Rok Gomišček (email@example.com)
English (including the homework and, by consent of students, the exam).
The course starts on Wednesday, Oct 3, 2018. Lectures are each Wednesday from 8:15 (sharp!) to 11:00 at P19.
The grade is composed from grade on the homework and grade from the final exam. To grant approach to the final exam, students have to score higher than 60% with homework. The course is completed successfully if both homework and exam scores are above 60%. Homeworks may include bonuses; we take these into account in the final grade of homework but do not consider them when grading the final exam. That is, you have to score better than 60% in the final exam to pass the course. The final course score in points is computed as max[min(HW+15, EX), min(HW, EX+15)], where HW is a score from homework and EX is a score from the exam, both expressed in the scale from 0 to 100. Example: student's score is 85% for homework, 65% at the exam, the final score in points is 80%. One more example: exam score was 90%, homework 65%, final grade in points is 80%. Score is rounded to an integer and then translated to a course grade by the following rule: below or equal to 60 -> 5, from 61 to 68 -> 6, from 69 to 76 -> 7, from 77 to 84 -> 8, from 85 to 92 -> 9, from 93 -> 10. Grade 5 is negative (fail) and grades 6 and above are positive (pass). There's no oral exam, except for students who would like to change their final grades (note: this could go both directions, students who will not be prepared at the oral exam will fail the course).
Homework will include solving exercises on rosalind and working on a project as a bonus (20%).
Homework submission is through rosalind, as indicated in the description of the homework. Submission deadline is strict, homework cannot be submitted after the deadline. Homeworks have a strict deadline. For each day after the grade is multiplied by 0.9.
Project are submitted as Github repositories with all the code and documentation. The project final report, with summaries and figures, should be written in the README.md file in the repository.
- Nello Cristianini, Matthew W. Hahn (2007) Introduction to computational genomics: A case study approach, Cambridge University Press, Cambridge, UK. (FRI library, Amazon)
- Durbin et al. (1998) Biological sequence analysis, Cambridge University Press (selected chapters)
- Koza (1992), John R. Genetic programming: on the programming of computers by means of natural selection. Vol. 1. MIT press (Supplementary material on genetic algorithms).
Fun Stuff to Read
- Larry Gonick & Mark Wheelis (2005) The Cartoon Guide to Genetics, Harper, New York. (FRI library, Amazon).
- James D. Watson, Andrew Berry (2004) DNA: The Secret of Life, Arrow Books, UK. (also in Slovene: DNK, skrivnost življenja, Modrijan, Ljubljana, 2007).
Exams in years 2012 to 2016. Notice that we have been updating the course every year, so that the exam topics can change.
- PyCharm, IDE for Python
- J Demšar (2009) Python za programerje (in Slovene, sorry, there are plenty of other books for learning Python, like Fluent Python)
- 31 January 2019, from 13:00 to 15:00 in P01 (and P19 if needed)
- 14 February 2019, from 12:00 to 14:00 in P19 (and P18 if needed)
- 21 August 2019, from 9:00 to 11:00 in P22