some more networkapi functions ?

[yewalenikhil65]

Based on #318

for now, i have written this in a form of tutorial ! Should this be in tutorial form Or should we add some more networkapi functions for incidence matrix of complexes , complex stoichiometric matrix , outgoing matrix, Laplacian matrix and so on?

[isaacsas]

@yewalenikhil65 very nice! I think it would make more sense though to add some of these intermediate matrix representations to the API, and then have the tutorial show something cool one can do using them. What do you think?

[yewalenikhil65]

@yewalenikhil65 very nice! I think it would make more sense though to add some of these intermediate matrix representations to the API, and then have the tutorial show something cool one can do using them. What do you think?

Yes, i think having these matrices as output of some networkapi functions makes sense. I shall add these matrices into networkapi after testing more tonight.. As for tutorial to do something nice using them, i will do that in few days soon.

[yewalenikhil65]

@isaacsas , added a complexstoichmat function to networkapi. Please check for improvements if any in the loops. I would suggest to not quickly merge, as i plan to come soon with brief tutorial of application of this function to some problem.

[isaacsas]

Could you also add tests for some examples to make sure the returned matrices are all correct?

[yewalenikhil65]

Could you also add tests for some examples to make sure the returned matrices are all correct?

Yup, .. any suggestion on what kind of reactions i should preferably use for tests ?

[isaacsas]

I'd suggest systems with a variety of reactions, including non-mass action reactions if they make sense, and where you know the answer (either from a paper, or from working it out by hand).

[isaacsas]

@yewalenikhil65 will take a look later in the week, I’m swamped through Thursday currently.

[yewalenikhil65]

@yewalenikhil65 will take a look later in the week, I’m swamped through Thursday currently.

No problem

[yewalenikhil65]

Hi @isaacsas
Didn't get time to follow up this later in past month(COVID issues at home)

There example is missing a demonstration for the use of these functions. Will start to work on it this week.

[isaacsas]

@yewalenikhil65 what is the status on this PR? Are you done with it? (Your last comment said there was more you planned to do.)

[yewalenikhil65]

@yewalenikhil65 what is the status on this PR? Are you done with it? (Your last comment said there was more you planned to do.)

hi @isaacsas wrapping it up here yewalenikhil65#2 (comment)
would you please take a look and suggest/improve it ?
should this be okay as a tutorial for demo of these new functions ?

[yewalenikhil65]

@isaacsas closing this PR , and will come up with new PR with functions + proposed tutorial

[isaacsas]

@yewalenikhil65 sorry for my delays with this one. If you feel this is done and in good shape I can review; I just wasn't clear if you had further updates you intended to make or not!

I'll look through your comment -- somehow I missed that in the previous discussion.

[yewalenikhil65]

@yewalenikhil65 sorry for my delays with this one. If you feel this is done and in good shape I can review; I just wasn't clear if you had further updates you intended to make or not!

I'll look through your comment -- somehow I missed that in the previous discussion.

@isaacsas sure.. please do review yewalenikhil65#2 (comment) , so that we can decide whether it goes well with the complex-stoichiomatrices matrices functions in networkapi.jl that i proposed earlier.
I will add a new PR for this one.