Hi.
I am coding according to the pycotools3 documentation (release 12, Jan 2019).
First, i tried to code for importing all the dependencies. it worked.
Second, i tried to built michaelis_menten model according to the documentation.
It showed error by saying that "you should use loada in place of BuildAntimony" (files showing
errors are m_m modelerr1.png and m_m modelerr1-extended.png).
Third, when i use loada. it started showing some positional error in copasi file (related error showing file is m_m modelerr2.png .
Thank you so much in advance for your suggestion.

*My system is Ubuntu 16.04.
I downloaded Anaconda3 (2019.03) with python 3.6 on my ubuntu machine.
Obviously, downloaded pycotools3 using "pip install pycotools3".
My work is on chemical kinetics and model prediction, but i am doing the michaelis_menten model coding to see how pycotools3 works accroding to the given doc, prior to begin my project.

Thanks
Vibha

Hey Ciaran,

What's the difference between PyCoTools and the python bindings for COPASI (https://github.com/copasi/COPASI/tree/develop/copasi/bindings/python/examples)?

My goal is to take a model that I've built in COPASI using the GUI, and do a bunch of automated parameter scans, and collect the resulting time-course data for subsequent analysis. I read your 2018 Bioinformatics paper, but the section where you compare PyCoTools to the command line interface was very brief.

Thanks,
Dan

Hi,
I am trying to perform model selection using tasks.MultiModelFit, but it shows the Attribute error saying "AttributeError: module 'pycotools3.tasks' has no attribute 'MultiModelFit' ".

Also while running time course, it reflects name error. I am attaching here the screen shot for you to take a look.

I am working with pycotools 3 and COPASI 4.24. Thanks for your time.

Vibha
I

Hi!

I'm curious why pycotools3 is not recognizing my SBML file as an SBMl file?

Any idea?

Thank you!

Best regards,
Brad

pip install pycotools3 getting installation error, which throwing out No matching distribution for tesbml>=5.15.0.1 (from tellurium->pycotools3) (from versions: none)

Hi Mr Welsh,
I am again stuck in building model in pycotools3. Generally, it builds the model with mol as species's concentration and liters as compartment unit. I need to convert the compartment unit in femtoliters and species in nmol.
I build models using antimony. I have gone through pycotools3 master's documentation and found the conversion documentation for species. But i am not sure how to apply these in building models. I am seeking your suugestions in this regard.

Thank you for your time and help.

Vibha

I've double checked and made sure the xml file I have is an SBML file, yet I'm still getting the above error.

Any ideas? Thanks!

Hello!

I performed the calculations for obtaining the profile likelihood as in the docs. Parsing the output gives the report for multi_parameter_estimation. I looked into the code, found the report_type keyword, but i couldn't figure out where to use it during the Parameter Estimation configuration.

Hello!

I was wondering if it is possible to retrieve the differential equations, e.g. as is done here in COPASI:

using Pycotools3.

This is very important for me, because I would like to pipeline these equations directly into a "scientific machine learning" platform that will using the equations alongside experimental data to determine missing parts of the diff eqs for my master's thesis in bioinformatics.

Thank you very much for your time and attention! And thanks for the great tool!

Best,
Brad