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Chapter Response
This form is a place to respond after reading a chapter of Full Spectrum Bioinformatics.
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Foreword
Introduction
Using the Command Line - An Adventurous Introduction to the Command Line
Using the Command Line - Excercise: Duck vs. Yeast
Exploring Python
Exploring Python - Data Types
Exploring Python - Syntax
Project Design
Project Design - How to not repeatedly reformat 96 references by hand: Zotero for Beginners (Dr. Mushtaq Bilal)
Biological Sequences
Biological Sequences - Representing Sequences as Python Strings
Biological Sequences - Using For Loops and If statements to analyze biological sequences
Biological Sequences - Parsing FASTA files
Biological Sequences - Error Messages in Python
Biological Sequences - Exercise - Error Bingo
Biological Sequences - Capstone - Testing for Depletion of CG dinucleotides in the human genome
Omics - An Introduction to 'Omics
Omics - Working with Tabular 'Omic data in Python using Pandas
Omics - Simulating the Effects of Sequencing Depth on Estimates of Biodiversity
Omics - Joining and Filtering Data in Pandas
Omics - Calculating Beta Diversity
Omics - Calculating Alpha Diversity
Alignment and Phylogenetics
Alignment and Phylogenetics - Local Alignment with the Needleman-Wunsch algorithm
Alignment and Phylogenetics - Representing Phylogenetic Trees using Python Classes
Alignment and Phylogenetics - Implementing a Birth-Death model of Speciation and Extinction
Visualization
Visualization - Exercise - The Wrath of Tufte
Simulation
Simulation - Simulating Evolution by Mutation, Selection, and Genetic Drift
Statistics
Statistics - Linear Models - a statistical Swiss Army Knife
Statistics - Monte Carlo statistics and the fundamental unity of statistical tests
Statistics - Rank Transformations
Statistics - Monte Carlo simulations of effect size, sample size and significance
Statistics - Dealing with Multiple Comparisons
Statistics - Exercise - Revising your writing about statistical results
Multivariate statistics and Machine Learning
Presenting Research
Polishing and Publishing
Careers that draw on Bioinformatics
Careers that draw on Bioinformatics - Fighting for an Inclusive Workplace
Careers that draw on Bioinformatics - Science and Authoritarianism
Other
Bioinformatics Vignette - Nia Prabhu - Using For Loops and Dictionaries to Compare Nucleotide Composition in Pandemic and Non-Pandemic Causing Influenza Strains
Bioinformatics Vignette - Aziz Bajouri - Using Set Objects to Find Circular RNAs Associated with Multiple Diseases
Bioinformatics Vignette - Ayomikun Akinrinade - Using k-Nearest Neighbor and Binary Decision Tree Algorithms to Predict Enzyme Function from Protein Sequences
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