| 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 |
| MBG1002 | Introduction to Bioinformatics | Spring | 3 | 0 | 3 | 5 |
| 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 Lecturer(s): |
Prof. Dr. SÜREYYA AKYÜZ Dr. Öğr. Üyesi SERKAN AYVAZ |
| Recommended Optional Program Components: | There is none. |
| Course Objectives: | This course aims to prepare the students to work in the interdisciplinary area, bioinformatics that marry the advances in high-performance computing with the exploiting information resources of the human genome and related data. |
|
The students who have succeeded in this course; 1. Recognize the working in interdisciplinary teams of biologists, biochemists, medical researchers, geneticists, and computer engineers. 2. Perform sophisticated searches over enormous databases, and to interpret results. 3. Perform genomic comparisons, display genes and large genomic regions in Genome Browsers. 4. Recognize the basic bioinformatics problems and their solutions, including: fragment assembly, gene finding, protein folding and microarray studies. 5. Anayze the results in probabilistic terms using statistical significance. 6. Recognize the sequencing techniques, inherent computational problems, possible solutions. 7. Define Markov Model building and its usage for gene prediction. 8. Define computational methods for analysis of microarray data, and discuss the interpretations of gene expression from this data. 9. Discuss ethical, legal, and social issues associated with the Human Genome Project and its outcomes. |
| Bioinformatics is a rapidly growing field that integrates molecular biology, statistics, and computer science. This course is devoted to the mathematical models and computer algorithms of DNA and protein sequence analysis. In this course, the students will learn many of the popular tools for performing bioinformatics analysis and you will be introduced to the thinking that drives these algorithms. Various existing bioinformatics methods will be critically described and the strengths and limitations of each will be discussed. |
| Week | Subject | Related Preparation |
| 1) | Introduction: Probability and statistics in a nut shell. | |
| 2) | Analysis of nucleic acid and protein sequences. | |
| 3) | Molecular Biology Databases on the Web. | |
| 4) | Bioinformatics softwares on the internet | |
| 5) | How the Genome is Studied, Maps and Sequences, The Human Genome Project | |
| 6) | Sequencing: Next Gen, Exome, Shotgun | |
| 7) | Fragment Assembly Problem; Sequence Alignment Models: Shortest Common Superstring, Reconstruction, Multicontig, Graph Model | |
| 8) | Restriction mapping: a) Double Digest Problem, b) Partial Digest Problem | |
| 9) | Computational Gene Hunting, Gene finding methods; sequence patterns, Hidden Markov Models. | |
| 10) | Bioinformatics approaches to gene expression | |
| 11) | Protein folding problem | |
| 12) | Genome Rearrangements | |
| 13) | Suffix trees I | |
| 14) | Suffix trees II |
| Course Notes / Textbooks: | Biyoinformatik ders notları haftalık olarak verilecektir. Course material will be supplied weekly. |
| References: | 1) Pevsner J., Bioinformatics and Functional Genomics, Wiley-Liss, 2009 2) Mount D.W., Bioinformatics: Sequence and Genome Analysis (2nd edition), Cold Spring Harbor Laboratory Press, 2004 3) Krane D.E., Raymer M.L., Fundamental Concepts of Bioinformatics, Benjamin Cummings, 2003 4) Setubal C., Meidanis J., Introduction to Computational Molecular Biology, PWS Publishing, 1997" |
| Semester Requirements | Number of Activities | Level of Contribution |
| Homework Assignments | 2 | % 15 |
| Project | 1 | % 20 |
| Midterms | 1 | % 25 |
| Final | 1 | % 40 |
| Total | % 100 | |
| PERCENTAGE OF SEMESTER WORK | % 40 | |
| PERCENTAGE OF FINAL WORK | % 60 | |
| Total | % 100 | |
| Activities | Number of Activities | Duration (Hours) | Workload |
| Course Hours | 14 | 3 | 42 |
| Study Hours Out of Class | 14 | 5 | 70 |
| Project | 1 | 10 | 10 |
| Midterms | 1 | 2 | 2 |
| Final | 1 | 2 | 2 |
| Total Workload | 126 | ||
| 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 |