SubjectsSubjects(version: 853)
Course, academic year 2019/2020
  
Practical Classes in Bioinformatics II - M143011
Title: Praktikum z bioinformatiky II
Guaranteed by: Department of Informatics and Chemistry (143)
Actual: from 2019
Semester: summer
Points: summer s.:2
E-Credits: summer s.:2
Examination process: summer s.:
Hours per week, examination: summer s.:0/2 MC [hours/week]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type: Master's (post-Bachelor)
Guarantor: Znamenáček Jiří Ing.
Examination dates   Schedule   
Annotation -
Last update: Znamenáček Jiří Ing. (22.02.2018)
This is the follow-up course for "Practical Classes in Bioinformatics I" and continues in exercising practical bioinformatics programming.
Aim of the course -
Last update: Znamenáček Jiří Ing. (22.02.2018)

Students will be able to:

Use existing bioinformatics tools for their own work.

Understand the principles of the most important bioinformatics challenges.

Solve basic bioinformatics problems using Python programming language.

Literature -
Last update: Znamenáček Jiří Ing. (05.11.2018)

R: Libeskind-Hadas, Ran; Bush, Eliot: "Computing for Biologists: Python Programming and Principles". Cambridge University Press, 2014. ISBN 978-1107642188

R: Mareš, Martin; Valla, Tomáš: "Průvodce labyrintem algoritmů". CZ.NIC, 2017. ISBN 978-80-88168-22-5

R: Jones, Neil C.; Pevzner, Pavel A.: "An Introduction to Bioinformatics Algorithms". The MIT Press, 2004. ISBN 978-0262101066

A: Antao, Tiago: "Bioinformatics with Python Cookbook". Packt Publishing, 2015. ISBN 978-1782175117

A: Wróblewski, Piotr: "Algoritmy". Computer Press, 2017. ISBN 978-80-251-4126

A: Bassi, Sebastian: "Python for Bioinformatics". Chapman and Hall/CRC, 2009. ISBN 978-1584889298

A: Compeau, Phillip; Pevzner, Pavel: "Bioinformatics Algorithms: An Active Learning Approach". Active Learning Publishers, 2014. ISBN 978-0990374602

A: Pilgrim, Mark: "Ponořme se do Python(u) 3". CZ.NIC, 2011. ISBN 978-80-904248-2-1

A: Stevens, Tim J.; Boucher, Wayne: "Python Programming for Biology: Bioinformatics and Beyond". Cambridge University Press, 2015. ISBN 978-0521720090

A: Haddock, Steven H.D.; Dunn, Casey W.: "Practical Computing for Biologists". Sinauer Associates, 2010. ISBN 978-0878933914

Learning resources -
Last update: Znamenáček Jiří Ing. (14.02.2018)

web pages of the course at http://vyuka.ookami.cz

Requirements to the exam -
Last update: Znamenáček Jiří Ing. (14.02.2018)

A graded credit: homeworks and presentation on the given subject

Syllabus -
Last update: Znamenáček Jiří Ing. (15.02.2018)

1-2. Algorithm complexity II. Problémy třídy složitosti P a NP.

3-5. Protein folding. RNA structure.

6-8. Graph algorithms. Genome assembly.

9. Phylogenetics.

10. Genové regulatory networks.

11-14. Neural networks. Machine learning.

Registration requirements -
Last update: Znamenáček Jiří Ing. (14.02.2018)

Practical Classes in Bioinformatics I

Course completion requirements -
Last update: Znamenáček Jiří Ing. (14.02.2018)

Students will be graded by the work done on home exercises and the presentation on the given subject.

Teaching methods
Activity Credits Hours
Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi 1 28
Účast na seminářích 1 28
2 / 2 56 / 56
Coursework assessment
Form Significance
Homework preparation 40
Defense of an individual project 60

 
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