1 Content

1.1 Review

Make sure you actually know everything outlined here,
including Bash, VMs, Containers, Git, Standard Input/Output (I/O), etc.:
../../ClassGeneral.html

1.2 Schedule and due dates

The schedule and due dates will be updated as we progress through the semester (on Canvas).
Please check back regularly for changes.

1.3 Topic outline

1.3.1 Introduction, big picture, review, technical setup

Content/Inspiration.html
Content/eScience.html
Content/PlatformTools.html
Content/PythonReview.html
Content/BioReview.html
Content/BioInfoBasics.html

1.3.2 Biological sequence processing

To get the relevant files for this section, start up the class VM,
navigate to a directory you want to store the lecture notes in, and then:
git clone https://gitlab.com/bio-data/sequence-informatics.git
As I add lectures, or improve old ones, they’ll be updated in the repo,
so you can just do this is the repo to get the latest notebook scripts:
git pull

A file notebook.ipynb, notebook.md, or notebook.py is an example name for a Jupyter notebook,
which can be opened on your computer with jupyter lab (detailed in previous lectures).

Introduction.py
Biological-information.py

Pairwise-alignment.py
https://vimeo.com/674616839
https://vimeo.com/677007265
https://vimeo.com/677007892
https://vimeo.com/680727824

Database-searching.py
https://vimeo.com/680730089
https://vimeo.com/682719141

Multiple-sequence-alignment.py
https://vimeo.com/685957644
https://vimeo.com/685957698
https://vimeo.com/685957751
https://vimeo.com/687727294

Phylogeny-reconstruction.py
https://vimeo.com/692413491
https://vimeo.com/692413573

Sequence-mapping-and-clustering.py
https://vimeo.com/692413680
https://vimeo.com/692413878
https://vimeo.com/696706898
https://vimeo.com/696707009

Biological-diversity.py
https://vimeo.com/700484079
https://vimeo.com/700484242

Machine-learning.py

A fun recent example of a large genomics project employing some neat machine learning analyses to the data:
https://zoonomiaproject.org/
A pop news article about it:
https://www.vice.com/en/article/4a3wwg/scientists-sequenced-dna-of-nearly-every-mammal-on-earth-in-unprecedented-project
One paper using theses methods to understand the genetics of brain size expansion throughout evolution:
https://www.science.org/doi/10.1126/science.abm7993