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) and some non mandatory measurements options (.mflux, .mmet, .tvar, .cntsr, .opt). Let an example MTF set has 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 is that NA measurements are simulated and are present in the vectorssimulated unscaled labeling measurements
andsimulated scaled labeling measurements
in the result kvh file.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 the following files in the same directory thatmynetwok.*
:
mynetwork.ftbl
- FTBL is a previously used format as a front-end format. It is still in use but behind the scenes. This file can be necessary as entry for
ftbl2*
utilities.mynetwork.log
- contains the run-time output from various scripts, in particular, it contains a report on convergence history during the fitting process. It can be helpful for identifying potential problems, but if everything is going well, the user does not have to examine the content of this file;
mynetwork.err
- contains the warning and error messages. Normally, this file should be empty (0 byte size);
mynetwork_res.kvh
- contains all the results. KVH format is a lightweight plain text format for hierarchically structured data. It can be seen in a text editor or in a spreadsheet software as its fields are tab separated. It can also be processed by user’s custom software for post-processing, graphics output and alike. If
influx_si
is run on a series of starting points, there will be generated a common result filemynetwork_res.kvh
which contains common information to all starting points but also a series of kvh files, one by starting point, e.g.mynetwork_res.V1.kvh
,mynetwork_res.V2.kvh
and so on;mynetwork.pres.csv
- contains a matrix of fitted parameters and final cost values. Each column corresponds to a particular starting point if run with
--fseries
and /or--iseries
options. Ifinflux_si
was run without these options, the file will contain only one column corresponding to the starting point defined in themynetwork.tvar
file or to the random starting point.edge.netflux.mynetwok
,edge.xchflux.mynetwok
,node.log2pool.mynetwork
as the middle name of these files suggest, they can be used to map the corresponding values on the network graph in the cytoscape software.
Note
All these files are silently overwritten if already exist. So take care to copy your results elsewhere if you want to protect them from overwriting.
- custom files (e.g.
mynetwork.pdf
)- These files can be produced by user supplied scripts that are executed at the end of
influx_si
simulations. For example, we provide a scriptplot_ilab.R
which can be used to plot label kinetics simulated byinflux_i
. One or many of such custom scripts can be given in .opt file, fieldposttreat_R
(cf. e_coli_i.opt for example)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. 2 - Extract and use the numerical results from the
mynetwork_res.kvh
file. - 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 mappingedge.netflux.mynetwok.attrs
,edge.xchflux.mynetwok.attrs
ornode.log2pool.mynetwork.attrs
on graphical attributes like edge width, color etc. in cytoscape.