Rok Gomišček (firstname.lastname@example.org)
English (including the homework and, by consent of students, the exam).
The course starts on Wednesday, Oct 9, 2019. Lectures are each Wednesday from 11:15 (sharp!) to 14:00 at P22.
The course grade is composed from grade on the homework and grade from the final exam. The grade for the homework will be composed from the grade from Rosalind challenges (50%) and grade from mini projects (50%). To grant approach to the final exam, students have to score higher than 60% on rosalind and higher than 60% with the projects. 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 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.
Project report has to be prepared in LaTeX (template; also available in Slovene: template).
Students will have to submit both the report and the associated code.
Please see individual homework for a description for submissions.
- 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).
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)
Exam dates will be announced later in the semester.