Biocomputing

Course provider:
Faculty of Life Sciences, The University of Manchester

Course contact:
Azzam Maki (azzam.maki@man.ac.uk)

Summary:
Computational biology, or Biocomputing, is concerned with the development of methods for the efficient storage and processing of biological data. A large part of the work of computational biologists thus consists of the management and analysis of strings of characters. These strings may be nucleic acid or protein sequences, or their annotation. This module introduces perl, for data processing, and database design. Participants must have some prior programming experience.

Syllabus:

Unix Understand the basics of the unix operating system

Data interchange and display Understand the use of markup languages for documents and data

CGI and perl Use perl in a web application

Relational database design Understand and apply the principles of relational database design

The data:user interface Reflect on the needs of the data user

Assessment

To qualify for course credits you need to submit the following::

First assessment: for this assessment you should submit:

core project: design a web form and write a CGI script to return some results to the user.(40%)

Second assessment: for this assessment you should submit:

core project: design of a database for a relational database management system.(50%)

Use PHP to create and design a web front page for your database (10%).

You will be assessed on your contributions to the discussion of the design of each project, and also on your individual implementation.

The members of the course team retain the right to viva any participant on any piece of work submitted.

Further details:
All the course materials are provided within the Virtual Learning Environment. The tools provided will allow you to navigate and search through course notes, protocols, practicals and references to useful texts and URLs.
Within the course you will be provided with course notes as Web pages. These will be used to provide the necessary background to the focus of the course, which is problem-based learning. You will interact with the members of the course team, and with other learners, through study rooms, email, and 'chat rooms' for on-line tutorials.

Technical requirements:
To take the course you will need access to a computer with a Java-enabled browser. This means that you will need Netscape 3.0 or above or Internet Explorer, version 4.
To be able to work on our server (Bio-Linux), it is recommended to have Linux emulator on your machine. Cygwin is a Linux-like environment for Windows, which enable you to run Linux GUI (x windows) programs on your PC. You'll provided with full instruction on installing this software in the course. Alternative to Cygwin you might prefer to install SSH and a secured file transfer program (PSFTP) or (WinSCP 3.5 for windows) for your work on the course server (Bio-Linux).
For the section of the course covering database design , we prefer that you do the project on our server using MySQL. But you might need, as well, to have a copy of Microsoft Access installed on your machine.
We would also prefer that you return your text documents to us as Microsoft Word files.

Recommended reading :
Two essentials book are needed: one to cover Perl and CGI section; the other to cover Relational database design section:
Mastering Perl for Bioinformatics,James Tisdall, O'REILLY (2003)
Beginning Perl for Bioinformatics , James Tisdall , O'REILLY (2001)
Learning Perl (3rd Edition), Randal L. Schwartz et al. O'Reilly & Associates (2001)
Database Solutions, Thomas Connolly and Carolyn Begg, Addison-Wesley (2000)
Useful texts
Unix in a Nutshell : System V v 2.0 Daniel Gilly & Mike Loukides, O'Reilly & Associates (1995)
Unix is a Four Letter Word..., Christopher C. Taylor, http://unix.t-a-y-l-o-r.com/
NCSA (at UIUC) Beginner's Guide to HTML, http://www.ncsa.uiuc.edu/General/Internet/WWW/HTMLPrimerAll.html
Biological Mark-up Language Tutorial, http://www.rdcormia.com/COIN79/Bio_XML_overview/bio-xml_intro.html

Course provider:	Faculty of Life Sciences, The University of Manchester
Course contact:	Azzam Maki (azzam.maki@man.ac.uk)
Summary:	Computational biology, or Biocomputing, is concerned with the development of methods for the efficient storage and processing of biological data. A large part of the work of computational biologists thus consists of the management and analysis of strings of characters. These strings may be nucleic acid or protein sequences, or their annotation. This module introduces perl, for data processing, and database design. Participants must have some prior programming experience.
Syllabus:
	Unix	Understand the basics of the unix operating system
Data interchange and display	Understand the use of markup languages for documents and data
CGI and perl	Use perl in a web application
Relational database design	Understand and apply the principles of relational database design
The data:user interface	Reflect on the needs of the data user
Assessment	To qualify for course credits you need to submit the following:: First assessment: for this assessment you should submit: core project: design a web form and write a CGI script to return some results to the user.(40%) Second assessment: for this assessment you should submit: core project: design of a database for a relational database management system.(50%) Use PHP to create and design a web front page for your database (10%). You will be assessed on your contributions to the discussion of the design of each project, and also on your individual implementation. The members of the course team retain the right to viva any participant on any piece of work submitted.
Further details:	All the course materials are provided within the Virtual Learning Environment. The tools provided will allow you to navigate and search through course notes, protocols, practicals and references to useful texts and URLs. Within the course you will be provided with course notes as Web pages. These will be used to provide the necessary background to the focus of the course, which is problem-based learning. You will interact with the members of the course team, and with other learners, through study rooms, email, and 'chat rooms' for on-line tutorials.
Technical requirements:	To take the course you will need access to a computer with a Java-enabled browser. This means that you will need Netscape 3.0 or above or Internet Explorer, version 4. To be able to work on our server (Bio-Linux), it is recommended to have Linux emulator on your machine. Cygwin is a Linux-like environment for Windows, which enable you to run Linux GUI (x windows) programs on your PC. You'll provided with full instruction on installing this software in the course. Alternative to Cygwin you might prefer to install SSH and a secured file transfer program (PSFTP) or (WinSCP 3.5 for windows) for your work on the course server (Bio-Linux). For the section of the course covering database design , we prefer that you do the project on our server using MySQL. But you might need, as well, to have a copy of Microsoft Access installed on your machine. We would also prefer that you return your text documents to us as Microsoft Word files.
Recommended reading :	Two essentials book are needed: one to cover Perl and CGI section; the other to cover Relational database design section: Mastering Perl for Bioinformatics,James Tisdall, O'REILLY (2003) Beginning Perl for Bioinformatics , James Tisdall , O'REILLY (2001) Learning Perl (3rd Edition), Randal L. Schwartz et al. O'Reilly & Associates (2001) Database Solutions, Thomas Connolly and Carolyn Begg, Addison-Wesley (2000) Useful texts Unix in a Nutshell : System V v 2.0 Daniel Gilly & Mike Loukides, O'Reilly & Associates (1995) Unix is a Four Letter Word..., Christopher C. Taylor, http://unix.t-a-y-l-o-r.com/ NCSA (at UIUC) Beginner's Guide to HTML, http://www.ncsa.uiuc.edu/General/Internet/WWW/HTMLPrimerAll.html Biological Mark-up Language Tutorial, http://www.rdcormia.com/COIN79/Bio_XML_overview/bio-xml_intro.html

Back to module page

Updated 2 July 2009 by Heather Vincent