Syllabus for |
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TDA507 - Computational methods in bioinformatics
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| Beräkningsmetoder inom bioinformatik |
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| Syllabus adopted 2015-02-02 by Head of Programme (or corresponding) |
| Owner: MPALG |
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7,5 Credits
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| Grading: TH - Five, Four, Three, Fail |
| Education cycle: Second-cycle |
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Major subject: Bioengineering, Computer Science and Engineering, Information Technology
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Department: 37 - COMPUTER SCIENCE AND ENGINEERING
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Teaching language: English
Open for exchange students: Yes
Block schedule:
A
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Credit distribution |
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Examination dates |
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Sp1 |
Sp2 |
Sp3 |
Sp4 |
Summer course |
No Sp |
| 0113 |
Written and oral assignments |
7,5 c |
Grading: TH |
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7,5 c
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In programs
MPALG COMPUTER SCIENCE - ALGORITHMS, LANGUAGES AND LOGIC, MSC PROGR, Year 1 (elective)
MPALG COMPUTER SCIENCE - ALGORITHMS, LANGUAGES AND LOGIC, MSC PROGR, Year 2 (elective)
MPCAS COMPLEX ADAPTIVE SYSTEMS, MSC PROGR, Year 1 (compulsory elective)
MPCAS COMPLEX ADAPTIVE SYSTEMS, MSC PROGR, Year 2 (elective)
TKITE SOFTWARE ENGINEERING, Year 3 (elective)
Examiner:
Graham Kemp
Replaces
TDA505
Three-dimensional structure TDA506
Structural bioinformatics
Go to Course Homepage
Eligibility:
In order to be eligible for a second cycle course the applicant needs to fulfil the general and specific entry requirements of the programme that owns the course. (If the second cycle course is owned by a first cycle programme, second cycle entry requirements apply.)
Exemption from the eligibility requirement:
Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling these requirements.
Course specific prerequisites
To be eligible for the course the student should have successfully completed 90 hec of studies within the subject Computer Science or equivalent. Furthermore, the student should have successfully completed a course in Programming and in Discrete Mathematics.
Aim
This course demonstrates how computational methods that have possibly been presented in other computing courses can be applied to solve problems in an application area.
We look at problems related to the analysis of biological sequence data (sequence bioinformatics) and macromolecular structures (structural bioinformatics). Computing scientists need to be able to understand problems that originate in areas that may be unfamiliar to them, and to identify computational methods and approaches that can be used to solve them. Biological concepts needed to understand the problems will be introduced.
This is an advanced level course which uses research articles as the main reference materials. Reading research articles is valuable training for scientists and researchers.
These demonstrate how to present ideas and methods, and how to critically evaluate them. Developing skill in reading research articles is useful preparation for future scientific investigations, and one's own scientific writing can improve through reading.
Learning outcomes (after completion of the course the student should be able to)
Knowledge and understanding - describe bioinformatics problems and computational approaches to solving them.
Skills and abilities- implement computational solutions to problems in bioinformatics.
Judgement and approach- summarise problems and methods described in research articles
- critically discuss different methods that address the same task
- identify situations where methods can be applied across different application areas
Content
Computational methods and concepts featured in this course include: dynamic programming; heuristic algorithms; graph partitioning; image skeletonisation, smoothing and edge detection; clustering; sub-matrix matching; geometric hashing; constraint logic programming; Monte Carlo optimisation; simulated annealing; self-avoiding walks.
Biological problems featured in this course include: sequence alignment; domain assignment; structure comparison; comparative modelling; protein folding; fold recognition; finding channels; molecular docking; protein design.
Organisation
Lectures and programming assignments.
Literature
Lecture handouts; web-based resources; selected research articles.
Examination including compulsory elements
The course is examined by individual programming assignments, written assignments and oral presentations.