zaneveld/full_spectrum_bioinformatics: Full Spectrum Bioinformatics Development Release 2022.3.0

What's Changed

The 2022.3.1 Release of Full Spectrum Bioinformatics greatly expands the scope and maturity of the text, including contributions from 3 undergraduate co-authors. This text has now been used to support multiple classes, and has 35 sections that are linked from the table of content and ready for classroom use.

Here are some of the major changes:

The text has several new sections: -- An overview of python syntax now overviews how to recognize python syntax before we dive into studying the details -- A first chapter on sequence alignment now covers Needleman-Wunsch alignment, both as worked by hand using a simple example, and an implementation in numpy. -- The text now discusses linear models, with accompanying illustrations as well as figures -- An Error Bingo exercise now encourages students to intentionally trigger and learn from errors
-- An extensive section has been added discussing common errors in python, why they most commonly occur, and how to fix them.

-- 3 undergraduate contributors have added Bioinformatics Vignettes showing how to apply the principles in the text to biological problems:

- Nia Prabhu (nucleotide composition) 
- Aziz Bajouri (set analysis) 
- Ayomikun Akinrinade (machine learning)

-- A section has been added on revising writing about statistical results -- An initial draft section on visualizing correlation has been added showing how a scatterplot can be revised to add linear regression results, 95% confidence intervals, and to better meet recommendations for data visualization. -- The Data Sources page has been greatly updated, and now includes logos for linked resources

New Draft Sections: -- A draft section on student activism and fighting for an inclusive workplace has been added. -- A draft section on network analysis has several in-progress code commits (not yet linked from main table of contents)

Other changes: -- Full Spectrum Bioinformatics has now adopted a code of conduct -- Many minor fixes -- Exercises have been added to many sections that previously lacked them -- The exercise on calculating CG content in the human genome has been updated -- Several chapters have been updated to include Feedback links that were previously missing -- Unused Jupyter Book files have been removed

Full Changelog: https://github.com/zaneveld/full_spectrum_bioinformatics/compare/release-2020.12.1...release-2022.3.1