Forum:Asking for content suggestions for updated bioinformatics book

Question

[tiagoantao]

Hi,

I am the author of Bioinformatics with Python Cookbook . I am considering doing a third edition, given that there has been a few new libraries and formats in recent years.

I was wondering a few things: Do you think its worthwhile doing a new edition? If so what new content you would like so see? Any updates to existing content?

I would really value the community input to decide in what terms to go forward. If you prefer, we also have questions in surveymonkey format.

Many thanks for any input

[Dunois]

A section on Snakemake and another on general purpose sequence visualization tools?

[jared.andrews07]

If you have no content on single cell analysis, then you could definitely add a section on that (using scanpy). Though that could likely be its own entire book as well, so scope would be a concern.

[ATpoint]

Not sure what content is in there by now, but in general integration of user code with something like Jupyter Notebooks and some basics on reproducibility and containerization (even if it is "only" plain conda and version control via the environment.yml files) could be a plus. I think the common rookie error in any analysis code is to have a giant monolithic script on some laptop or workstation, but no awareness at all on documenting package versions and obtaining the same results when porting these scripts to another machine/OS. I am not sure though whether this is still what you have in mind, as this could well be a separate book on general good practices in data analysis. Maybe a small chapter that motivates the topic, and then references to other sources?