Postgraduate Course: Building a Bioinformatics Workstation (PGBI11058)
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 | 10 |
| Home subject area | Postgraduate |
Other subject area | None |
| Course website |
None |
Taught in Gaelic? | No |
| Course description | Bioinformaticians commonly work in environments where there is no centralised computer infrastructure and no specialist help to support the development of such an infrastructure.
The ability to set up a functioning bioinformatics workstation in the absence of any external support is an absolutely essential skills for bioinformaticians to have.
In this course we will teach students how to develop their own workstation and how to establish a functioning bioinformatics application that can be accessed (with approriate levels of security) across the internet. |
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
| Not being delivered |
Summary of Intended Learning Outcomes
- Students will have the ability to establish a working Linus server system given a blank system and a set of install disks.
- Students will be able to write a small shell script that automates a data download process
- Students will be able to install MySQL, establish a database within this system and insert, edit and retrieve data from this database using SQL.
- Students will be able to establish an instance of Blast and use this to query a locally installed sequence database.
- Students will be able to write a basic web interface to Blast and use this to query their locally installed Blast instance. |
Assessment Information
Students will be assessed by:
1. Examination (50%)
2. Practical Assessment of their ability to develop a functioning bioinformatics workstation (50%) |
Special Arrangements
| None |
Additional Information
| Academic description |
Not entered |
| Syllabus |
* Establishing a Linux server within a virtual host
* Professional issues of system management including aspects of network and data security, protection and management
* Installing, configuring and running the Apache web server and the Tomcat servlet container
* Writing and running shell scripts
* TCPIP networking, including security and networking protocols
* Installing Blast and associated data
* Establishing an instance of the MySQL database including installing and querying data using MySQL
* Building a web interface using Perl and Php and interfacing with Blast and MySQL |
| Transferable skills |
Not entered |
| Reading list |
Not entered |
| Study Abroad |
Not entered |
| Study Pattern |
Not entered |
| Keywords | BBW |
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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