Postgraduate Course: Bioinformatics Programming and System Management (PGBI11095)
Course Outline
| School | School of Biological Sciences |
College | College of Science and Engineering |
| Course type | Standard |
Availability | Available to all students |
| Credit level (Normal year taken) | SCQF Level 11 (Postgraduate) |
Credits | 20 |
| Home subject area | Postgraduate |
Other subject area | None |
| Course website |
None |
Taught in Gaelic? | No |
| Course description | The 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.
The course help students attain expert proficiency in
1 a knowledge of modern computer systems, the working of the internet, virtualisation, the grid and the cloud
2 a knowledge of the ¿ecology¿ of biological and bioinformatic data and knowledge bases available on the internet, 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 available for bioinformatics programming
5 an ability to write working bioinformatics programmes in python (or other competent programming language)
6 an understanding of the role of object-oriented programming in bioinformatics, and a working knowledge of programming in java
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Entry Requirements (not applicable to Visiting Students)
| Pre-requisites |
|
Co-requisites | |
| Prohibited Combinations | |
Other requirements | None |
| Additional Costs | None |
Information for Visiting Students
| Pre-requisites | None |
| Displayed in Visiting Students Prospectus? | No |
Course Delivery Information
|
| Delivery period: 2013/14 Semester 1, Available to all students (SV1)
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Learn enabled: Yes |
Quota: None |
Web Timetable |
Web Timetable |
| Course Start Date |
16/09/2013 |
| Breakdown of Learning and Teaching activities (Further Info) |
Total Hours:
200
(
Lecture Hours 20,
Seminar/Tutorial Hours 12,
Supervised Practical/Workshop/Studio Hours 8,
Programme Level Learning and Teaching Hours 4,
Directed Learning and Independent Learning Hours
156 )
|
| Additional Notes |
|
| Breakdown of Assessment Methods (Further Info) |
Written Exam
30 %,
Coursework
70 %,
Practical Exam
0 %
|
| Exam Information |
| Exam Diet |
Paper Name |
Hours:Minutes |
|
|
| Main Exam Diet S1 (December) | Bioinformatics Programming and System Management | 3:00 | | |
Summary of Intended Learning Outcomes
1 a knowledge of modern computer systems, the working of the internet, virtualisation, the grid and the cloud
2 a knowledge of the ¿ecology¿ of biological and bioinformatic data and knowledgebases available on the internet, 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 write working bioinformatics programmes in python
6 an ability to write working object-oriented bioinformatics programmes in java
|
Assessment Information
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%)
|
Special Arrangements
| None |
Additional Information
| Academic description |
Not entered |
| Syllabus |
1 Introduction. The unix environment. Real and virtual machines, 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 Versioning software (github); 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
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| Transferable skills |
Systems administration
Core principles of programming
Working in teams and on shared infrastructures
Time management
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| Reading list |
Not entered |
| Study Abroad |
Not entered |
| Study Pattern |
- lectures (~20)
- tutorials (~12)
- hands-on workshops (~4)
- demonstrations (~4)
- group work
- self-learning
- homework exercises
- assessed exercises
|
| Keywords | BPSM |
Contacts
| Course organiser | Prof Mark Blaxter
Tel: (0131 6)50 6760
Email: Mark.Blaxter@ed.ac.uk |
Course secretary | Miss Vicky Mactaggart
Tel: (0131 6)51 7052
Email: Vicky.Mactaggart@ed.ac.uk |
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