Syllabus for Informatics Toolbox for Systematics

Systematikens verktygslåda - informatik

Syllabus

  • 5 credits
  • Course code: 1BG395
  • Education cycle: Second cycle
  • Main field(s) of study and in-depth level: Biology A1F, Applied Biotechnology A1F
  • Grading system: Fail (U), Pass (3), Pass with credit (4), Pass with distinction (5)
  • Established: 2012-03-08
  • Established by:
  • Revised: 2021-02-11
  • Revised by: The Faculty Board of Science and Technology
  • Applies from: week 30, 2021
  • Entry requirements: 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. English language proficiency that corresponds to English studies at upper secondary (high school) level in Sweden ("English 6").
  • Responsible department: Biology Education Centre

Learning outcomes

The course intends to give the student a set tool (in the form of Perl, relation databases 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, relation databases and R
  • design simple relation databases
  • write new or modify existing code (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 relation databases; common database types, design of relational databases, 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, program packages in R, interface with databases.
- Programming for the web; Apache web server, HTML, Perl programming for the web and CSS.

Instruction

The teaching is given in the form of e-teaching

Assessment

Course parts: Theory 2 credits, Lab practicals 3 credits
The theory part is examined through active participation in web seminars and web fora. The lab practicals are examiend through assignments.

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.

Reading list

Reading list

Applies from: week 30, 2021

Some titles may be available electronically through the University library.

  • Bessant, Conrad; Oakley, Darren; Shadforth, Ian Building bioinformatics solutions : with Perl, R, and SQL

    Second edition.: Oxford, United Kingdom: Oxford University Press, 2014

    Find in the library