Seminar on Bioinformatics
| Year | Semester | Date | Period | Language | In charge |
|---|---|---|---|---|---|
| 2016 | autumn | 12.09-12.12. | 1-2 | English | Esko Ukkonen |
Lectures
| Time | Room | Lecturer | Date |
|---|---|---|---|
| Mon 14-16 | C220 | Esko Ukkonen | 12.09.2016-17.10.2016 |
| Mon 14-16 | C220 | Esko Ukkonen | 31.10.2016-12.12.2016 |
General
The main focus area of the seminar will be the so-called computational pan-genomics, a very recent special area of bioinformatics. Besides this, a student in this seminar may conduct a seminar project on his/her own topic within bioinformatics.
The word pan-genome refers to any collection of genomic sequences to be analyzed jointly or to be used as a reference. These sequences can be linked in a graph-like structure, or simply constitute sets of (aligned or unaligned) sequences. Questions about effcient data structures, algorithms and statistical methods to perform bioinformatic analyses of pan-genomes give rise to the discipline of computational pan-genomics. Computational pan-genomics therefore intersects with many other bioinformatics disciplines. In particular it is related to metagenomics, which studies the entirety of genetic material sampled from an environment; to comparative genomics, which is concerned with retracing evolution by analyzing genome sequences; and to population genetics, whose main subject is the change of a population's genetic composition in response to various evolutionary forces and migration.
The seminar is suitable for students with basic knowledge of algorithms and /or probabilistic modeling and/or bioinformatics (course "Algorithms in Bionformatics"or "Biological Sequence Analysis").
Also see the global learning objectives of seminars at the department: http://www.cs.helsinki.fi/en/courses/seminaarien-ennakkoilmoittautuminen/matrix
This seminar will work in English.
Completing the course
Participants must have completed the course Scientific writing or have equivalent skills. A maximum of 12 students will be elected for the seminar on the basis of their application and previous studies.
Students are expected to actively participate in the seminar work: the working include studying scientific sources, writing reports and giving presentations, reading the reports of other participants and evaluating them, and actively following presentations.
The detailed schedule of the seminar will be fixed in the first sessions. There will be 2-hour sessions in the first part of the seminar and a couple of longer, full day sessions at the end. The seminar requires independent home work throughout the semester.
Each student will have three roles in the seminar: (1) a writer and speaker, (2) reviewer of two other reports, (3) audience for the rest of the reports and oral presentations.
The grading will be based on each student's own written work, oral presentation, and commentary on the reports of others as well as activeness in general. To pass the seminar, each of these components must be passed. Active attendance of seminar meetings is obligatory (absense from at most two meetings is accepted (will affect grading)).
Literature and material
T. Marschall et al.: Computational Pan-Genomics: Status, Promises and Challenges (http://www.biorxiv.org/content/early/2016/03/29/043430.abstract)
More literature will be listed here later.