Postgraduate Course: Bioinformatics Programming and System Management (PGBI11095)
|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
|Summary||The course will provide Bioinformatics MSc (and other postgraduate) students with a working overview of computer systems, programming and software components advantageous to a career in bioinformatics, or graduate research. The course comprises examples of the different ways we could use bioinformatics software and environments and introduces the programming language Python.
(Note that the order and number of course components given below may change)
The UNIX environment: system administration, using AWK, accessing ECDF (Edinburgh Compute and Data Facility)
The Bioinformatic web: Databases, servers, web services, file formats, workflow management systems
git and github
BLAST: using BLAST to explore biological data
Relational (SQL) databases
Programming in Python
Course Delivery Information
|Academic year 2020/21, Not available to visiting students (SS1)
|Learning and Teaching activities (Further Info)
Lecture Hours 20,
Supervised Practical/Workshop/Studio Hours 40,
Programme Level Learning and Teaching Hours 4,
Directed Learning and Independent Learning Hours
|Assessment (Further Info)
|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 an open-book exam in the December diet (30%)
||Written feedback will be given for both assessments. Additional feedback may also be given in week 11. Written feedback will be provided for the exam.
||Hours & Minutes
|Main Exam Diet S1 (December)||3:00|
On completion of this course, the student will be able to:
- A knowledge of how computer systems, online tools and high-performance compute interact to enable bioinformatics experiments
- A knowledge of the biological and bioinformatic data and knowledge bases "ecosystem", and the application and use of workflow management systems.
- A working knowledge of UNIX command line and basic systems administration.
- 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.
- An ability to design and write working bioinformatics programmes in Python.
|It would be helpful if students could ensure they know their way around the Windows or UNIX graphical desktop. Most of the course will be taught using the UNIX command line - we strongly advise students to familiarize themselves with the UNIX command line before the course starts in order to get the most out of the teaching sessions. |
You can work through introductory UNIX workbooks online for free:
There is no required text but students may find the following useful:
The NCBI BLAST tutorials at
|Graduate Attributes and Skills
Core principles of programming
Working in teams and on shared infrastructures
|Course organiser||Dr Alasdair Ivens
Tel: (0131 6)513605
|Course secretary||Ms Louise Robertson
Tel: (0131 6)50 5988