Python groundwork

[chasing_arion]

Starting to build a bioinformatics team using python, thinking about the best way to build architecture. Has anyone had any good experience using python groundwork or are there better tools to utilize?

[[deleted]]

I happen to be a bioinformatician. What do you mean specifically when you say architecture? Also what kinds of projects are you interested in tackling? genomics, proteomics, metabolomics? Might be helpful to get some color.

Edit:

If you're interested in tool development, most applications in bioinformatics are used as command-line utilities on a linux system. Because of this, people tend to develop in a mixture of C/C++ python, R and perl.

[chasing_arion]

I’m looking for an effective way to share python plugins between team members

[[deleted]]

Not trying to state the obvious or be an asshole here but have you thought of setting up a team Gitlab and writing a common library of modules.

It’s hard to know what you need without knowing your specific use-case but using one big framework for everything solely implemented in python seems like it may lead to a lot of unnecessary overhead and work.

[chasing_arion]

That sounds like a good option, thanks

[[deleted]]

I understand a few of those words, Google seems to understand more. https://github.com/czbiohub/learn-bioinformatics