MATHEMATICS | |||||
Bachelor | TR-NQF-HE: Level 6 | QF-EHEA: First Cycle | EQF-LLL: Level 6 |
Course Code | Course Name | Semester | Theoretical | Practical | Credit | ECTS |
MBG4059 | Computational Methods in Bioinformatics | Spring Fall |
3 | 0 | 3 | 6 |
This catalog is for information purposes. Course status is determined by the relevant department at the beginning of semester. |
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. |
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. |
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. |
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 |
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. |
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 |
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 |
No Effect | 1 Lowest | 2 Low | 3 Average | 4 High | 5 Highest |
Program Outcomes | Level of Contribution | |
1) | To have a grasp of basic mathematics, applied mathematics and theories and applications in Mathematics | |
2) | To be able to understand and assess mathematical proofs and construct appropriate proofs of their own and also define and analyze problems and to find solutions based on scientific methods, | |
3) | To be able to apply mathematics in real life with interdisciplinary approach and to discover their potentials, | |
4) | To be able to acquire necessary information and to make modeling in any field that mathematics is used and to improve herself/himself, | 4 |
5) | To be able to tell theoretical and technical information easily to both experts in detail and non-experts in basic and comprehensible way, | |
6) | To be familiar with computer programs used in the fields of mathematics and to be able to use at least one of them effectively at the European Computer Driving Licence Advanced Level, | |
7) | To be able to behave in accordance with social, scientific and ethical values in each step of the projects involved and to be able to introduce and apply projects in terms of civic engagement, | |
8) | To be able to evaluate all processes effectively and to have enough awareness about quality management by being conscious and having intellectual background in the universal sense, | 4 |
9) | By having a way of abstract thinking, to be able to connect concrete events and to transfer solutions, to be able to design experiments, collect data, and analyze results by scientific methods and to interfere, | |
10) | To be able to continue lifelong learning by renewing the knowledge, the abilities and the competencies which have been developed during the program, and being conscious about lifelong learning, | |
11) | To be able to adapt and transfer the knowledge gained in the areas of mathematics ; such as algebra, analysis, number theory, mathematical logic, geometry and topology to the level of secondary school, | |
12) | To be able to conduct a research either as an individual or as a team member, and to be effective in each related step of the project, to take role in the decision process, to plan and manage the project by using time effectively. |