Postgraduate Course: Bioinformatics Programming and System Management (PGBI11095)
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 | 20 |
ECTS Credits | 10 |
| Summary | The Bioinformatics Programming and System Management (BPSM) course is a compulsory component of the Bioinformatics MSc programme, and is designed to provide you with a working overview of computer systems, programming and software components advantageous to whatever you wish to do with your bioinformatics career, whether that is setting up your own business, or working for a big pharmaceutical company, or in the academic environment, going on to do a PhD and running a research group. Each of you is coming from a different viewpoint/background, and with the Bioinformatics degree, we try to maximise the opportunities for you, whatever it is you have chosen. |
| Course description |
The BPSM course comprises examples of the different ways we could use bioinformatics software in the Linux environment, as well as introducing the Python programming language. It is important to note that we start everyone off at level zero: we assume that you have no experience of using computers to answer biological questions! Remember, this is BIO-informatics, so the emphasis is very much on using the tools and procedures we learn to help you analyse, and more importantly, interpret, biological data. We do not attempt to make you into IT managers that could go straight into some large accounting firm: if that is really what you want to do, this is not the course (or perhaps degree) for you!
What sort of things do we do? The course is structured such that we have two three-hour lecture/workshops per week, and we do those in person. Within each of these, a topic is covered, you do some exercises on that topic, and then at the end of each session, we go through possible answers to the exercises, answer questions, etc.
We start our journey learning some of the more useful Linux commands for use on our course servers, and over subsequent lessons, the complexity increases, including SQL, BLAST, and learning how to use git and GitHub, culminating in the first assessment task, which involves writing a programme that interacts with the user. When you get your marks back, there will be detailed feedback given.
Towards the second half of the semester, we learn about Python, and how to use it. The emphasis here is learning how to write your own Python code, not just use modules that are already out there on the shelf. The second course assignment also involves writing a user-interactive biological programme, but this time in Python, and drawing on all that has been learnt over the course of the Semester; once again, you will get detailed feedback on what you have submitted for the assignment. The final assessment component is the exam in December, for which more details will be made available during the course itself.
The BPSM course is, as already mentioned, a compulsory component of the MSc Bioinformatics degree. The degree has several compulsory components, but also several elective courses: the ones you get to choose. When it comes to doing your project, you will get to actually use/integrate all the knowledge that you have gained over the course of the two semesters, so if there is ever anything you don't understand when doing a course, please just ask straight away....we are here to help you, whichever course it is!
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Course Delivery Information
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| Academic year 2024/25, Not available to visiting students (SS1)
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Quota: 50 |
| 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 )
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| Assessment (Further Info) |
Written Exam
30 %,
Coursework
70 %,
Practical Exam
0 %
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| 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 closed book in person exam in the December diet (30%)
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| Feedback |
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. |
| Exam Information |
| Exam Diet |
Paper Name |
Hours & Minutes |
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| Main Exam Diet S1 (December) | | 3:00 | |
Learning Outcomes
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.
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Reading List
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:
http://www.ed.ac.uk/schools-departments/information-services/help-consultancy/is-skills/catalogue/program-op-sys-catalogue/unix1
There is no required text but students may find the following 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/
SQL
https://www.lynda.com/SQL-tutorials/SQL-Essential-Training/139988-2.html
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Additional Information
| Graduate Attributes and Skills |
Systems administration
Core principles of programming
Working in teams and on shared infrastructures
Time management
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| Keywords | BPSM |
Contacts
| Course organiser | Dr Alasdair Ivens
Tel: (0131 6)513605
Email: Al.Ivens@ed.ac.uk |
Course secretary | Ms Louise Robertson
Tel: (0131 6)50 5988
Email: Louise.K.M.Robertson@ed.ac.uk |
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