IV114 Bioinformatics and Systems Biology Project

Faculty of Informatics
Autumn 2022
Extent and Intensity
0/1/1. 2 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
Teacher(s)
doc. Ing. Matej Lexa, Ph.D. (lecturer)
Mgr. Marie Krátká (seminar tutor)
Guaranteed by
doc. Ing. Matej Lexa, Ph.D.
Department of Machine Learning and Data Processing – Faculty of Informatics
Supplier department: Department of Machine Learning and Data Processing – Faculty of Informatics
Timetable
Mon 14:00–15:50 B410
Prerequisites
The students should have finished IV107 Bioinformatics I, be acquainted with NGS/sequencing data processing tools and have elementary programming skills in any programming language/environment (optimally UNIX with C/C++/Java and Perl/Python) or consent of the lecturer
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
In this course the students will:
get acquainted with DNA nanopore sequencing
be able to select appropriate bioinformatic tools for a given problem
be able to carry out independent analysis of bioinformatic data
present their results to their colleagues
Learning outcomes
In this course the students will:
get acquainted with DNA nanopore sequencing
be able to select appropriate bioinformatic tools for a given problem
be able to carry out independent analysis of bioinformatic data
present their results to their colleagues
Syllabus
  • Familiarization with DNA sequencing using minION technology
  • Preparation of student proposals in pairs (selection of material for sequencing; preparation of bioinformatic tools and pipelines)
  • Analysis phase (DNA sequencing and data collection; data processing by filtration, mapping and assembly; visualization)
  • Student mini-conference and optional participation in paper writing (depending on quality of results)
Literature
  • ZVELEBIL, Marketa J. and Jeremy O. BAUM. Understanding bioinformatics. New York, N.Y.: Garland Science, 2008, xxiii, 772. ISBN 9780815340249. info
Teaching methods
student projects, their presentation and class discussion
Assessment methods
written project proposal and summary, presentation of project results
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, Autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, Autumn 2021, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (Autumn 2022, recent)
  • Permalink: https://is.muni.cz/course/fi/autumn2022/IV114