Update/Simplify README

README.Rmd

@@ -75,30 +75,16 @@ TODO
 
 The full documentation including illustrative examples is available [here](https://waschina.github.io/cobrar/).
 
-The following (very brief) example illustrates how to use `cobrar` to perform flux balance analysis for a core metabolism model of *Escherichia coli*. In a first simulation, fluxes and growth are predicted for the default constraints of the model, which represents a minimal medium with glucose as the sole carbon source and the presence of oxygen. The second simulation performs the same flux balance analysis but without oxygen to simulate an anoxic growth environment.
+A simple Flux Balance Analysis (FBA) for the core metabolism of *Escherichia coli*:
 
 
 ```{r example}
-# First, load the cobrar package and the metabolic model:
 library(cobrar)
+
 fpath <- system.file("extdata", "e_coli_core.xml", package="cobrar")
 mod <- readSBMLmod(fpath)
 
-# Next, perform simulation 1: Aerobic growth of E. coli
-res_aero <- fba(mod)
-
-# Finally, simulation 2: Anaerobic growth of E. coli
-mod <- changeBounds(mod, react = "EX_o2_e", lb = 0) # before: -1000
-res_anaero <- fba(mod)
-
-# Report simulation results (i.e., growth and acetate production)
-cat("[Aerobic growth]\n",
-    " Growth rate:        ", res_aero@obj,"\n",
-    " Acetate production: ", res_aero@fluxes[mod@react_id == "EX_ac_e"],"\n\n",
-    "[Anaerobic growth]\n",
-    " Growth rate:        ", res_anaero@obj,"\n",
-    " Acetate prodcution: ", res_anaero@fluxes[mod@react_id == "EX_ac_e"],"\n",
-    sep = "")
+fba(mod)
 ```
 
 ## Key differences to sybil
@@ -124,7 +110,7 @@ cat("[Aerobic growth]\n",
 
 - *cobrar* exports SBML files level 3 version 2 with `fbc` version 3 and `groups` version 1. 
 - Group assignments are only supported for reactions.
-- currently only glpk is supported as solver. A plugin for IBM's ILOG CPLEX is planned.
+- GLPK is the default solver and is required to build the package. A plugin for IBM's ILOG CPLEX is available [here](https://github.com/Waschina/cobrarCPLEX).
 - *Multiple objectives*. The SBML standard with its `fbc` extension allows to specify more than one objective (class `ListOfObjectives`). However, *cobrar* can only handle one current objective function per model, which is defined as an objective coefficient vector in slot `obj_coef` of an object of class `modelorg`. Note that when reading SBML models, *cobrar* will only use the first objective defined in the SBML document.
 
 ## References

README.md

@@ -82,46 +82,25 @@ TODO
 The full documentation including illustrative examples is available
 [here](https://waschina.github.io/cobrar/).
 
-The following (very brief) example illustrates how to use `cobrar` to
-perform flux balance analysis for a core metabolism model of
-*Escherichia coli*. In a first simulation, fluxes and growth are
-predicted for the default constraints of the model, which represents a
-minimal medium with glucose as the sole carbon source and the presence
-of oxygen. The second simulation performs the same flux balance analysis
-but without oxygen to simulate an anoxic growth environment.
+A simple Flux Balance Analysis (FBA) for the core metabolism of
+*Escherichia coli*:
 
 ``` r
-# First, load the cobrar package and the metabolic model:
 library(cobrar)
 #> Loading required package: Matrix
 #> cobrar uses...
-#>  - libSBML (v. 5.18.0)
-#>  - glpk (v. 4.65)
+#>  - libSBML (v. 5.19.0)
+#>  - glpk (v. 5.0)
+
 fpath <- system.file("extdata", "e_coli_core.xml", package="cobrar")
 mod <- readSBMLmod(fpath)
 
-# Next, perform simulation 1: Aerobic growth of E. coli
-res_aero <- fba(mod)
-
-# Finally, simulation 2: Anaerobic growth of E. coli
-mod <- changeBounds(mod, react = "EX_o2_e", lb = 0) # before: -1000
-res_anaero <- fba(mod)
-
-# Report simulation results (i.e., growth and acetate production)
-cat("[Aerobic growth]\n",
-    " Growth rate:        ", res_aero@obj,"\n",
-    " Acetate production: ", res_aero@fluxes[mod@react_id == "EX_ac_e"],"\n\n",
-    "[Anaerobic growth]\n",
-    " Growth rate:        ", res_anaero@obj,"\n",
-    " Acetate prodcution: ", res_anaero@fluxes[mod@react_id == "EX_ac_e"],"\n",
-    sep = "")
-#> [Aerobic growth]
-#>  Growth rate:        0.8739215
-#>  Acetate production: 0
-#> 
-#> [Anaerobic growth]
-#>  Growth rate:        0.2116629
-#>  Acetate prodcution: 8.503585
+fba(mod)
+#> algorithm:              FBA 
+#> generic status:         solution is optimal 
+#> solver status message:  optimization process was successful 
+#> Objective fct. value:   0.8739215 
+#> Secondary objective:    NA
 ```
 
 ## Key differences to sybil
@@ -163,8 +142,9 @@ cat("[Aerobic growth]\n",
 - *cobrar* exports SBML files level 3 version 2 with `fbc` version 3 and
   `groups` version 1.
 - Group assignments are only supported for reactions.
-- currently only glpk is supported as solver. A plugin for IBM’s ILOG
-  CPLEX is planned.
+- GLPK is the default solver and is required to build the package. A
+  plugin for IBM’s ILOG CPLEX is available
+  [here](https://github.com/Waschina/cobrarCPLEX).
 - *Multiple objectives*. The SBML standard with its `fbc` extension
   allows to specify more than one objective (class `ListOfObjectives`).
   However, *cobrar* can only handle one current objective function per