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Information
| Code | BT508 |
| Name | Bioinfomatics Software Development with Python |
| Term | 2024-2025 Academic Year |
| Term | Spring |
| Duration (T+A) | 4-0 (T-A) (17 Week) |
| ECTS | 6 ECTS |
| National Credit | 4 National Credit |
| Teaching Language | Türkçe |
| Level | Yüksek Lisans Dersi |
| Type | Normal |
| Mode of study | Yüz Yüze Öğretim |
| Catalog Information Coordinator | Prof. Dr. ZEYNEL CEBECİ |
| Course Instructor |
1 |
Course Goal / Objective
This course aims to develop bioinformatics software with Python programming language.
Course Content
This course covers coding with Python programming language and bioinformatics software development.
Course Precondition
Programming knowledge and experience with one of the high-level programming languages, i.e, R, Fortran, C/C++ etc.
Resources
Bassi, S. (2016). Python for bioinformatics. Chapman and Hall/CRC. Model, M. L. (2009). Bioinformatics Programming Using Python: Practical Programming for Biological Data. O'Reilly Media, Inc.
Notes
Biopython Tutorial. URL https://www.tutorialspoint.com/biopython/index.htm
Course Learning Outcomes
| Order | Course Learning Outcomes |
|---|---|
| LO01 | Learns coding with Python. |
| LO02 | Codes software for bioinformatics. |
| LO03 | Learns OOP essentials. |
| LO04 | Learns debugging and fixing of the codes. |
Relation with Program Learning Outcome
| Order | Type | Program Learning Outcomes | Level |
|---|---|---|---|
| PLO01 | Bilgi - Kuramsal, Olgusal | Based on the undergraduate level qualifications, develops and deepens the knowledge in the same or different field at the level of expertise and analyzes and interprets them using statistical methods. | 4 |
| PLO02 | Beceriler - Bilişsel, Uygulamalı | To identifiy the interdisciplinary interaction of the field and to solve use of the methods. | 3 |
| PLO03 | Beceriler - Bilişsel, Uygulamalı | Interpret the knowledge gained in the field by integrating the information from different disciplines and creates new information | |
| PLO04 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | Develops new strategic approaches for solving complex problems that are encountered in applications related to the field. | |
| PLO05 | Yetkinlikler - Öğrenme Yetkinliği | To teach the social, scientific, cultural and ethical values during the collection, interpretation, implementation and announcement of the data related to the field. | 3 |
| PLO06 | Yetkinlikler - İletişim ve Sosyal Yetkinlik | To solve the problems encountered in the field and cominicate by using research methods. | 3 |
| PLO07 | Yetkinlikler - Alana Özgü Yetkinlik | To gain the ability to develop and deepen the knowledge in the field of biotechnology | 2 |
| PLO08 | Yetkinlikler - Alana Özgü Yetkinlik | Establishes functional interaction by using strategic decision-making processes in solving the problems encountered in the field. | |
| PLO09 | Yetkinlikler - Öğrenme Yetkinliği | Knows the ethical rules to be considered while obtaining biotechnological products. | |
| PLO10 | Yetkinlikler - İletişim ve Sosyal Yetkinlik | He / she defends his / her original opinions in discussing the subjects in his / her field and establishes an effective communication showing his / her competence in the field. |
Week Plan
| Week | Topic | Preparation | Methods |
|---|---|---|---|
| 1 | Python fundamentals , installation and working environment | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 2 | Data types | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 3 | Variables and types of variables | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 4 | Simple expressions | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 5 | Advanced data types, Containers | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 6 | Loops | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 7 | Functions | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 8 | Mid-Term Exam | Preparation for the exam | Ölçme Yöntemleri: Ödev |
| 9 | Exceptions | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 10 | Code organization | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 11 | Input/Output files | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 12 | Interacting with the other elements | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 13 | Regular expressions | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 14 | Introduction to functional programming | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 15 | Introduction to object-oriented programming | Searching for the learning resources on the Internet, reading the tutorials, lecture notes and textbooks, and problem solving related with the topic. | Öğretim Yöntemleri: Alıştırma ve Uygulama, Anlatım |
| 16 | Term Exams | Preparation for the exam | Ölçme Yöntemleri: Ödev |
| 17 | Term Exams | Preparation for the exam | Ölçme Yöntemleri: Ödev |
Student Workload - ECTS
| Works | Number | Time (Hour) | Workload (Hour) |
|---|---|---|---|
| Course Related Works | |||
| Class Time (Exam weeks are excluded) | 14 | 4 | 56 |
| Out of Class Study (Preliminary Work, Practice) | 14 | 4 | 56 |
| Assesment Related Works | |||
| Homeworks, Projects, Others | 0 | 0 | 0 |
| Mid-term Exams (Written, Oral, etc.) | 1 | 12 | 12 |
| Final Exam | 1 | 28 | 28 |
| Total Workload (Hour) | 152 | ||
| Total Workload / 25 (h) | 6,08 | ||
| ECTS | 6 ECTS | ||