TÜRKÇE
ENGLISH
Information
| Code | VTS142 |
| Name | Basics of Bioinformatics |
| Term | 2024-2025 Academic Year |
| Semester | 2. Semester |
| Duration (T+A) | 2-0 (T-A) (17 Week) |
| ECTS | 4 ECTS |
| National Credit | 2 National Credit |
| Teaching Language | Türkçe |
| Level | Lisans Dersi |
| Type | Normal |
| Label | GC General Culture Courses E Elective |
| Mode of study | Yüz Yüze Öğretim |
| Catalog Information Coordinator | Dr. Öğr. Üyesi SİNAN KANDIR |
| Course Instructor |
Dr. Öğr. Üyesi SİNAN KANDIR
(A Group)
(Ins. in Charge)
|
Course Goal / Objective
This course aims to provide students with fundamental theoretical knowledge and practical skills in accessing data using web-based infrastructures in bioinformatics. In particular, the course focuses on how biological databases are accessed, analyzed, and applied within veterinary medicine.
Course Content
Bioinformatics concept and its applications, information theory, collection of data, its manipulation and allocation, creation of a database and its usage, analysis of protein and nucleotide databases, primer design, interpretation of nucleotide sequence analysis results and bioinformatics in veterinary medicine.
Course Precondition
None
Resources
Introduction to Bioinformatics, Arthur M. Lesk, Oxford University Press, New York, 2002. Bioinformatics : A Practical Approach, Shui Qing Ye, Chapman and Hall/CRC, London, 2007. Bioinformatics, ed. Jonathan M. Keith, Humana press, London, 2008.
Notes
Relevant literature, lecture notes, presentations, and topic-related video materials.
Course Learning Outcomes
| Order | Course Learning Outcomes |
|---|---|
| LO01 | Explains the fundamental concepts of bioinformatics and its applications in veterinary medicine. |
| LO02 | Recognizes bioinformatics databases related to veterinary genetics (OMIM, Ensembl, NCBI). |
| LO03 | Describes the fundamental principles of DNA and protein sequence analysis. |
| LO04 | Identifies biological data formats such as FASTA and GenBank. |
| LO05 | Explains the core functionalities of commonly used bioinformatics software like BLAST. |
| LO06 | Develops basic skills in interpreting bioinformatics data. |
| LO07 | Defines bioinformatics applications in veterinary medicine and explains the use of genetic databases. |
| LO08 | Gains awareness of ethical regulations and data security in bioinformatics. |
| LO09 | Follows recent developments in veterinary bioinformatics applications. |
Relation with Program Learning Outcome
| Order | Type | Program Learning Outcomes | Level |
|---|---|---|---|
| PLO01 | Bilgi - Kuramsal, Olgusal | Distinguishes animal species and breeds based on their structural (morphological), functional (physiological, biochemical) and behavioral characteristics and whether they can be consumed for food purposes. | |
| PLO02 | Bilgi - Kuramsal, Olgusal | Explains the sources, physical and chemical properties and preparation of drugs. | |
| PLO03 | Bilgi - Kuramsal, Olgusal | Describes the effects and side effects of medications on patients | |
| PLO04 | Bilgi - Kuramsal, Olgusal | Explains the formation mechanisms of animal diseases and their pathological effects on the body. | |
| PLO05 | Bilgi - Kuramsal, Olgusal | It makes efficiency evaluations among animal breeds and, when necessary, carries out selection, hybridization and artificial insemination at a level that can carry out breeding work. | |
| PLO06 | Bilgi - Kuramsal, Olgusal | Disposes of dead animal material, tissue samples, medical and chemical waste appropriately in accordance with international, national laws and regulations. | |
| PLO07 | Beceriler - Bilişsel, Uygulamalı | It determines the correct approach area for the patient by evaluating the examination, operation etc. practices in the clinic according to the topographic anatomy. | |
| PLO08 | Beceriler - Bilişsel, Uygulamalı | Uses biochemical parameters in diagnostic processes by evaluating the information obtained with cause-effect relationships. | 2 |
| PLO09 | Beceriler - Bilişsel, Uygulamalı | Writes prescriptions in accordance with diagnosis and treatment protocols for diseases and poisoning in animals. | 4 |
| PLO10 | Beceriler - Bilişsel, Uygulamalı | Implements necessary measures, including biosecurity, to control infectious diseases. | |
| PLO11 | Beceriler - Bilişsel, Uygulamalı | Performs necropsy to evaluate findings in dead animals, directs tissues to the necessary laboratory according to appropriate storage methods and prepares a report. | 1 |
| PLO12 | Beceriler - Bilişsel, Uygulamalı | Monitors patients in the post-operative process according to the main treatment methods of surgical diseases in animal species. | |
| PLO13 | Beceriler - Bilişsel, Uygulamalı | Applies sedation, anesthesia and pain management methods safely according to animal species. | |
| PLO14 | Beceriler - Bilişsel, Uygulamalı | Correctly applies biosafety principles such as sterilization of clinical and laboratory equipment and clothing. | |
| PLO15 | Beceriler - Bilişsel, Uygulamalı | It regulates the care and feeding protocols according to animal species and supervises the consumption of animal foods produced for human consumption or foods containing animal products in their composition. | |
| PLO16 | Beceriler - Bilişsel, Uygulamalı | Evaluates laboratory results of animal diseases and applies correct diagnosis, prognosis and treatment methods based on the data obtained. | |
| PLO17 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | He/she is conscious of performing his/her profession by being aware of his/her powers and responsibilities. | |
| PLO18 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | Examines scientific techniques and methods according to facts related to veterinary services and takes analysis or methodological responsibility for problems. | 3 |
| PLO19 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | It uses adequate technology in the hygienic production, manufacturing, processing, consumption and sales of food by conducting health control of animal food products produced for human consumption. | |
| PLO20 | Yetkinlikler - Öğrenme Yetkinliği | Lists the methods of producing and using scientific knowledge in his/her professional field. | 5 |
| PLO21 | Yetkinlikler - Öğrenme Yetkinliği | Uses updated legislation regarding veterinary services when necessary. | |
| PLO22 | Yetkinlikler - Öğrenme Yetkinliği | Performs an examination appropriate to the case, applying the contribution of imaging methods to diagnosis and radiation safety in accordance with current regulations. | |
| PLO23 | Yetkinlikler - Öğrenme Yetkinliği | Keeps clinical and patient records using proper and scientific methods. | |
| PLO24 | Yetkinlikler - Öğrenme Yetkinliği | By observing the basic principles of medicine, it develops management methods and appropriate management plans for animal production enterprises. | |
| PLO25 | Yetkinlikler - İletişim ve Sosyal Yetkinlik | Implement social projects and plans with social awareness, based on professional skills and authority with a computer usage license, advanced computer software. | 4 |
| PLO26 | Yetkinlikler - İletişim ve Sosyal Yetkinlik | Works in cooperation with other colleagues by following the world agenda within the framework of professional ethics and deontology rules. | |
| PLO27 | Yetkinlikler - Alana Özgü Yetkinlik | Produces solutions to field-specific problems in line with scientific data/evidence. | 3 |
| PLO28 | Yetkinlikler - Alana Özgü Yetkinlik | He/she has the ethical values of the veterinary profession and defends these values. | |
| PLO29 | Yetkinlikler - Alana Özgü Yetkinlik | Takes appropriate precautions by clinically recognizing zoonosis and notifiable diseases. | |
| PLO30 | Yetkinlikler - Alana Özgü Yetkinlik | Determines the methods of diagnosis, prevention, treatment and operation of diseases in different animal species. | |
| PLO31 | Yetkinlikler - Alana Özgü Yetkinlik | In emergency cases, intervenes in all animals and applies first aid methods. | |
| PLO32 | Yetkinlikler - Alana Özgü Yetkinlik | Makes judgments on animal husbandry principles and breeding by assessing the physical condition, welfare and rearing conditions of domestic animals, communicating appropriately with animal owners and colleagues. | |
| PLO33 | Yetkinlikler - Alana Özgü Yetkinlik | Independently interprets articles and presentations published in other scientific fields related to Veterinary Medicine to maintain professional development and skills. | |
| PLO34 | Yetkinlikler - Alana Özgü Yetkinlik | When necessary, euthanizes animals using appropriate methods and respecting the feelings of animal owners. | |
| PLO35 | Yetkinlikler - Alana Özgü Yetkinlik | By mastering the concepts of occupational safety in terms of the workplace and the personnel working with it, they have the competence to apply and defend it. |
Week Plan
| Week | Topic | Preparation | Methods |
|---|---|---|---|
| 1 | Fundamental Concepts of Bioinformatics | Reviewing course materials (books, articles, lecture notes) | Öğretim Yöntemleri: Anlatım, Tartışma |
| 2 | Introduction to Bioinformatics Tools and Basic Algorithms | Reading about bioinformatics fundamentals, reviewing resources | Öğretim Yöntemleri: Anlatım, Soru-Cevap |
| 3 | Bioinformatics Tools - Gene Databases | Exploring web-based bioinformatics tools | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Gösterip Yaptırma |
| 4 | Bioinformatics Tools - Omics Databases | Researching and utilizing bioinformatics tools | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Gösterip Yaptırma |
| 5 | Literature Review and Modern Bioinformatics Tools | Literature review in bioinformatics, understanding omics databases | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Örnek Olay, Gösterip Yaptırma |
| 6 | FASTA and GenBank File Formats | Accessing omics databases and retrieving data | Öğretim Yöntemleri: Anlatım, Örnek Olay, Grup Çalışması |
| 7 | BLAST and Sequence Alignment Techniques | Accessing databases and analyzing retrieved data | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Gösterip Yaptırma |
| 8 | Mid-Term Exam | Reviewing previous topics | Ölçme Yöntemleri: Yazılı Sınav, Sözlü Sınav, Ödev, Proje / Tasarım |
| 9 | Application of Bioinformatics Tools in Veterinary Medicine | Reviewing articles on clinical bioinformatics, group work | Öğretim Yöntemleri: Anlatım, Grup Çalışması, Beyin Fırtınası |
| 10 | Gene Databases for Pet Animals | Accessing databases, case studies, and group work | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Gösterip Yaptırma |
| 11 | OMIM databases | Accessing OMIM database, studying hereditary diseases | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Gösterip Yaptırma |
| 12 | Gene databases of livestock animals | Using bioinformatics tools to access omics data of farm animals | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Gösterip Yaptırma |
| 13 | Gene databases of poultry | Using bioinformatics tools to access omics data of poultry | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Gösterip Yaptırma |
| 14 | Omics databases and precision veterinary medicine | Understanding precision medicine concepts and group studies on hereditary diseases | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Beyin Fırtınası |
| 15 | Application of Artificial Intelligence in Bioinformatics | Utilizing modern AI applications in bioinformatics | Öğretim Yöntemleri: Anlatım, Gösterip Yaptırma, Tartışma |
| 16 | Term Exams | Reviewing previous topics | Ölçme Yöntemleri: Yazılı Sınav, Sözlü Sınav, Ödev, Proje / Tasarım, Performans Değerlendirmesi |
| 17 | Term Exams | Reviewing previous topics | Ölçme Yöntemleri: Yazılı Sınav, Sözlü Sınav, Ödev, Proje / Tasarım, Performans Değerlendirmesi |
Student Workload - ECTS
| Works | Number | Time (Hour) | Workload (Hour) |
|---|---|---|---|
| Course Related Works | |||
| Class Time (Exam weeks are excluded) | 14 | 2 | 28 |
| Out of Class Study (Preliminary Work, Practice) | 14 | 4 | 56 |
| Assesment Related Works | |||
| Homeworks, Projects, Others | 1 | 10 | 10 |
| Mid-term Exams (Written, Oral, etc.) | 1 | 2 | 2 |
| Final Exam | 1 | 4 | 4 |
| Total Workload (Hour) | 100 | ||
| Total Workload / 25 (h) | 4,00 | ||
| ECTS | 4 ECTS | ||