Syllabus for Informatics Toolbox for Systematics

Learning outcomes

The course intends to give the student a set tool (in the form of Perl, MySQL and R) to handle, store, structure, analyse and visualise data in a molecular-systematic project.

On completion of the course, the student should be able to:

• choose and apply existing applications in Perl, MySQL and R
• design simple databases in MySQL
• write new or modify existing scripts (in Perl, SQL and R) to solve simple problems
• outline solutions to information flow based on Perl, R and SQL for a systematic research project

Content

The course presents and applies the most popular open environments in bioinformatics to design practical solutions to concrete problems within the systematics.

- Automation of bioinformatic data management; application of bioinformatics, from process to algorithm, to solve problems through programming

- Biological databases with MySQL; common database types, design of relational databases, configuration of MySQL server, data management with SQL

- Automation with Perl; basic syntax and logic, references, subroutines and modules, regular expressions, file management, Perl DBI

- Numerical data analysis with R; data structures, import of data, visualisation, programs in R, multivariate data analysis (clustering, PCA, classification) in R, program package in R, interface with MySQL

- Programming for the web; Apache web server, HTML and XHTML, CGI with Perl, CSS, Ecmascript, visualisation with Perl, CGI and R

Instruction

The teaching is given in the form of e-teaching

Assessment

Parts of the course: Theory 2 HE credits, Practice 3 HE credits

The theory part is examined by a computer-based test

If there are special reasons for doing so, an examiner may make an exception from the method of assessment indicated and allow a student to be assessed by another method. An example of special reasons might be a certificate regarding special pedagogical support from the disability coordinator of the university.