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DEGREE REGULATIONS & PROGRAMMES OF STUDY 2017/2018

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DRPS : Course Catalogue : School of Biological Sciences : Postgraduate

Postgraduate Course: Bioinformatics Programming and System Management (PGBI11095)

Course Outline
SchoolSchool of Biological Sciences CollegeCollege of Science and Engineering
Credit level (Normal year taken)SCQF Level 11 (Postgraduate) AvailabilityAvailable to all students
SCQF Credits20 ECTS Credits10
SummaryThe course will provide Bioinformatics MSc (and other postgraduate) students with a working knowledge of computer systems, programming and software essential to a career in bioinformatics, or in graduate research.
Course description Course Description / Syllabus

1 Introduction. The unix environment.System Administration, ECDF
2 The Bioinformatic web: Databases, servers, webservices, file formats
3 BLAST: Installing software, Command line scripting, Grid computing
4 Programming in python 1
5 Programming in python 2
6 Programming in python 3
7 Programming in python 4
8 Programming in python 5
9 Programming in python 6
10 Relational (SQL) databases
11 Programming in python 6: advanced topics 1
12 Programming in python 8: advanced topics 2
13 Programming in python 9: advanced topics 3
14 Workflow management systems (Galaxy, GeneProf)
15 Programming in java 1
16 Programming in java 2
17 Programming in java 3
18 Programming in java 4
19 Programming in java 5
20 Programming in java 6
Entry Requirements (not applicable to Visiting Students)
Pre-requisites Co-requisites
Prohibited Combinations Students MUST NOT also be taking Bioinformatics (PGBI11006)
Other requirements None
Information for Visiting Students
Pre-requisitesNone
High Demand Course? Yes
Course Delivery Information
Academic year 2017/18, Available to all students (SV1) Quota:  43
Course Start Semester 1
Timetable Timetable
Learning and Teaching activities (Further Info) Total Hours: 200 ( Lecture Hours 20, Supervised Practical/Workshop/Studio Hours 40, Programme Level Learning and Teaching Hours 4, Directed Learning and Independent Learning Hours 136 )
Assessment (Further Info) Written Exam 30 %, Coursework 70 %, Practical Exam 0 %
Additional Information (Assessment) The course will be assessed by 2 in-course assessments consisting of directed programming exercises producing working, well annotated code and associated support documentation (2 x 35%) and a written exam in the December diet (30%)
Feedback Not entered
Exam Information
Exam Diet Paper Name Hours & Minutes
Main Exam Diet S1 (December)Bioinformatics Programming and System Management3:00
Learning Outcomes
On completion of this course, the student will be able to:
  1. a knowledge of how computer systems, online tools and high-performance compute interact to enable bioinformatics experiments
  2. a knowledge of the biological and bioinformatic data and knowledgebases "ecosystem", and the application and use of workflow management systems
  3. a working knowledge of UNIX command line and systems administration
  4. an understanding of the core principles of scientific programming, including an understanding of the importance of code versioning and appreciation of the different kinds of programming language
  5. an ability to design and write working bioinformatics programmes in Python and Java
Reading List
There is no required text but students may find the following very useful:

Python
http://pythonforbiologists.com

UNIX
http://www.ubuntu.com/desktop
http://www.ee.surrey.ac.uk/Teaching/Unix/index.html

The NCBI BLAST tutorials at
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs
especially
http://www.ncbi.nlm.nih.gov/books/NBK21097/

Java
http://docs.oracle.com/javase/tutorial/
(for reference only)

SQL
http://sql.learncodethehardway.org/book/
Additional Information
Graduate Attributes and Skills Systems administration
Core principles of programming
Working in teams and on shared infrastructures
Time management
KeywordsBPSM
Contacts
Course organiserDr Alasdair Ivens
Tel:
Email:
Course secretaryMiss Emma Currie
Tel: (0131 6)50 5988
Email:
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