Syllabus for Informatics Toolbox for Systematics
Systematikens verktygslåda - informatik
A revised version of the syllabus is available.
- 5 credits
- Course code: 1BG395
- Education cycle: Second cycle
Main field(s) of study and in-depth level:
Applied Biotechnology A1F
- Grading system: Fail (U), Pass (3), Pass with credit (4), Pass with distinction (5)
- Established: 2012-03-08
- Established by:
- Revised: 2018-08-30
- Revised by: The Faculty Board of Science and Technology
- Applies from: Autumn 2019
150 credits including (1) 60 credits in biology and 30 credits in chemistry or 30 credits in earth science, or (2) 90 credits in biology, in both cases including Fundamental and Molecular Systematics, 10 credits, or Evolutionary Patterns, 15 credits. Proficiency in English equivalent to the Swedish upper secondary course English 6.
- Responsible department: Biology Education Centre
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
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
The teaching is given in the form of e-teaching
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.
- Latest syllabus (applies from Autumn 2023)
- Previous syllabus (applies from Autumn 2021)
- Previous syllabus (applies from Autumn 2019)
- Previous syllabus (applies from Autumn 2012)
Applies from: Autumn 2019
Some titles may be available electronically through the University library.
Building bioinformatics solutions : with Perl, R, and SQL
Second edition.: Oxford, United Kingdom: Oxford University Press, 2014