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Full Spectrum Bioinformatics Development Release 2020.12.1

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@zaneveld zaneveld released this 08 Dec 20:43
· 240 commits to master since this release
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This is an initial development release of the Full Spectrum Bioinformatics online textbook. This is not a full release of the entire planned textbook, but rather an incremental development release of some content that is sufficiently developed that it has been used in classes.

Some current features include:
-- A series of open-access Jupyter Notebooks discussing topics in Bioinformatics.
-- Links to Google Colab to allow students to run notebooks in a browser without installing software
-- An outline table of contents shows planned sections, with sections that are in beta status available as live links.
-- This release includes 21 new sections, covering topics ranging from sequence analysis to how to revise one's writing about statistical results:

Foreword
The Command Line
Using the Command Line
Exercise: Little Brother is Missing
Exploring Python
Exploring Python
A Tour of Python Data Types
Project Design
Using Literature Surveys to Ask Good Questions and Propose Testable Hypotheses
Biological Sequences
An introduction to Biological Sequences
Representing and Manipulating Biological Sequences as Python Strings
Analyzing Biological Sequences with For Loops and If Statements
Reading and writing FASTA files using Python
'Omics
An Introduction to 'Omics
Working with Tabular 'Omic data in Python using Pandas
Phylogenetic Trees
Representing Phylogenetic Trees with Python Classes
Generating Trees Using Birth-Death Models
Simulation
Simulating the Population Genetics of Natural Selection and Genetic Drift
Statistics
Rank Transformations
Monte Carlo simulation of Effect Size, Sample Size, and Significance
Dealing with Multiple Comparisons
Exercise: Revising your writing about statistical results
Polishing and Publishing
Presenting Research
Careers that draw on Bioinformatics
Applying for Grants

NOTE: this is very similar to release-2020.12.0, other than minor edits to the readme but I need to re-release to trigger Zenodo to generate a DOI.