Practical Bioinformatics for Biologists 20/21

Faculteit Science and Engineering
Jaar 2019/20
Vakcode WMLS15005
Vaknaam Practical Bioinformatics for Biologists 20/21
Niveau(s) master
Voertaal Engels
Periode semester I b
ECTS 5
Rooster rooster.rug.nl

Uitgebreide vaknaam Practical Bioinformatics for Biologists 20/21
Leerdoelen At the end of the course, the student is able to:
1) Understand and describe the origin(s) and properties of “big data”, in particular those coming from the ‘Omics
technologies’, evaluate the challenges they are posing in modern biology applications, and basic principles and
applications of bioinformatics.
2) Master a Linux/Unix environment: navigate and use the file system, including understanding directory
structure/permissions, and creating/editing/removing files. Work on remote computers and High Performance Computing (HPC) cluster. Install and run several types of software in this environment.
3) Handle, manage, explore, and extract information from big and complex data files (e.g. personal and public databases) using basic functionality and options of building block data analysis tools included in Unix-like operating systems.
4) Design and implement custom tools using scripting programming languages (e.g., Shell, R and/or Python) to explore, analyse, and visualize data.
5) Design and implement analytic pipeline consisting of combining, automatizing, and wrapping tasks/analyses using general command-line tools to address specific problems.
6) Integrate personal data or data from public databases into a concrete case study example and design (a) workflow(s) to address a given biological research question, choose the most appropriate method for its implementation, and reflect on the biological implications of results.
Omschrijving Practical Bioinformatics for Biologists (PBfB) introduces students to use general computational tools to work more effectively on a
daily basis. It pulls together a broad range of free powerful, and flexible tools that are applicable to geneticists, molecular biologists,
ecologists, oceanographers, physiologists, and anyone interested or in need of bioinformatics in their research. It features practical
use of bioinformatic techniques to solve real analysis problems.
PBfB will cover the “nuts and bolts” of data centered computing tasks in a Unix/Linux environment. Basics of using such an
environment, including installing and running software on remote machines will be introduced. Students will become familiar with
command line tools to explore and analyze data, and explore the use of scripting languages such as Python and R to (a) write
custom analysis tools as needed and (b) act as “glue” to make effective pipelines of other tools. Practical use of databases and
how to retrieve data from remote public databases will be introduced. Various data visualization technics, including among other GIS
tools, will be introduced using R statistical language.
Topics address in PBfB will use concrete example taken from various field, for example data from Next Generation Sequencing (NGS) technologies in genetics and molecular biology, as well as remote sensing and oceanographic data widely used in environmental ecological and evolutionary biology.
The course consists of short lectures featuring new concepts and examples interspersed with practical computer exercises and individual assignments. During the last week, students will prepare a project assignment in small groups featuring the use of the skills learned during the course and aiming at solving a concrete example. Students will present and explain their pipeline and results to the group in an oral presentation during the last days of the course.
Uren per week 40
Onderwijsvorm Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC), Werkcollege (T)
(During the first 3 weeks, presence to the course is mandatory since the students will have a combination of short lectures, tutorials and personal exercises. The final day of the course is project presentation day, and is also mandatory, since each student will present his project to the class.)
Toetsvorm Opdracht (AST), Practisch werk (PR)
(Final grade =(0.15 x PR1) + (0.15 x PR2) + (0.15 x PR3) + (0.55 x Opdr) PR1, PR2, PR3 = practical exercises of week 1, 2 and 3 AST = 1-week personal project with a short report, an online GIT repository & presentation. Final grade is the weighted average of the grades for the assignments of the first three weeks (each contributing 15%) and the grade for the personal project of the final week.)
Vaksoort master
Coördinator M.C. Fontaine, PhD.
Docent(en) M.C. Fontaine, PhD.
Verplichte literatuur
Titel Auteur ISBN Prijs
Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. O'Reilly Media; 1 edition (July 23, 2015) Vince Buffalo €  32,00
Practical computing for biologists. (1sted.) Haddock S.H.D. and Dunn C.W. 978-0878933914 ca. €  60,00
Course material provided to students via Nestor including also the course website (to be announced)
Entreevoorwaarden No a priori knowledge of bioinformatics is required for the course, but students are expected to have elementary computer skills and be comfortable with a computer.

Open for all with Bachelor or Master in Biological Sciences. Students belonging to the GELIFES MSc Biology: Marine Biology, Behavioural Neuroscience or Ecology and Evolution have first choice.
Opmerkingen Students are expected to bring their own personal laptops for the course. In the case a student would not have a laptop, one can be
provided during the course.
Specific instructions are send a few weeks ahead of the course on how to set-up the computer. Students should follow carefully and
meticulously those instructions
Opgenomen in
Opleiding Jaar Periode Type
MSc Biology: Modelling in the Life Sciences  (Electives/Optional modules) - semester I b keuze
MSc Biology: Research  (Compulsory master courses) - semester I b keuze
MSc Biology: Science, Business and Policy  (Compulsory master courses) - semester I b keuze
MSc Biomedical Sciences: Biology of Ageing  ( Master Courses) - semester I b keuzegroep
MSc Biomedical Sciences: Biology of Cancer and Immune System  (Electives ) - semester I b keuze
MSc Biomedical Sciences: Biology of Food and Nutrition  (Electives (10 ECTS)) - semester I b keuze
MSc Biomedical Sciences: Neuroscience  (Electives (10 ECTS)) - semester I b keuze
MSc Biomedical Sciences: Research  (Electives) - semester I b keuze
MSc Biomedical Sciences: Science, Business and Policy  (Electives (10 ECTS)) - semester I b keuze
MSc Biomolecular Sciences  (Electives/Optional modules) - semester I b keuze
MSc Ecology and Evolution: Ecology and Conservation  (Electives/optional modules) - semester I b keuze
MSc Ecology and Evolution: Evolutionary Biology  (Electives/optional modules) - semester I b keuze
MSc Marine Biology: Research  (Compulsory master courses) - semester I b keuze
Tweejaarlijkse vakken  (Even jaren) - semester I b -