pysb/pysb

Python framework for Systems Biology modeling

Rodrigo Santibáñez

@glucksfall

you could convert the kappa model into ODEs with KaDE (part of the kappatools)

what I do is convert kappa into sbml with KaDE and then use libroadrunner to simulate

Zelun Li

@lzl0719

Sorry, could you point me to the documentation? I couldn't find it?

Rodrigo Santibáñez

@glucksfall

try this https://kappalanguage.org/sites/kappalanguage.org/files/inline-files/Kappa_Manual.pdf

Zelun Li

@lzl0719

Sorry for having so many questions, is there any way to do sensitivity analysis with this?

Rodrigo Santibáñez

@glucksfall

I believe pysb has a function to do SA, and I'm developing a package to do SA from kappa models

Zelun Li

@lzl0719

Yes, but if I want to use Expression in my model, I will need to use Kappa simulator for my model, is that right?

Rodrigo Santibáñez

@glucksfall

maybe not...

KaDE --ode-backend sbml model.kappa (after the correction)

and use tools such as copasi to analyse the model

libroadrunner could perform metabolic control analysis that is a type of SA

Rodrigo Santibáñez

@glucksfall

network.xml

that's the output of kade

Zelun Li

@lzl0719

Do I need to install something to use KaDE?

Rodrigo Santibáñez

@glucksfall

yeap... download the compiled kappatools from the github

otherwise, good luck installing opam and other things to compile from source

Zelun Li

@lzl0719

And I would also need to install libroadrunner? is there a version for Linux?

Rodrigo Santibáñez

@glucksfall

is a python package

Princeofthebow

@Princeofthebow

Hi there pretty new to Pysb and I'm trying to start to use if for some calculations.

I have encoutered however the following error:

FileNotFoundError: [WinError 2] The system cannot find the file specified when running the tutorial code.

I'm using biogennet 2.5.1, may this be the issue?

This is the code I'm trying to run

from pysb import *
from pysb.simulator import ScipyOdeSimulator

Model()
Monomer('A')
Parameter('k', 3.0)
Rule('synthesize_A', None >> A(), k)
t = [0, 10, 20, 30, 40, 50, 60]

simulator = ScipyOdeSimulator(model)
simresult = simulator.run()
print(simresult.species)

Rodrigo Santibáñez

@glucksfall

Hi @Princeofthebow, there is a small problem with your code (missing t in ScipyOdeSimulator:

from pysb import *
from pysb.simulator import ScipyOdeSimulator

Model()
Monomer('A')
Parameter('k', 3.0)
Rule('synthesize_A', None >> A(), k)
t = [0, 10, 20, 30, 40, 50, 60]

simulator = ScipyOdeSimulator(model, t)
simresult = simulator.run()
print(simresult.species)

You need to add BNG2.pl to the path. You could use from pysb.pathfinder import set_path and then set_path('bng', path_to_BNG2.pl)

Rodrigo Santibáñez

@glucksfall

if you installed BNG2 with conda, something like this should work set_path('bng', 'C:/Users/gluck/Anaconda3/share/bionetgen') (change gluck by your user)

Princeofthebow

@Princeofthebow

OK - cool I did not know biogennet used pearl so I will have to install that as well

I did though succesfully add the .pl to the path and only after doing so it gave me the error you see.

I'll check after installing pearl

BTW I'm running everyhting from Jupyter, no Anaconda

Princeofthebow

@Princeofthebow

Ok excellent, both needed fixing and now it works!

Rodrigo Santibáñez

@glucksfall

Great to know!! Feel free to ask anything. BTW, I'm a user of pySB, not part of the dev team.

Princeofthebow

@Princeofthebow

Cool thanks

I'm actaully getting into it as I woudl like to run gillespie via GPUs

have you ever used this functionality?

Rodrigo Santibáñez

@glucksfall

No, but I would like to do that.

Princeofthebow

@Princeofthebow

cool I'll tryo to keep you in the loop with a MVE if I get somewhere :-)

Rodrigo Santibáñez

@glucksfall

sure, no problem at all

Princeofthebow

@Princeofthebow

Hi sorry it is me again, I ahve some trouble in understading how the rule definitions work(I'm an engineer and I'm not too familiar with some concepts)

I would need to model this reaction

where R(A) is a function that depdends non linearly on A

does anybody know how to do it in pysb?

Rodrigo Santibáñez

@glucksfall

using Expression: https://pysb.readthedocs.io/en/stable/faq.html#rule-and-reaction-rate-laws

Princeofthebow

@Princeofthebow

ow wow thanks I had not spotted that

Rodrigo Santibáñez

@glucksfall

no problem ;)

Princeofthebow

@Princeofthebow

Hi I tried it but it results on an error

from pysb import *
from pysb.pathfinder import set_path
from pysb.simulator import ScipyOdeSimulator
set_path('bng', 'C:\Program Files\BNG')

Model()
Monomer('A',['a'])
Observable('A_total', A())
Parameter('Hcoeff',1.0)
Expression('kf_A', A_total*Hcoeff)
Rule('bindA', A(a=None) + A(a=None) >> A(a=1) % A(a=1), kf_A)
Parameter('A0',20)
Initial(A(a=None),A0)

simres = ScipyOdeSimulator(model, tspan=[0,20]).run()

This is the error I get:

AttributeError: 'str' object has no attribute 'args'

Is there some problem with my code?

Rodrigo Santibáñez

@glucksfall

Oh... right. Sorry, I forgot to mention. Last week, another user asked the same about Expression. It seems there is a problem when converting the model into ODEs. The solution, if you could read the conversation history, was export the model into kappa, edit by hand because the observable must be before the parameter that use the observable, and simulate the model using the command line (KaSim).

Princeofthebow

@Princeofthebow

ok that looks tough as I am totally new to this. I simply submitted an issue on the github. Lets see where it gets

rAntonioH

@rAntonioh

hi, i'm trying to set the max_stoich option in BioNetGen using pysb, however generate_network(Model, cleanup=False, **{'max_stoich':3}) results in the following error:

AttributeError: type object 'Model' has no attribute 'rules'

this is of course not 'True' because i have written rules, any advice on how to address this?

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