of
influx_si
binaries is in the PATH variable.An
influx_si
run will produce result files inmynetwok_res
directory. The detailed description of these files can be found in the next section. However, general idea is that simulated measurements are written in the files similar to MTF format with.sim
(as “simulated”) suffix appended, e.g.mynetwork.miso.sim
.Note
It can be helpful to do some “dry runs” by executing
$ influx_s.py --noopt --pref mynetworkbefore collecting actual measurement data to see if intended measurements will be sufficient to well define all fluxes, or at least the fluxes of interest. It is possible to do so because the measurement values in the .miso file have no impact on flux SD calculation when
--noopt
option is used. So it can be used any values, even NA at this moment. On the contrary,SD
values set in .miso file, must be realistic. It is generally not a problem as they express measurements errors and are more or less known for a given measurement method.It is worthwhile to stress that a “dry run” is done for some presumed free flux values. If they reveal to be very different from actual flux values, it can happen that a network considered as well defined at moment of “dry run” turned into a badly defined network with actual measurement data and corresponding estimated fluxes. So it is important to do his best to guess the most realistic free fluxes for “dry runs” and log their values in .tvar file.
See warning and error messages in
mynetwork.err
if any. Correct what has to be corrected and retry p. 2Extract and use the numerical results from the
mynetwork_res/*.sim
files.Optionally, visualize net fluxes (or exchange fluxes or logarithm of metabolite concentrations \(\log_2(M)\)) in cytoscape using
ftbl2xgmml
to produce a .xgmml file and then mapping files frommynetwork_res/tmp
(edge.netflux.mynetwok.attrs
,edge.xchflux.mynetwok.attrs
ornode.log2pool.mynetwork.attrs
) to graphical attributes like edge width, color etc. in cytoscape.