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 | Available to all students |
| SCQF Credits | 20 |
ECTS Credits | 10 |
| Summary |
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 will 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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| Course description |
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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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-requisites | None |
Course Delivery Information
|
| Academic year 2014/15, Available to all students (SV1)
|
Quota: 23 |
| 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 Management | 3:00 | |
Learning Outcomes
¿ a knowledge of modern computer systems, the working of the internet, virtualisation, the grid and the cloud
¿ 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
¿ a working knowledge of UNIX command line and 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 write working bioinformatics programmes in python
an ability to write working object-oriented bioinformatics programmes in 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/
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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 | Mr Martin Jones
Tel: (0131 6)50 7403
Email: martin.jones@ed.ac.uk |
Course secretary | Miss Vicky Mactaggart
Tel: (0131 6)51 7052
Email: Vicky.Mactaggart@ed.ac.uk |
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