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. |
| Course description |
Course Description / Syllabus
1 Introduction. The unix environment.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 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 |
| High Demand Course? |
Yes |
Course Delivery Information
|
| Academic year 2016/17, Available to all students (SV1)
|
Quota: 43 |
| 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
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 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
|
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
|
| Keywords | BPSM |
Contacts
| Course organiser | Dr Alasdair Ivens
Tel:
Email: Al.Ivens@ed.ac.uk |
Course secretary | Miss Emma Currie
Tel: (0131 6)50 5988
Email: Emma.Currie@ed.ac.uk |
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