pycotools3: code for michaelis_menten model creation is not working about pycotools3 HOT 6 CLOSED

Hello,

The documentation you are referring to sounds a bit old (12 Jan 2019?). I've developed the project more recently than that so my first suggestion would be to just ensure you are using the most up to date version of everything. You can find the documentation here. Also, try ensuring you are using the most recent pycotools.

$ pip uninstall pycotools3

then

$ pip install pycotools3 --no-cache-dir

the --no-cache-dir option just forces pip to redownload the package, rather than using a cached version.

I've tried the following on my own machine, which works as expected.

Let me know how it goes - all the best

Ciaran

import os
import site
from pycotools3 import model, tasks, viz

working_directory = <input working directory here>
if not os.path.isdir(working_directory):
    os.makedirs(working_directory)

copasi_file = os.path.join(working_directory, 'michaelis_menten.cps')

if os.path.isfile(copasi_file):
    os.remove(copasi_file)

antimony_string = """
model michaelis_menten()
    compartment cell = 1.0
    var E in cell
    var S in cell
    var ES in cell
    var P in cell

    kf = 0.1
    kb = 1
    kcat = 0.3
    E = 75
    S = 1000

    SBindE: S + E => ES; kf*S*E
    ESUnbind: ES => S + E; kb*ES
    ProdForm: ES => P + E; kcat*ES
end
"""

with model.BuildAntimony(copasi_file) as loader:
    mm = loader.load(antimony_string)

from pycotools3.

from pycotools3.

Hi Vibha,

I've tested pycotools3 on both Copasi 4.24 and 4.25 and behavior is the same as far as I can tell so you're best off using the most recent version.

As for Python, I've also tested this on 3.7 but ran into troubles because of a dependency (tellurium). I haven't chased this up for a while so it may work. If you wanted to quickly test it, it would be a simple case of writing a script (or notebook) that works on Python 3.6, then switching to a Python 3.7 environment and seeing if it works. However, for the time being, 3.6 works well enough.

Jupyter notebooks also work well enough. These days I tend to just use Pycharm, but notebooks are the preference for many.

Pycotools dependencies should install themselves with pycotools. The only exception is COPASI itself. The assumption is that you already have COPASI installed and the path to the copasi/bin folder (i.e. where the copasi binaries are kept) are in your path environment variable. An easy way to test this is to run the command CopasiUI and see if it opens the COPASI GUI.

Good luck,

Ciaran

from pycotools3.

from pycotools3.

from pycotools3.

Hi Vibha,

It looks like there are syntax errors in your antimony model - In antimony, parenthesis are reserved for functions. I suspect this will work if you were to just remove them from your variable naming.

You can find some documentation here.

Something else that can be helpful is to build you model in COPASI, export the SBML and then use a tellurium function tellurium.tellurium.sbmlToAntimony(sbml) here to create an antimony string. I found this useful when I was learning how to use Antimony.

Ciaran

from pycotools3.