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CiaranWelsh / pycotools3

A Python toolbox for COPASI
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Question about pycotools vs. python bindings for COPASI #12

Open danolson1 opened 3 years ago

danolson1 commented 3 years ago

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

CiaranWelsh commented 3 years ago

Hi Dan,

Pycotools3 is basically a “layer” on top of COPASI that talk to COPASI by modifying the xml while the python bindings for COPASI are a swig generated mirror of the COPASI code that works in python. Swig basically exposes pointers to the actual COPASI code in python, so while pycotools3 uses Copasi, the python binding are copasi.

Hope this helps,

Ciaran

On Tue, 9 Feb 2021 at 16:54, danolson1 notifications@github.com wrote:

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

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