MBG4059 Computational Methods in BioinformaticsBahçeşehir UniversityDegree Programs ENERGY SYSTEMS ENGINEERINGGeneral Information For StudentsDiploma SupplementErasmus Policy StatementNational QualificationsBologna Commission
ENERGY SYSTEMS ENGINEERING
Bachelor TR-NQF-HE: Level 6 QF-EHEA: First Cycle EQF-LLL: Level 6

Course Introduction and Application Information

Course Code Course Name Semester Theoretical Practical Credit ECTS
MBG4059 Computational Methods in Bioinformatics Fall 3 0 3 6
This catalog is for information purposes. Course status is determined by the relevant department at the beginning of semester.

Basic information

Language of instruction: English
Type of course: Non-Departmental Elective
Course Level: Bachelor’s Degree (First Cycle)
Mode of Delivery: Face to face
Course Coordinator : Dr. Öğr. Üyesi ELIZABETH HEMOND
Course Objectives: The goal of this course is to provide an understanding of the fundamental computational methods used in bioinformatics and the set of algorithms that have important applications both inside and outside of the bioinformatics field.

Learning Outcomes

The students who have succeeded in this course;
1. Recognize the fundamental models of computation useful in modeling nucleic acid and protein sequences.
2. Design and implement algorithms useful for analyzing various molecular biology data.
3. Discuss Genetic Algorithm and its applications in bioinformatics.
4. Discuss Greedy Algorithms and its applications in bioinformatics.
5. Discuss Gibbs sampling and its applications in bioinformatics.
6. Recognize Expectation Maximization and its applications in bioinformatics.
7. Recognize Hidden Markov models and its applications in bioinformatics.
8. Define Bayesian networks and its applications in bioinformatics.
9. Define graphs and its applications in bioinformatics.

Course Content

This course will provide a broad and thorough background in computational methods and algorithms that are widely used in bioinformatics applications. Various existing methods will be critically described and the strengths and limitations of each will be discussed.

Weekly Detailed Course Contents

Week Subject Related Preparation
1) A brief introduction to computational complexity and algorithm design techniques
2) Exact sequence search algorithms
3) Rabin-Karp algorithm, pattern matching, suffix trees
4) Elements of dynamic programming, Manhattan tourist problem, k-band algorithm
5) Approximate string matching, divide and conquer algorithms
6) Branch and bound search
7) Genetic Algorithm
8) Greedy Algorithms
9) Gibbs sampling
10) Expectation Maximization
11) Hidden Markov models
12) Bayesian networks
13) Graphs
14) Review

Sources

Course Notes / Textbooks: Haftalık ders notları iletilecektir.
Weekly course notes will be provided.
References: An Introduction to Bioinformatics Algorithms (Computational Molecular Biology), Neil Jones and Pavel Pevzner, MIT Press, 2004.

Evaluation System

Semester Requirements Number of Activities Level of Contribution
Homework Assignments 2 % 10
Project 1 % 15
Midterms 1 % 25
Final 1 % 50
Total % 100
PERCENTAGE OF SEMESTER WORK % 35
PERCENTAGE OF FINAL WORK % 65
Total % 100

ECTS / Workload Table

Activities Number of Activities Duration (Hours) Workload
Course Hours 14 3 42
Study Hours Out of Class 14 6 84
Presentations / Seminar 5 4 20
Midterms 1 2 2
Final 1 2 2
Total Workload 150

Contribution of Learning Outcomes to Programme Outcomes

No Effect 1 Lowest 2 Low 3 Average 4 High 5 Highest
           
Program Outcomes Level of Contribution
1) Build up a body of knowledge in mathematics, science and Energy Systems Engineering subjects; use theoretical and applied information in these areas to model and solve complex engineering problems.
2) Ability to identify, formulate, and solve complex Energy Systems Engineering problems; select and apply proper modeling and analysis methods for this purpose.
3) Ability to design complex Energy systems, processes, devices or products under realistic constraints and conditions, in such a way as to meet the desired result; apply modern design methods for this purpose.
4) Ability to devise, select, and use modern techniques and tools needed for solving complex problems in Energy Systems Engineering practice; employ information technologies effectively.
5) Ability to design and conduct numerical or pysical experiments, collect data, analyze and interpret results for investigating the complex problems specific to Energy Systems Engineering.
6) Ability to cooperate efficiently in intra-disciplinary and multi-disciplinary teams; and show self-reliance when working on Energy Systems-related problems
7) Ability to communicate effectively in English and Turkish (if he/she is a Turkish citizen), both orally and in writing. Write and understand reports, prepare design and production reports, deliver effective presentations, give and receive clear and understandable instructions.
8) Recognize the need for life-long learning; show ability to access information, to follow developments in science and technology, and to continuously educate oneself.
9) Develop an awareness of professional and ethical responsibility, and behave accordingly. Be informed about the standards used in Energy Systems Engineering applications.
10) Learn about business life practices such as project management, risk management, and change management; develop an awareness of entrepreneurship, innovation, and sustainable development.
11) Acquire knowledge about the effects of practices of Energys Systems Engineering on health, environment, security in universal and social scope, and the contemporary problems of Energys Systems engineering; is aware of the legal consequences of Energys Systems engineering solutions.