This is the home page for class SDS 348, Computational Biology and Bioinformatics. All relevant course materials will be posted here.

Syllabus: SDS348_syllabus_spring2019.pdf

Lectures

1. Jan 22, 2019 – Introduction, R Markdown

2. Jan 24, 2019 – R review

3. Jan 29, 2019 – Data visualization with ggplot2

4. Jan 31, 2019 – Data visualization with ggplot2

5. Feb 5, 2019 – Working with tidy data

6. Feb 7, 2019 – Working with tidy data

7. Feb 12, 2019 – Working with tidy data

8. Feb 14, 2019 – Rearranging data tables with tidyr

9. Feb 19, 2019 – Principal Components Analysis (PCA)

10. Feb 21, 2019 – k-means clustering

11. Feb 26, 2019 – Binary prediction/logistic regression

12. Feb 28, 2019 – Sensitivity/Specificity, ROC curves

13. Mar 5, 2019 – Training and test data sets, cross-validation

14. Mar 7, 2019 – Introduction to python, basic data structures

15. Mar 12, 2019 – Control flow in python

16. Mar 14, 2019 – Functions in python

17. Mar 26, 2019 – More on python data structures, classes

18. Mar 28, 2019 – Working with files

19. Apr 2, 2019 – Introduction to Biopython

20. Apr 4, 2019 – Working with gene features and genomes

21. Apr 9, 2019 – Running queries on Entrez

22. Apr 11, 2019 – Regular expressions

23. Apr. 16, 2019 – Using regular expressions to analyze data

24. Apr. 18, 2019 – Using regular expressions to analyze data

25. Apr. 23, 2019 – Aligning sequences

26. Apr. 25, 2019 – Global and local alignments, BLAST

27. Apr. 30, 2019 – Multiple sequence alignments and phylogenetic trees

28. May 2, 2019 – Working with protein structures

29. May 7, 2019 – Plotting geospatial data

30. May 9, 2019 – Making animated plots

Homeworks

All homeworks are due by 4:00pm on the day they are due. Homeworks need to be submitted as pdf files on Canvas.

Labs

1. Jan 23, 2019

2. Jan 30, 2019

3. Feb 6, 2019

4. Feb 13, 2019

5. Feb 20, 2019

6. Feb 27, 2019

7. Mar 6, 2019

8. Mar 13, 2019

9. Mar 27, 2019

10. Apr 3, 2019

11. Apr 10, 2019

12. Apr 17, 2019

13. Apr 24, 2019

14. May 1, 2019

Projects

All projects are due by 4:00pm on the day they are due. Projects need to be submitted on Canvas, both in pdf format and as source code (plus data where needed).