Blog of Andrés Aravena
Course Homepage:

# Computing in Molecular Biology 2

13 February 2018

This course is an introduction to Quantitative Thinking. We will use the tools we learned in the previous course and apply them to model real data and to simulate scientific experiments as a way to understand them.

The forum of the course is at https://groups.google.com/d/forum/iu-cmb. You can also participate writing an email to iu-cmb@googlegroups.com.

## Homework

All quizzes and homework should be sent to andres.aravena+cmb@istanbul.edu.tr before the deadline to get a grade. Please be careful, otherwise you will get a grade zero.

• Homework 2. Functions in R. (Deadline: Wednesday 28 of February at 9:00).
• Homework 3 (Deadline: Wednesday 18 of April at 9:00).
• Homework 4. How many persons with epilepsy in our course?. (Deadline: Wednesday 25 of April at 9:00).
• Exercises for Final Exam. Prepare yourself for the exam with practice and perseverance. (Deadline: Exam day, of course).

## Classes

Here you find the slides that have been used in classes. Notice that usually they are not published immediately, so you better take good notes. We recommend taking notes with pen and paper using the Cornell Method.

• Class 1: Introduction to Scientific Computing. Motivation of the course. [Slides]. (Feb 14, 2018).

• Class 2: Quiz 1. Turtle graphics. [Document]. (Feb 16, 2018).

• Class 3: Turtle Graphics. From Scratch to R. [triangle1.R], [triangle_loop.R], [triangle_loop2.R], [variable-star.R], [star1.R], [Slides]. (Feb 21, 2018).

• Class 4: Decomposition, Patterns, Abstraction, Algorithms. Functions: a key element of Computational Thinking. [draw_star.R], [Slides]. (Feb 23, 2018).

• Class 5: Step by Step into Functions of Functions. Using RStudio Debugger, and something about recursive functions. [draw_star_xy.R], [facto.R], [Slides]. (Feb 23, 2018).

• Class 6: Quiz 2. Rabbits, thin people and trees. [Document]. (Mar 2, 2018).

• Class 7: Learning from our mistakes. Taking lessons from the quiz answers. Drawing genomic data. [sample-stick-person.R], [stick-person-2.R], [sample-tree.R], [simple-tree.R], [Slides]. (Mar 7, 2018).

• Class 8: Genomic data. Working with DNA sequences. [gc_content.R], [Slides]. (Mar 9, 2018).

• Class 9: Local and Global Statistics on DNA. Finding the Origin of Replication. [Slides]. (Mar 14, 2018).

• Class 10: Cumulative sums. And an introduction to Systems Theory. [class10.R], [Slides]. (Mar 16, 2018).

• Class 11: Dynamic Systems. Making water is like growing cells. [class11.R], [Slides]. (Mar 21, 2018).

• Class 12: Quiz 3. Rehearsal for midterm. [quiz3.R], [Document]. (Mar 23, 2018).

• Class 13: Can we Predict the Future?. Deterministic and Non-deterministic Systems. Chaos and randomness. [Slides]. (Apr 11, 2018).

• Class 14: Probabilities. Basic definitions and concepts. [Slides]. (Apr 13, 2018).

• Class 15: Probability distributions. Also, solution of the homework. [Slides]. (Apr 18, 2018).

• Class 16: Quiz 4. Practice of Decomposition, Pattern Matching, Abstraction and Algorithm Design. [quiz4.R], [Document]. (Apr 20, 2018).

• Class 17: Events. Confidence intervals, and answer to homework 4. [Slides]. (Apr 25, 2018).

• Class 18: Practical Simulations. Is this variation caused by chance or something else?. [class18.R], [Slides]. (Apr 27, 2018).

• Class 19: More Simulations. Defining p-value and Run Length. [Slides]. (May 2, 2018).

• Class 20: Experiment Design. Simulating to plan a DNA sequencing project. [Slides]. (May 4, 2018).

• Class 21: Genetic algorithms. Solving hard questions using Nature’s ideas. Also, end of experimental design. [Slides]. (May 9, 2018).

• Class 22: Practicing Genetic algorithms. Solving hard problems step by step. [Slides]. (May 11, 2018).

• Class 23: Summary of the course. The big picture. Why we did all of this. [class23.R], [Slides]. (May 16, 2018).

• Class 24: Quiz 5. Practice for Exam. [quiz-5.R], [Document]. (May 18, 2018).

## Attendance

By regulation from the Rectory, students need to attend at least 70% of the classes. The attendance book is updated every week and can be seen in Google Sheets.

## References

• Polya, G. and Conway, John H. How to Solve It: A New Aspect of Mathematical Method. Princeton Science Library.

• Wilson et al. “Best Practices for Scientific Computing.” PLoS Biology 12,1 (2014).

• Stefan et al. “The Quantitative Methods Boot Camp: Teaching Quantitative Thinking and Computing Skills to Graduate Students in the Life Sciences”. PLoS Comput. Biol. 11, 1–12 (2015).

• Elson D, Chargaff E (1952). On the deoxyribonucleic acid content of sea urchin gametes. Experientia 8 (4): 143–145.

• Chargaff E, Lipshitz R, Green C (1952). Composition of the deoxypentose nucleic acids of four genera of sea-urchin. J Biol Chem 195 (1): 155–160.

• Roten C-AH, Gamba P, Barblan J-L, Karamata D. Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes. Nucleic Acids Research. 2002;30(1):142-144.

• Zeeberg, Barry R, Joseph Riss, David W Kane, Kimberly J Bussey, Edward Uchio, W Marston Linehan, J Carl Barrett, and John N Weinstein. Mistaken Identifiers: Gene Name Errors Can Be Introduced Inadvertently When Using Excel in Bioinformatics. BMC Bioinformatics 5 (2004): 80. doi:10.1186/1471-2105-5-80.

• Babylonian astronomers computed position of Jupiter with geometric methods January 29, 2016 https://phys.org/news/2016-01-babylonian-astronomers-position-jupiter-geometric.html
• Ossendrijver, Mathieu. Ancient Babylonian Astronomers Calculated Jupiter’s Position from the Area under a Time-Velocity Graph. Science (New York, N.Y.) 351, no. 6272 (January 29, 2016): 482–84. doi:10.1126/science.aad8085.

Originally published at https://anaraven.bitbucket.io/blog/2018/cmb2/