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Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS MBG 6110 BIOINFORMATICS SCRIPTING AND PROGRAMMING ELECTIVE 3 0 0 12

Offered By

Molecular Biology and Genetics

Level of Course Unit

Third Cycle Programmes (Doctorate Degree)

Course Coordinator

ASSISTANT PROFESSOR GÖKHAN KARAKÜLAH

Offered to

Molecular Biology and Genetics Biomedicine and Health Technologies

Course Objective

This course aims to to provide students with scripting and programming skills for biological data analysis.

Learning Outcomes of the Course Unit

1   To be able to work with Linux command line 2   To be able to develop Bash scripts 3   To be able to use Python programming language for biological data analysis 4   To be able to access programmatically public databases to extract useful information with Python programming language 5   To be able to develop analysis pipelines for biological data analysis with Bash or Python

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description 1 Introduction to Linux 2 Bash scripting 3 Python strings, text, numbers, dates, and times 4 Iterators and generators 5 Files and I/O 6 Functions 7 Modules and Packages 8 Sequence objects and I/O 9 MIDTERM 10 Multiple sequence alignment and BLAST 11 Accessing public databases with BioPython 12 Pathway analysis 13 Sequence motif analysis 14 Cluster analysis 15 Supervised learning methods 16 Assignment Presentations

Recomended or Required Reading

Textbook(s): 1. Biopython Tutorial and Cookbook, Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczy ski 2. Beazley, David, and Brian K. Jones. Python cookbook. " O'Reilly Media, Inc.", 2013.

Planned Learning Activities and Teaching Methods

Face -to- Face Theoretical lectures with PowerPoint presentation and assignment presentations by students

Assessment Methods

Successful / Unsuccessful *** Resit Exam is Not Administered in Institutions Where Resit is not Applicable.

Further Notes About Assessment Methods

None

Assessment Criteria

To be announced.

Language of Instruction

English

Course Policies and Rules

To be announced.

Contact Details for the Lecturer(s)

gokhan.karakulah@deu.edu.tr

Office Hours

To be announced.

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours) Lectures 14 3 42 Preparation before/after weekly lectures 14 6 84 Preparation for Mid-term Exam 1 30 30 Preparation for Final Exam 1 37 37 Preparing Individual Assignments 12 5 60 Preparing Presentations 2 20 40 Final 1 3 3 Mid-term 1 4 4 TOTAL WORKLOAD (hours) 300

Contribution of Learning Outcomes to Programme Outcomes

PO/LO PO.1 PO.2 PO.3 PO.4 PO.5 PO.6 PO.7 PO.8 LO.1 3 LO.2 3 LO.3 3 LO.4 3 LO.5 3