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 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 two programming languages: Python and Java. |
| Course description |
Course Description/Syllabus
Note that the order 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, webservices, file formats, workflow management systems
BLAST: using BLAST to explore biological data
Relational (SQL) databases
Programming in Python (nine lectures)
Programming in Java (six lectures)
Advised preparatory work
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
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Course Delivery Information
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| Academic year 2018/19, Not available to visiting students (SS1)
|
Quota: 49 |
| 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 |
Written feedback will be given for both assessments. Additional feedback will also be given in week 11. Written feedback will be provided for the exam. |
| Exam Information |
| Exam Diet |
Paper Name |
Hours & Minutes |
|
| Main Exam Diet S1 (December) | Bioinformatics Programming and System Management | 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 knowledgebases "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 and Java
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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/
https://www.lynda.com/SQL-tutorials/SQL-Essential-Training/139988-2.html |
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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