Open jotech opened 3 years ago
external enzymes can be added either by defining diffusion and transport partial differential equations using the reactran package or by simply adding the external enzymes as an pseudo-organism which is metabolic model containing just the enzymatic reactions + exchange reactions. As an example, I used this code to model an sucrose invertase that splits sucrose to glucose and fructose:
suc <- sybil::modelorg(id = "sucrase", name = "sucrase")
suc@mod_desc <- "external enzyme"
suc <- addReact(suc, id="EX_cpd00076_e0", met=c("cpd00076[e0]"), Scoef=c(-1))
suc <- addReact(suc, id="EX_cpd00027_e0", met=c("cpd00027[e0]"), Scoef=c(-1))
suc <- addReact(suc, id="EX_cpd00082_e0", met=c("cpd00082[e0]"), Scoef=c(-1))
suc <- addReact(suc, id="sucrose_invertase", met=c("cpd00027[e0]", "cpd00082[e0]", "cpd00076[e0]"), Scoef=c(1,1,-1))
suc@lowbnd <- c(-10,-10,-10,0)
suc <- changeObjFunc(suc, react="sucrose_invertase", obj_coef = 1)
arena <- Arena(n=20,m=20)
arena <- addOrg(arena, Human(suc, maxweight=Inf, cellweight_mean=0.01), amount=10)
Hope this provides some help how it could be tackled!
Thanks a lot, @jotech. It is very helpful!
One question is what is "Human(suc, maxweight=Inf, cellweight_mean=0.01)"? Is "Human" a function? Thanks again!
All the best, Xuejian
Hello! Is there any way where I can pair the external enzyme to the model organism? For example, I wanted to pair the external enzyme with the model so that the products metabolized by the external enzyme can be consumed by the organism. Thank you for your help! Shraddha
How can I add an extra enzyme, amylase 3.2.1.1, into the BacArean system using addSubs() ? Thank you!
Best, Xuejian
Originally posted by @XuejianXiong in https://github.com/euba/BacArena/issues/161#issuecomment-808322625