Programming in Bioinformatics

Course Description

COURSE CONTENT

Programming skills are now in strong demand in biology research and are an important new laboratory skill. The Perl (BioPerl) language makes it possible to start writing real programs quickly, BioJava and BioPython are becoming standard tools in lofe sciences. The programming language includes a collection of "protocols", or programming techniques, which can be useful in bioinformatics. There are certain operations with DNA and protein sequences and also protocols with which DNA can be translated into proteins. The essence of bioinformatics is dealing with large quantities of information. Because of that it is necessary to build biological databases. Biological databases allow the organisation of data, completeness and integrity, transformation from one form to another and efficient search through the data to find the desired information. The MySQL database is the world’s most popular, and some might argue, the best open source database. One can interface with MySQL using most popular programming languages, including PHP, Perl and Java. The SQL language is the universally accepted mechanism for accessing and manipulating data stored in a relational database. It is a text-based language where instead of the mathematical notations there are words from the English language.

LEARNING OUTCOMES

• students will learn basics of computer programming including core syntax of programming language
• students will learn basic Java language syntax, design programming flowcharts and control execution of source code. Students will get to know basic and most common Java classes.
• students will get to know basic bioinformatic algortihms, develop their own algortihms and deploy them in Java programming language.
• upon course completion, students will be able to solve biological problems independently, applying their knowledge of bioinformatics and computing.