Postgraduate Course: Bioinformatics Algorithms (PGBI11057)
Course Outline
School  School of Biological Sciences 
College  College of Science and Engineering 
Credit level (Normal year taken)  SCQF Level 11 (Postgraduate) 
Availability  Not available to visiting students 
SCQF Credits  10 
ECTS Credits  5 
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. 
Course description 
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 SmithWaterman local sequence alignment
 Graphbased algorithms
 Clustering and Treebased 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)
Prerequisites 

Corequisites  
Prohibited Combinations  
Other requirements  None 
Course Delivery Information

Academic year 2018/19, Not available to visiting students (SS1)

Quota: 42 
Course Start 
Semester 2 
Timetable 
Timetable 
Learning and Teaching activities (Further Info) 
Total Hours:
100
(
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
76 )

Assessment (Further Info) 
Written Exam
80 %,
Coursework
20 %,
Practical Exam
0 %

Additional Information (Assessment) 
1. Examination (80%)
2. Written Assessment (20%) 
Feedback 
Written feedback will be given for both the exam and ICA. 
Exam Information 
Exam Diet 
Paper Name 
Hours & Minutes 

Main Exam Diet S2 (April/May)   2:00  
Learning Outcomes
On completion of this course, the student will be able to:
 characterise a given algorithm class and describe the basic properties of this algorithm.
 write a computer programme encoding a given algorithm using a programming language of their choice.
 select an appropriate algorithm to solve a given task.

Additional Information
Graduate Attributes and Skills 
Not entered 
Keywords  BioinfAlgor 
Contacts
Course organiser  Dr Simon Tomlinson
Tel: (0131 6)51 7252
Email: simon.tomlinson@ed.ac.uk 
Course secretary  Ms Louise Robertson
Tel: (0131 6)50 5988
Email: Louise.K.M.Robertson@ed.ac.uk 

