Postgraduate Course: Bioinformatics Algorithms (PGBI11057)
|School||School of Biological Sciences
||College||College of Science and Engineering
|Credit level (Normal year taken)||SCQF Level 11 (Postgraduate)
||Availability||Available to all students
|Summary||Algorithms are a set of rules that allow a problem to be solved, often encoded in a computer programme. Algorithms are ubiquitous in bioinformatics and are often at the interface of computer science and biology.
All bioinformatics students need a good understanding of algorithms, in order to select appropriate methods to solve a given task, to understand the outputs of bioinformatics software and to write software that solves particular bioinformatics problems.
The course has a strong practical component that concentrates on the implementation of algorithms using the Java programming language (by default). We use the implementation of algorithms to explore the properties of algorithms in a bioinformatics setting.
In this course we will cover:
- The theory of algorithms - e.g. how to formally describe an algorithm, what makes a good algorithm, classes of algorithm.
- The implementation of algorithms in software applications
- Searching algorithms - both exhaustive and heuristic
- Dynamic programming algorithms ¿ eg Smith-Waterman local sequence alignment
- Graph-based algorithms
- Clustering and Tree-based algorithms
- Finding sequence patterns with algorithms
- Hidden Markov Models
- Genetic Algorithms
- Running algorithms on compute clusters concentrating on MapReduce and Apache Hadoop.
Entry Requirements (not applicable to Visiting Students)
||Other requirements|| None
Information for Visiting Students
|High Demand Course?
Course Delivery Information
|Academic year 2015/16, Available to all students (SV1)
|Learning and Teaching activities (Further Info)
Lecture Hours 10,
Supervised Practical/Workshop/Studio Hours 10,
Summative Assessment Hours 2,
Programme Level Learning and Teaching Hours 2,
Directed Learning and Independent Learning Hours
|Assessment (Further Info)
|Additional Information (Assessment)
||1. Examination (80%)
2. Written Assessment (20%)
||Hours & Minutes
|Main Exam Diet S2 (April/May)||Bioinformatics Algorithms||2:00|
On completion of this course, the student will be able to:
- Students will be able to characterise a given algorithm class and describe the basic properties of this algorithm.
- Students will be able to write a computer programme encoding a given algorithm using a programming language of their choice.
- Students will be able to select an appropriate algorithm to solve a given task.
|Graduate Attributes and Skills
|Course organiser||Dr Simon Tomlinson
Tel: (0131 6)51 7252
|Course secretary||Miss Vicky Mactaggart
Tel: (0131 6)51 7052
© Copyright 2015 The University of Edinburgh - 18 January 2016 4:32 am