SBIA10210U Applied Programming for Biosciences

Many different areas of biosciences struggle with two large challenges. Firstly the amount of data that can be generated by just one experiment in very short time can be huge and a meaningful filtering can only be carried out by computational means. Secondly, processing of data can often at best be made with existing webservers, but even in that case output data from one webserver often needs to be converted and filtered to be suitable for input to another and given the quantities of data this is often not feasible to do by hand. Knowing basic programming is therefore an essential skill for a person working in the biosciences.

The aim of the course is to make the students able to analyze and process large biological data sets by writing and running Perl programs.
The course gives an introduction to data processing and filtering using the
programming language Perl. Thus the course also introduce the programming language Perl itself. The course is aimed at students with no prior programming experience. 

The course will cover how to learn new concepts in the Perl language.
The outset is specific cases of biosciences by analyzing and redesigning existing pre-designed code that process data from the specific cases. Various ways to acquire information (for example perldoc)

With outset in the cases the pre-designed code will be analyzed and concepts introduced as the different code pieces are introduced through their specific applications. The cases will complement each other concepts and the technical level will be increased from case to case. Through the cases it will also be demonstrated how to design a modular chain of programs of which some can be used in multiple contexts. Some Perl programs can for example be general by converting one data format to another and can therefore be reused in
multiple contexts. Overall the most common and useful features of the language will be introduced. Including:
* Printing to the screen.
* Single value variables (scalars).
* Multivalue variables like arrays and hashes.
* The if else control structure.
* The while, for and foreach loops.
* Reading data into the program using the general operator '<>', or reading from a file.
* Writing results to a file.
* A basic introduction to using Perl's powerful pattern matching method called regular expressions.

The course will also introduce how to write well structured code. This will include splitting code into smaller subroutines and the usage of packages.