Practical Bioinformatics for Biologists

Faculteit Science and Engineering
Jaar 2021/22
Vakcode WMBY008-05
Vaknaam Practical Bioinformatics for Biologists
Niveau(s) master
Voertaal Engels
Periode semester I b (06-12-2021 till 26-12-2021)

Uitgebreide vaknaam Practical Bioinformatics for Biologists
Leerdoelen At the end of the course, the student is able to:

1) understand and characterize the origin(s) and properties of big data;, in particular data obtained using 'omics technologies; evaluate and solve challenges in analyses of big data in modern biological applications, as well as the basic principles and applications of bioinformatics.

2) connect with and work remotely on high performance computing clusters; master a Linux/Unix environment: navigate and use the file system, such as; understanding directory structure/permissions, and creating/editing/removing files as well as install and execute software.

3) manage, extract and explore information contained in large, complex data files using the basic functions and options included in standard 'nix data analysis tools.

4) design, implement and automate custom pipelines using scripting languages (e.g., BASH, R and/or Python) to explore, analyse, and visualize data.

5) develop data analysis pipelines and apply those to her/his own research data or publicly accessible data in a case study and critically evaluate and assess the results in a biological context.
Omschrijving Practical Bioinformatics for Biologists (PBfB) introduces students to general computational tools in order to enable to design and execute efficient computations. PBfB presents a broad range of open-source, free and flexible computational tools applicable to geneticists, molecular biologists, ecologists, oceanographers, physiologists, or anyone with an interest or need for bioinformatics in their research. PBfB emphasizes the practical application of bioinformatic methods to solve real-life analyses.

PBfB covers data -centered computing in a Unix/Linux environment. PBfB introduces the basics of a 'nix environment, such as; remote installation and execution of software. Students will be familiar with command line tools to explore and analyze data as well as the use of scripting languages such as Python and R to (a) code custom analyses and (b) to design effective pipelines of existing software. The use of databases and retrieval of data from public on-line databases will be introduced. Data visualization techniques will be introduced using the statistical language R.

Topics addressed in PBfB will employ practical example from different research fields, e.g., Next Generation Sequencing (NGS) data in genetics and molecular biology, as well as remote sensing and oceanographic data widely used in spatial ecological and evolutionary biology.

The course consists of short lectures featuring new concepts and examples as well as practical computer exercises and individual assignments. In the last week, students will conduct a project assignment in small groups implementing the use of skills acquired during the course, aimed at solving real-life analyses. Students will present their pipeline and results to the class 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 two 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 mandatory, since each student will present his project to the class.)
Toetsvorm Opdracht (AST), Practisch werk (PR)
(Final grade =(0.25 x PR1)+(0.25 x PR2)+(0.50 x AST) PR1 and PR2 = practical exercises during week 1 and 2 AST = one-week (3rd week) personal project concluding in a short report, an on-line repository & presentation. Final grade is the weighted average of the grades for the assignments of the first three weeks (each contributing 25%) and the personal project (50%).)
Vaksoort master
Coördinator prof. dr. P.J. Palsboll
Docent(en) prof. dr. H.L. Dugdale , Guest lecturer ,prof. dr. P.J. Palsboll ,dr. J.P. van der Zee
Verplichte literatuur
Titel Auteur ISBN Prijs
Course material provided to students via Nestor including also the course website (to be announced)
Computing Skills for Biologists. Princeton University Press. 2019 S. Allesina & M. Wilmes 9780691167299
Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. O'Reilly Media; 1st Edition 2015 Vince Buffalo 978-1449367374 €  32,00
Entreevoorwaarden No prior knowledge of bioinformatics is required for the course, but students are expected to have elementary computer skills and be comfortable with a computer.
Opmerkingen The course is highly recommended for students planning to take other, computational courses in the Master program, such as Meta-analyses in Ecology (WMBY013-05), Principles of Population Genetics in Natural Populations (WMMB005-05), Practical Modeling for Biologists (WMBY009-05), Mathematical Models in Ecology and Evolution (WMEV013-06), and in general for students in evolutionary biology and genetics/genomics.

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.

The course is limited to 25 students.
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
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