Welcome to CNApy Discussions!

[sthiele]

👋 Welcome!

We’re using Discussions as a place to connect with other members of our community. We hope that you:

• Ask questions you’re wondering about.
• Share ideas.
• Engage with other community members.
• Welcome others and are open-minded. Remember that this is a community we
  build together 💪.

To get started, comment below with an introduction of yourself and tell us about what you do with this community.

[galib96]

Hi, I am a grad student and using cnapy GUI for Elementary flux modes analysis.

Is it possible to use cnapy inside jupyter notebook so that generated flux data can be imported/exported and analyzed in python?

[Paulocracy]

Hello Galib!
It's certainly possible to start CNApy inside a Jupyter notebook by using cnapy.py's content in a Jupyter cell, however, as of now, there wouldn't be much use to it as CNApy doesn't generate much output on its own.
However, with the latest CNApy version 1.1.6, you can save the reaction list (including shown fluxes for a specific EFM analysis) concent to your system's clipboard by right-clicking on the list's column captions. Alternatively, you can also directly store this list as a CSV file or Excel XLSX under the "Clipboard" menu entry. These files (or clipboard content) can then be loaded into Python using e.g. pandas, csv or openpyxl.
If you have further suggestions or questions feel free to post them, we're always looking for feedback and ideas :-)

[axelvonkamp]

For elementary model analysis in particular you can also use the efmtool-link package independent of CNApy. It has an example Jupyter notebook efmtool_link.ipynb included.