Update README.md

Added Google Colab links for all chapters!
zaneveld · Nov 24, 2020 · f32fd37 · f32fd37
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Showing 1 changed file with 22 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -10,21 +10,30 @@ This text is currently in early prototype status. Chapters with content you can
      - [**Exercise**: Little Brother is Missing](content/03_the_command_line/exercise_little_brother_is_missing.ipynb) 
 - **Chapter 4. Exploring Python**
      - [Exploring Python](./content/04_exploring_python/exploring_python.ipynb)
+       [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/04_exploring_python/exploring_python.ipynb)
      - **Exercise**: Error Bingo
      - [A Tour of Python Data Types](./content/04_exploring_python/exploring_python_data_types.ipynb)
+       [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/04_exploring_python/exploring_python_data_types.ipynb)
      -  A Tour of Python Syntax (functions, conditions, iteration)
 - **Chapter 5. Project Design**
-     - [Using Literature Surveys to Ask Good Questions and Propose Testable Hypotheses](./content/05_project_design/project_design.ipynb)      
+     - [Using Literature Surveys to Ask Good Questions and Propose Testable Hypotheses](./content/05_project_design/project_design.ipynb)
+       [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/05_project_design/project_design.ipynb)
 - **Chapter 6. Biological Sequences**
      - [An introduction to Biological Sequences](./content/06_biological_sequences/biological_sequences.ipynb)
+       [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/06_biological_sequences/biological_sequences.ipynb)
      - [Representing and Manipulating Biological Sequences as Python Strings](./content/06_biological_sequences/representing_and_manipulating_biological_sequences_with_python_strings.ipynb)
-     - [Analyzing Biological Sequences with For Loops and If Statements](./content/06_biological_sequences/using_for_loops_to_analyze_biological_sequences.ipynb) 
+      [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/06_biological_sequences/representing_and_manipulating_biological_sequences_with_python_strings.ipynb)
+     - [Analyzing Biological Sequences with For Loops and If Statements](./content/06_biological_sequences/using_for_loops_to_analyze_biological_sequences.ipynb)
+       [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/06_biological_sequences/using_for_loops_to_analyze_biological_sequences.ipynb)
      -  [Reading and writing FASTA files using Python](./content/06_biological_sequences/reading_and_writing_fasta_files.ipynb)
+     [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/06_biological_sequences/reading_and_writing_fasta_files.ipynb)
 - **Chapter 7. 'Omics**
      -  [An Introduction to 'Omics](./content/07_tabular_omics_data/tabular_omics_data.ipynb) 
+        [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/07_tabular_omics_data/tabular_omics_data.ipynb)
      -  **In depth:** Characterizing Microbial Community Ecology
      -  **Exercise:** Microbiome change scenarios
      -  [Working with Tabular 'Omic data in Python using Pandas](./content/07_tabular_omics_data/analyzing_tabular_omics_data_in_pandas.ipynb)
+        [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/07_tabular_omics_data/analyzing_tabular_omics_data_in_pandas.ipynb)
      -   Analyzing Microbiome Alpha Diversity in Python
      -   Analyzing Microbiome Beta Diversity in Python
      -   Simulating the Effect of Sequencing Depth on Diversity Estimates
@@ -37,7 +46,9 @@ This text is currently in early prototype status. Chapters with content you can
      - **8b. Phylogenetics**
      - Tree thinking
      - [Representing Phylogenetic Trees with Python Classes](./content/08_phylogenetic_trees/phylogenetic_trees.ipynb)
+     [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/08_phylogenetic_trees/phylogenetic_trees.ipynb)
      - [Generating Trees Using Birth-Death Models](./content/08_phylogenetic_trees/birth_death_models.ipynb)
+     [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/08_phylogenetic_trees/birth_death_models.ipynb)
      - Working with Traits on Trees
      - Maximum Parsimony Ancestral State Reconstruction
      - Hidden State Prediction
@@ -48,14 +59,20 @@ This text is currently in early prototype status. Chapters with content you can
      - Representing Correlation
      - Representing Distribution
 - **Chapter 10. Simulation**
-     - [Simulating the Population Genetics of Natural Selection and Genetic Drift](./content/10_simulation/simulating_evolution.ipynb)     
+     - [Simulating the Population Genetics of Natural Selection and Genetic Drift](./content/10_simulation/simulating_evolution.ipynb)
+     [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/10_simulation/simulating_evolution.ipynb)
 - **Chapter 11. Statistics**
      - [Monte Carlo simulation and the Fundamental Unity of Statistical Hypothesis Tests](./content/11_statistics/monte_carlo_methods_and_the_fundamental_unity_of_statistical_tests.ipynb) 
+     [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/11_statistics/monte_carlo_methods_and_the_fundamental_unity_of_statistical_tests.ipynb)
      - Statistical Distributions and Parametric Tests
      - [Rank Transformations](./content/11_statistics/rank_based_methods.ipynb)
+     [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/11_statistics/rank_based_methods.ipynb)
      - [Monte Carlo simulation of Effect Size, Sample Size, and Significance](./content/11_statistics/effect_size_sample_size_and_significance.ipynb)
+     [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/11_statistics/effect_size_sample_size_and_significance.ipynb)
      - [Dealing with Multiple Comparisons](https://github.com/zaneveld/full_spectrum_bioinformatics/blob/master/content/11_statistics/dealing_with_multiple_comparisons.ipynb)
+     [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/11_statistics/dealing_with_multiple_comparisons.ipynb)
      - [**Exercise**: Revising your writing about statistical results](./content/11_statistics/exercise_revising_your_writing_about_statistical_results.ipynb)
+     [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/11_statistics/exercise_revising_your_writing_about_statistical_results.ipynb)
      - An Introduction to Maximum Likelihood optimization
      - The Best Model of A Cat is a Cat - model complexity, overfitting, and the AIC
      - An Introduction to Bayesian Approaches
@@ -69,6 +86,7 @@ This text is currently in early prototype status. Chapters with content you can
      - Presentations as Verbal Chess
 - **Chapter 14. Polishing and Publishing**
      - [Presenting Research](./content/13_presenting_research/12_Presenting_Research.ipynb)
+     [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/13_presenting_research/12_Presenting_Research.ipynb)
      - From Data to Conclusion: building a research manuscript brick by brick
      - Resistance is Futile: becoming a language Borg
      - **Exercise**: generating a targeted title using templating
@@ -80,6 +98,7 @@ This text is currently in early prototype status. Chapters with content you can
      - Fighting for an Inclusive Workplace
      - Open-source Science as Shield and Sword
      - [Applying for Grants](./content/13_presenting_research/applying_for_grants.ipynb)
+     [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/zaneveld/full_spectrum_bioinformatics/blob/master/content/13_presenting_research/applying_for_grants.ipynb)
 - **Appendices:**      
      - Appendix A - Data Sources for Bioinformatics Projects
      - Appendix B - Timesaving Starter Code