[Biopython-dev] Tutorial problems

Tiago Antao tra at popgen.net
Sat Dec 5 16:31:51 UTC 2015

On Sat, 5 Dec 2015 08:53:18 -0700
Vincent Davis <vincent at vincentdavis.net> wrote:

> I am interested in helping with this converting. Now that github will
> render Jupiter notebooks how about creating a new repo under the
> biopython github account for the notebooks?

[I have included biopython-dev in the response]

Your help would be most welcome!
If people are OK with the notebooks being under biopython, I can
transfer the project ASAP.

This all being said, I do not think a literal translation is working
very well. There are 3 issues that I think are worth addressing:

1. Some of the tutorial content is slightly broken, so it will need

2. Some of the content needs adaptation for a jupyter interactive
environment. I would suggest that you would make full use of your
creative license when adapting. Change if you think it makes sense to

3. I think, in the medium-term, it will make sense to develop
jupyter-only content to make full use of the interactive features in a
learning environment

This all being said, I believe that the current PDF tutorial reeks of
20th century lack of interactivity. It is difficult to see any advantage
of the current format against an interactive jupyter version... My real
suggestion would be to convert it (well, adapt it) and then make it the
official version.

PS - Note that there is a docker image for this (already under the
biopython umbrella - biopython-tutorial)

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