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| BIY4032 | Bioinformatics | 3+0+0 | ECTS:5 | | Year / Semester | Spring Semester | | Level of Course | First Cycle | | Status | Elective | | Department | DEPARTMENT of BIOLOGY | | Prerequisites and co-requisites | None | | Mode of Delivery | | | Contact Hours | 14 weeks - 3 hours of lectures per week | | Lecturer | Dr. Öğr. Üyesi Fulya AY | | Co-Lecturer | | | Language of instruction | Turkish | | Professional practise ( internship ) | None | | | | The aim of the course: | | The main objectives of this course are to provide the basic concepts and principles of related subjects using current methods and knowledges to students. |
| Learning Outcomes | CTPO | TOA | | Upon successful completion of the course, the students will be able to : | | | | LO - 1 : | understand how sequence information collected, stored and organized, managed and distributed | 4,9 | 1,3,4,5 | | LO - 2 : | use standard bioinformatic tools to access biological information | 4,9 | 1,3,4,5 | | LO - 3 : | understand the theoretical basis of the algorithms used in the programs for bioinformatics | 4,9 | 1,3,4,5 | | CTPO : Contribution to programme outcomes, TOA :Type of assessment (1: written exam, 2: Oral exam, 3: Homework assignment, 4: Laboratory exercise/exam, 5: Seminar / presentation, 6: Term paper), LO : Learning Outcome | | |
| Commonly used databases in molecular biology, genetics and related fields, homology search for genes and proteins, primer design, molecular operations, restriction mapping, structure prediction, contructing phylogenetic trees. |
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| Course Syllabus | | Week | Subject | Related Notes / Files | | Week 1 | Definition and Brief History of Bioinformatics Science | | | Week 2 | Definition and Brief History of Bioinformatics Science - Basic File Formats Used for Molecular Data Storage, Processing and Analysis (Fasta, embl, phylip etc.) | | | Week 3 | Basic File Formats Used for Molecular Data Storage, Processing and Analysis (Fasta, embl, phylip etc.) | | | Week 4 | Biological databases (NCBI, embl, ddbj, protein veritabanları vb.) | | | Week 5 | Adding sequences to databases and sequence analysis | | | Week 6 | PCR and primer design, FastPCR, oligo analyzer programs | | | Week 7 | Databases related to metabolic pathways (KEGG, MetaCyc, etc.) | | | Week 8 | Blast programs | | | Week 9 | Mid-term exam | | | Week 10 | Student Presentations | | | Week 11 | Student Presentations | | | Week 12 | SnapGene programı | | | Week 13 | Clustal W, Omega and sequence aligment | | | Week 14 | Bioedit and Mega programs, phylogentic trees | | | Week 15 | Signal P and protein databases | | | Week 16 | End-of-term exam | | | |
| 1 | Bioinformatics For Dummies, 2nd EditionBy Jean-Michel Claverie, Ph. D., Cedric Notredame, Ph.D. December 2006, 436pp, ISBN: 978-0-470-08985-9, JOHN WILEY. | | | 2 | Lecturer Notes | | | |
| 1 | Bioinformatics: A Biologist's Guide to Biocomputing and the Internet, January 2000, Hardcover, 200pp, ISBN: 188129918X, Eaton Publishing Company/Bio Techniques Boks. | | | |
| Method of Assessment | | Type of assessment | Week No | Date | Duration (hours) | Weight (%) | | Mid-term exam | 9 | 15/04/2024 | 60 | 30 | | Presentation | 11 | 29/04/2024 | 30 | 20 | | End-of-term exam | 16 | 03/06/2024 | 50 | 50 | | |
| Student Work Load and its Distribution | | Type of work | Duration (hours pw) | No of weeks / Number of activity | Hours in total per term | | Yüz yüze eğitim | 3 | 14 | 42 | | Sınıf dışı çalışma | 3 | 14 | 42 | | Laboratuar çalışması | 0 | 0 | 0 | | Arasınav için hazırlık | 2 | 7 | 14 | | Arasınav | 2 | 1 | 2 | | Uygulama | 2 | 1 | 2 | | Klinik Uygulama | 0 | 0 | 0 | | Ödev | 0 | 0 | 0 | | Proje | 3 | 7 | 21 | | Kısa sınav | 0 | 0 | 0 | | Dönem sonu sınavı için hazırlık | 5 | 2 | 10 | | Dönem sonu sınavı | 0 | 0 | 0 | | Diğer 1 | 3 | 5 | 15 | | Diğer 2 | 2 | 1 | 2 | | Total work load | | | 150 |
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