Feature suggestion: Pretty print an output which is displayed by jupyter/ipython `display`

BuildACell / bioCRNpyler

A modular compiler for biological chemical reaction networks

BSD 3-Clause "New" or "Revised" License

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Feature suggestion: Pretty print an output which is displayed by jupyter/ipython `display` #112

Open eldad-a opened 4 years ago

eldad-a commented 4 years ago

Allow a Jupyter display-able output, similar to those of pandas and sympy, for example:

Compiled CRNs could be pretty_printed to show up in the common form of a LaTeX

$$ \quad \quad E + S \underset{k_u}{\overset{kb}{\rightleftharpoons}}E:S \xrightarrow{k{cat}} E + P $$

or the jupyter display output of it (MathJax).

Simulation output would have a default plot method, similar to pandas DataFrames , or to the functionality provided by hvplot from the HoloViz ecosystem.

WilliamIX commented 4 years ago

Great idea about having a nice way to see reactions in latex [and I didn't know that could be printed as python output in jupyter]!

On the plotting front, we are currently moving in the opposite direction and having biocrnpyler be "simulator agnostic" [ie not reliant on bioscrape necessarily]. That said, there is a case to be made for easy plotting capabilities - but maybe we can include those in bioscrape?

WilliamIX commented 4 years ago

This is related to my comment on CRN From string