Error at tutorial visualization step

[lhdp0110]

When I enter the command:
[path-to-pysb]/pysb/tools/render_reactions.py [path-to-pysb-model-file]/mymodel.py > mymodel.dot
Replacing with appropriate path names as instructed, I get the following error:
NameError: name 'mymodel' is not defined

What may cause this? Thank you

[jmuhlich]

Could you provide the entire stack trace from your terminal? It would be helpful to see the exact line that's failing as well as everything leading up to it.

[lhdp0110]

Thank you for your reply, here is the entire error message:

`'C:/Users/.../anaconda3/pkgs/pysb-1.14.0-py_0/site-packages/pysb/tools/render_reactions.py' 'C:/Users/.../anaconda3/Scripts/PySB/mymodel.py' > mymodel.dot
Traceback (most recent call last):

Input In [14] in <cell line: 1>
'C:/Users/.../anaconda3/pkgs/pysb-1.14.0-py_0/site-packages/pysb/tools/render_reactions.py' 'C:/Users/.../anaconda3/Scripts/PySB/mymodel.py' > mymodel.dot

NameError: name 'mymodel' is not defined`

I ran this line interactively after running the following:

import the pysb module and all its methods and functions

from pysb import *

instantiate a model

Model()

declare monomers

Monomer('C8', ['b'])
Monomer('Bid', ['b', 'S'], {'S':['u', 't']})

input the parameter values

Parameter('kf', 1.0e-07)
Parameter('kr', 1.0e-03)
Parameter('kc', 1.0)

now input the rules

Rule('C8_Bid_bind', C8(b=None) + Bid(b=None, S='u') | C8(b=1) % Bid(b=1, S='u'), *[kf, kr])
Rule('tBid_from_C8Bid', C8(b=1) % Bid(b=1, S='u') >> C8(b=None) + Bid(b=None, S='t'), kc)

initial conditions

Parameter('C8_0', 1000)
Parameter('Bid_0', 10000)
Initial(C8(b=None), C8_0)
Initial(Bid(b=None, S='u'), Bid_0)

Observables

Observable('obsC8', C8(b=None))
Observable('obsBid', Bid(b=None, S='u'))
Observable('obstBid', Bid(b=None, S='t'))

import mymodel as m

(I'm sorry, I cannot figure out how to format the above code properly)
Is is possible that this is due to Graphviz or another requirement not being properly installed?

[jmuhlich]

It looks like you are entering the command as a cell in a Jupyter notebook. That command as written must be run from the shell instead. If you want to run the visualization from a notebook you'll need Python code:

First, delete the line import mymodel as m. The Model object is already available under the variable model. Next you will need to add the following import lines:

from IPython.display import SVG
import pygraphviz
import pysb.tools.render_reactions

Then we call the pysb render_reactions tool and store the result as a GraphViz graph object in g:

g = pygraphviz.AGraph(string=pysb.tools.render_reactions.run(model))

Finally we call graphviz to perform layout and SVG rendering, displaying the SVG inline in the notebook:

SVG(g.draw(prog="dot", format="svg"))