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Information
| Unit | INSTITUTE OF NATURAL AND APPLIED SCIENCES |
| BIOTECHNOLOGY (PhD) (INTERDISCIPLINARY) | |
| Code | BT042 |
| Name | Applications of Bioinformatics - II |
| Term | 2022-2023 Academic Year |
| Term | Spring |
| Duration (T+A) | 2-4 (T-A) (17 Week) |
| ECTS | 6 ECTS |
| National Credit | 4 National Credit |
| Teaching Language | Türkçe |
| Level | Doktora Dersi |
| Type | Normal |
| Mode of study | Yüz Yüze Öğretim |
| Catalog Information Coordinator | Doç. Dr. ATIL BİŞGİN |
| Course Instructor |
The current term course schedule has not been prepared yet.
|
Course Goal / Objective
Main purpose of this course is to give students an insight on bioinformatics utilization in molecular genetic testing
Course Content
This course is the follow-up of Applications of Bioinformatics - I and includes next generation sequening data processing, analyzing and choosing the right bioinformatics tool.
Course Precondition
Have a Applications of Bioinformatics - I lesson.
Resources
Bioinformatics related on Articles
Notes
Bioinformatics related on Articles/Books
Course Learning Outcomes
| Order | Course Learning Outcomes |
|---|---|
| LO01 | Having information about Next Generation Sequencing method |
| LO02 | Having information about Next Generation Sequencing systems |
| LO03 | Having information about Next Generation Sequencing data evaluation |
| LO04 | Having information about bioinformatics analysis of DNA and RNA based genetic changes |
| LO05 | Having information about NGS data quality controls |
| LO06 | Having information about databases and in-silico analysis tools |
| LO07 | Having information about NGS workflow. |
| LO08 | Having information about used biological materials in Next Generation Sequencing systems |
Relation with Program Learning Outcome
| Order | Type | Program Learning Outcomes | Level |
|---|---|---|---|
| PLO01 | Bilgi - Kuramsal, Olgusal | Develop and deepen the current and advanced knowledge in the field with original thought and / or research at the level of expertise based on the qualifications of the graduate and reach the original definitions that will bring innovation to the field. | 4 |
| PLO02 | Bilgi - Kuramsal, Olgusal | Understands the interdisciplinary interaction of the field; it achieves original results using knowledge requiring expertise in analysis, synthesis and evaluation of new and complex ideas. | |
| PLO03 | Beceriler - Bilişsel, Uygulamalı | Evaluates, uses and transfers new information in the field with a systematic approach. | 2 |
| PLO04 | Beceriler - Bilişsel, Uygulamalı | Makes critical analysis, synthesis and evaluation of new and complex thoughts. | 2 |
| PLO05 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | Makes leadership in environments that require the analysis of original and interdisciplinary problems. | |
| PLO06 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | It extends the limits of knowledge in its field by publishing at least one scientific article in its field in national and / or international refereed journals and / or producing or interpreting an original work. | |
| PLO07 | Yetkinlikler - Öğrenme Yetkinliği | Develops new ideas and methods related to the field by using high level mental processes such as creative and critical thinking, problem solving and decision making. | |
| PLO08 | 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. | |
| PLO09 | Yetkinlikler - Alana Özgü Yetkinlik | Conducts scientific research in national and international scientific research groups. | |
| PLO10 | Yetkinlikler - Alana Özgü Yetkinlik | Establishes functional interaction by using strategic decision making processes in solving problems encountered in the field. |
Week Plan
| Week | Topic | Preparation | Methods |
|---|---|---|---|
| 1 | Setting Up Trio Analysis | No need for preliminary preparation | Öğretim Yöntemleri: Gösteri, Deney / Laboratuvar |
| 2 | Analysis of Hereditary Workflows | No need for preliminary preparation | Öğretim Yöntemleri: Gösteri, Deney / Laboratuvar |
| 3 | Analysis of Somatic Workflows - 1: Fresh Samples to FFPE Samples | No need for preliminary preparation | Öğretim Yöntemleri: Gösteri, Deney / Laboratuvar |
| 4 | Analysis of Somatic Workflows - 2: Circulating cell-free DNA | No need for preliminary preparation | Öğretim Yöntemleri: Gösteri, Deney / Laboratuvar |
| 5 | Filtering Whole Exome Data | No need for preliminary preparation | Öğretim Yöntemleri: Gösteri, Deney / Laboratuvar |
| 6 | Filtering Whole Genome Data-2 | No need for preliminary preparation | Öğretim Yöntemleri: Anlatım, Gösteri, Deney / Laboratuvar |
| 7 | NGS and Databases in Clinical Diagnostics | No need for preliminary preparation | Öğretim Yöntemleri: Anlatım, Gösteri, Gösterip Yaptırma |
| 8 | Mid-Term Exam | No need for preliminary preparation | Ölçme Yöntemleri: Performans Değerlendirmesi |
| 9 | Legal Issues for Data Storage | No need for preliminary preparation | Öğretim Yöntemleri: Anlatım |
| 10 | Law on the Protection of Personal Data | No need for preliminary preparation | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma |
| 11 | Students' presentation | No need for preliminary preparation | Öğretim Yöntemleri: Anlatım |
| 12 | Students' presentation-2 | No need for preliminary preparation | Öğretim Yöntemleri: Anlatım |
| 13 | Students' presentation-3 | No need for preliminary preparation | Öğretim Yöntemleri: Anlatım |
| 14 | Data Mining | No need for preliminary preparation | Öğretim Yöntemleri: Anlatım |
| 15 | Clinical reporting | No need for preliminary preparation | Öğretim Yöntemleri: Anlatım, Gösteri |
| 16 | Term Exams | No need for preliminary preparation | Ölçme Yöntemleri: Ödev |
| 17 | Term Exams | No need for preliminary preparation | Ölçme Yöntemleri: Ödev |
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 | 0 | 0 | 0 |
| Mid-term Exams (Written, Oral, etc.) | 1 | 18 | 18 |
| Final Exam | 1 | 36 | 36 |
| Total Workload (Hour) | 138 | ||
| Total Workload / 25 (h) | 5,52 | ||
| ECTS | 6 ECTS | ||