biojulia / biojulia_handbook

Bio

This package has been depreceated. Full details are available here. You might still download and use this package, as we don't want old scripts to break. However going forward, know that this repository is archived and read only, no further updates or fixes will be committed. You should use the packages that replace Bio.jl - a list is available here.

biojulia_handbook's Issues

We forgot about BioTutorials.jl

Probably this stuff should go there, if we ever actually get to it :-(

BioJulia/BioTutorials#3

Setup autobuilds/autotests for the book code

Basically run Julia code snippets in CI to check everything still works.

Good examples are:

• Rustdoc https://doc.rust-lang.org/beta/rustdoc/documentation-tests.html
• OCaml mdx https://github.com/realworldocaml/mdx

Master Topic List

I thought it would be good to collect topic/lesson ideas in one place. Comment here and I'll add stuff to this first comment. If the list gets long enough I'll do some organization. Some ideas off the top of my head:

• search for, download, and examine gene sequences from NCBI
• search for, download, and examine articles with certain keywords from pubmed
• Get all subsequences of length N from a given protein/DNA/RNA sequence
• Parse a fasta file, and get all unique sequences (accounting for reverse compliments) and write that to a new fasta file
• Basically anything from rosalind.info
• ML/DL/RL for genomics
• Clean / align sequencing results

Please feel free to post other ideas and I'll add them to the list.