### General

#### Lecturers

Tomaž Curk (tomaz.curk@fri.uni-lj.si) and Blaž Zupan (blaz.zupan@fri.uni-lj.si)

#### Teaching Assistant

Rok Gomišček (rok.gomiscek@fri.uni-lj.si)

#### Course Language

English (including the homework and, by consent of students, the exam).

#### Dates

The course starts on Wednesday, Oct 9, 2019. Lectures are each Wednesday from 11:15 (sharp!) to 14:00 at P22.

#### Grading

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

Homework will include exercises on rosalind and three smaller projects, where solving rosalind will carry 40% and each project 20% of the homework points.

Enroll to the course on rosalind with your name and surname. Submit your solutions to the tasks until the deadline. Tasks have different scores.

Projects have a strict deadline. For each day after the grade is multiplied by 0.9.

#### Textbook

- Nello Cristianini, Matthew W. Hahn (2007) Introduction to computational genomics: A case study approach, Cambridge University Press, Cambridge, UK.
- 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).

#### Past Exams

Exams in years 2012 to 2016. Notice that we have been updating the course every year, so that the exam topics can change.

#### Python-Related Resources

- 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)

#### Exam dates

Exam dates will be announced later in the semester.

#### Other resources

**Homework**