that's the output of kade
otherwise, good luck installing opam and other things to compile from source
:)
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)
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)
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
I'm actaully getting into it as I woudl like to run gillespie via GPUs
have you ever used this functionality?
where R(A) is a function that depdends non linearly on A
does anybody know how to do it in pysb?
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?
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).
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?
Hi, everyone, I am new to pysb and have some questions about update monomer state in a list of complex, would anyone help me ? Thanks a lot ! I have a list of complex including(binding to) a common monomer. I create the list by SpeciesPatternMatcher. I would like to update the state of the particular monomer from 'u' to 'p' and create a corresponding list of complex, I am wondering if there is any easy way such as a function in library ? Thanks a lot !
@lu-250 The general pattern for this, with a monomer
A, binding site b, and phosphorylation site s, is Rule('r1', A(s='u') >> A(s='p'), kf). The left hand side of the rule, A(s='u'), determines what's matched by the rule. Note that no binding site is included in that rule, so the phosphorylation will apply regardless if A is bound or not. If you want the phosphorylation reaction to only apply to A units which are in complex, but you don't care what the binding partner is, you can use the ANY keyword to specify "any bond, but not unbound", i.e. Rule('r2', A(b=ANY, s='u') >> A(b=ANY, s='p'), kf). For a worked example including the ANY keyword, see the egfr_simple model: https://github.com/pysb/pysb/blob/master/pysb/examples/bngwiki_egfr_simple.py
just to make sure I understand it right, for your r1 example, if the rule only apply to monomer, not in complex, then the binding site need to be explicitly stated in rule as rule('r1', A(s = 'u', b = None) >> A (s = 'p', b = None), kf) , even though the binding site is not directly involved or changed in the reaction. Am I right ?
Thank you so much !