update scalaflux wf

Author: Pierre Millard

README.md

@@ -72,9 +72,9 @@ On Linux, install the R development package, usually called `r-devel` or `r-base
     This function builds a test model (network shown in Figure 1A of IsoSim publication), simulates labeling kinetics, and recalculates some fluxes from this theoretical dataset. Most of 
     the practical situations and features should be covered by these tests.
 
-  A folder `test` containing all the results should be created in the working directory (here `/home/usr/isosim/isosim/test/`), and no error should be displayed.
-  If an error is displayed at the compilation step, check that the set of R development tools is correctly installed. 
-  Please refers to IsoSim code or submit a new issue to our [GitHub issue tracker](https://github.com/MetaSys-LISBP/IsoSim/issues) for other problems.
+A folder `test` containing all the results should be created in the working directory (here `/home/usr/isosim/isosim/test/`), and no error should be displayed.
+If an error is displayed at the compilation step, check that the set of R development tools is correctly installed. 
+Please refers to IsoSim code or submit a new issue to our [GitHub issue tracker](https://github.com/MetaSys-LISBP/IsoSim/issues) for other problems.
 
 ## ScalaFlux: Scalable <sup>13</sup>C-metabolic flux analysis
 

doc/scalaflux_workflow.md

@@ -270,6 +270,7 @@ Results are saved in subfolder `res_fit_enr`:
 
   ```bash
   subsystem (list):
+    $name (str):                name of the subsystem
     $rxn_subnet (list):         definition of the [subnetwork](#construct-a-metabolic-model) of interest
     $meta_conc_subnet (vector): named vector of [initial metabolite concentrations](#simulate-labeling-dynamics)
     $kp_subnet (vector):        named vector of [model parameters](#simulate-labeling-dynamics)
@@ -321,13 +322,13 @@ Results are saved in subfolder `res_fit_enr`:
   > res_sub <- fit_subsystems(subsystem_1)
   ```
 
-  Or pass the list of subsystems to analyze all of them at once:
+  Or pass directly the full list of subsystems/datasets to analyze:
 
   ```bash
   > res_sub <- fit_subsystems(subsystems, mc.cores=numCores)
   ```
 
-  Flux calculation results are saved in subfolder `fit_subnet_n` (where `n` is the name of the subsystem, e.g. `subsystem_1$name`):
+  Flux calculation results are saved in subfolder `fit_subnet_n` (where `n` is the name of the subsystem, i.e. which is in `$name`):
 
   `results.pdf`: plot of exp. vs fitted labeling dynamics of all metabolites
   
@@ -337,7 +338,7 @@ Results are saved in subfolder `res_fit_enr`:
 
 - Save the complete flux calculation results:
 
-  To save detailed results (containing the network structure, experimental and fitted data, etc), run:
+  To save detailed results (containing the network structure, experimental data, optimization details, etc), run:
 
   ```bash
   > list2file(res_sub, file="results_minimal_subsystems.txt")