BIO9905FBI1 - Introduction to Bioinformatics for Biosystematics

Schedule, syllabus and examination date

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Course content

Basic programming skills are essential for handling large datasets and performing complex analyses in biosystematics. This course aims to provide the students with tools to solve practical problems often encountered in biosystematic research. The students will be introduced to programming using Python (www.python.org), R (www.r-project.org), and SQL (e.g., http://en.wikipedia.org/wiki/SQL). Other programming languages may be used for specific tasks.

Learning outcome

Upon completion of the course, the students should be comfortable working with a command-line interface, well oriented in the basics of Phyton, R and SQL programming, and familiar with methods for computerized process control and data analysis.

Admission

PhD candidates from the University of Oslo should apply for classes and register for examinations through Studentweb.

If a course has limited intake capacity, priority will be given to PhD candidates who follow an individual education plan where this particular course is included. Some national researchers’ schools may have specific rules for ranking applicants for courses with limited intake capacity.

PhD candidates who have been admitted to another higher education institution must apply for a position as a visiting student before August 1th.

In addition to registering through Studentweb, all students are requested to apply by filling the course registration form that you find at http://www.forbio.uio.no/events/courses/2016/bioinfointro_2016.html

The course is limited to 26 students. The course is arranged by the National research School in Biosystematics, ForBio. Priority will be given to members of ForBio.

Deadline for applications is August 1th.

Prerequisites

Recommended previous knowledge

Course participants are expected to have knowledge in evolutionary biology and phylogenetic analyses of molecular dat corresponding to BIO4200 - Molecular Evolution and BIO4210 - Phylogeny and Classification .

You will need a laptop throughout the course. Make sure you have administrator privilegies and can install software on the computer.

No programming experience is required but participants are expected to be familiar with the GNU/Linux environment and Bash (www.gnu.org/software/bash).

A two day introduction will be arranged for participants without experience of GNU/Linux and Bash. Specify that you would like to participate in the introduction in “Other information” in the application form.

Teaching

Lectures and computer exercises
Literature: Handouts

Schedule:

October 1-2 (Saturday-Sunday): Introduction to GNU/Linux and Bash.

October 3-7 (Monday-Friday): Python, R, SQL

All lectures and computer exercises will take place at the Auditorium of Lids hus, Natural history Museum, University of Oslo.

More information including a more detailed schedule will be sent to all participants in September.
Any questions before that can be sent by email to hugo.deboer@nhm.uio.no

Examination

Each student will present a written solution to a programming problem given by the teachers during the course. The solution should be delivered within two weeks after the course ends. The solution will be marked as passed/not passed.

Examination support material

No examination support material is allowed.

Grading scale

Grades are awarded on a pass/fail scale. Read more about the grading system.

Explanations and appeals

Special examination arrangements

Application form, deadline and requirements for special examination arrangements.

Facts about this course

Credits

5

Level

PhD

Teaching

Autumn 2016

Examination

Autumn 2016

Teaching language

English