add docs dependencies and skeleton

docs/Project.toml

@@ -1,4 +1,7 @@
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+SBML = "e5567a89-2604-4b09-9718-f5f78e97c3bb"

docs/src/metabolic-modeling.jl

@@ -16,3 +16,36 @@ import JuMP, SBML
 
 import Downloads: download
 
+download("http://bigg.ucsd.edu/static/models/e_coli_core.xml", "e_coli_core.xml")
+
+ecoli = SBML.readSBML("e_coli_core.xml")
+
+# Let's first build the constrained representation of the problem. First, we
+# will need a variable for each of the reactions in the model:
+
+c = C.allocate_variables(keys = Symbol.(keys(ecoli.reactions)));
+
+@test length(C.elems(c)) == length(ecoli.reactions) #src
+
+# The above operation returns a `ConstraintTree`. You can browse these as a
+# dictionary:
+C.elems(c)
+
+# ...or much more conveniently using the record dot syntax as properties:
+c.R_PFK
+
+# Operator `^` is used to name individual constraints and directories in the
+# hierarchy. Let us name our constraints as "fluxes" (which is a common name in
+# metabolic modeling) and explore the result:
+
+c = :fluxes^c;
+
+# We can see that there is now only a single "top-level directory" in the
+# constraint system:
+collect(keys(C.elems(c)))
+
+@test collect(keys(c)) == [:fluxes] #src
+@test issetequal(collect(keys(c.fluxes)), sort(Symbol.(collect(keys(ecoli.reactions))))) #src
+
+# ...which can be explored with the dot access again:
+c.fluxes.R_PFK