| EUROPEAN UNION RELATIONS | |||||
| 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 | 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 be able to examine, interpret data and assess ideas with the scientific methods in the area of EU studies. | 2 |
| 2) | To be able to inform authorities and institutions in the area of EU studies, to be able to transfer ideas and proposals supported by quantitative and qualitative data about the problems. | 2 |
| 3) | To be introduced to and to get involved in other disciplines that EU studies are strongly related with (political science, international relations, law, economics, sociology, etc.) and to be able to conduct multi-disciplinary research and analysis on European politics. | 3 |
| 4) | To be able to evaluate current news on European Union and Turkey-EU relations and identify, analyze current issues relating to the EU’s politics and policies. | 2 |
| 5) | To be able to use English in written and oral communication in general and in the field of EU studies in particular. | 1 |
| 6) | To have ethical, social and scientific values throughout the processes of collecting, interpreting, disseminating and implementing data related to EU studies. | 1 |
| 7) | To be able to assess the historical development, functioning of the institutions and decision-making system and common policies of the European Union throughout its economic and political integration in a supranational framework. | 2 |
| 8) | To be able to evaluate the current legal, financial and institutional changes that the EU is going through. | 2 |
| 9) | To explain the dynamics of enlargement processes of the EU by identifying the main actors and institutions involved and compare previous enlargement processes and accession process of Turkey. | 2 |
| 10) | To be able to analyze the influence of the EU on political, social and economic system of Turkey. | 2 |
| 11) | To acquire insight in EU project culture and to build up project preparation skills in line with EU format and develop the ability to work in groups and cooperate with peers. | 2 |
| 12) | To be able to recognize theories and concepts used by the discipline of international relations and relate them to the historical development of the EU as a unique post-War political project. | 3 |