CENG4525 Introduction to Bioinformatics¶
Fall 2023¶
Course Description¶
This course is a preliminary exploration into the field of bioinformatics, a discipline at the intersection of computer science and biology as the study of biological systems utilizing computer science principles. The course will address a variety of topics including biological data, databases, molecular evolution, structural biology, systems biology, molecular biology, biochemistry and diseases. Students will gain hands-on experience in writing and adapting code using the Python programming language. In addition, the course will introduce students to the fundamental aspects of bioinformatics as an academic field, covering topics such as the specification, construction, testing, documentation, evaluation of the efficiency and limitations of algorithms.
Learning objectives¶
The goal of this course is to introduce concepts of bioinformatics and modern scientific methods. Students completing the course should be able to:
- Understand basic biological mechanisms and features of biological data.
- Understand common problems of biology and possible solutions through computer science.
- Read, write, and modify computer code in the Python language for biological data.
- Understand the ideas behind the different bioinformatics algorithms.
- Design, implement, and debug scripts to perform bio-computational tasks.
- Model biological systems in a computational framework, and gain biological insights from those models in areas such as genetics, evolution, biochemistry and structural biology.
General Information¶
Instructor¶
Talip Zengin
E-mail: talipzengin@mu.edu.tr
Office: Faculty of Science, Department of Molecular Biology and Genetics
Office hours: Wednesday, Thursday, Friday, 10-12:00
Course Hours¶
Friday 14:30-17:15
Lab: C106
Course content and Readings¶
Course content and readings on bioinformatics will be taken from a variety of sources, with all readings posted on the course website.
Tentative Schedule¶
| Week | Date | Topic | |
|---|---|---|---|
| 1 | Oct 06 | Overview of Bioinformatics | |
| 2 | Oct 13 | Basic Biological Mechanisms and Data | |
| 3 | Oct 20 | Biological Databases & Accessing databases | |
| 4 | Oct 27 | DNA/RNA/Protein Sequences & Objects | |
| 5 | Nov 03 | Sequence Analysis: Transcription, Translation, Mutation | |
| 6 | Nov 10 | Sequence Analysis: Transcription, Translation, Mutation | |
| 7 | Nov 17 | Sequence Analysis: Sequence Alignments & Phylogenetics | |
| 8 | Nov 24 | Genome Analysis: Sequence Annotation | |
| 9 | Dec 01 | Transcriptome Analysis: RNAseq Data Analysis | |
| 10 | Dec 08 | Project Brainstorming & Planning | |
| 11 | Dec 15 | Project Proposals | |
| 12 | Dec 22 | Structural Biology | |
| 13 | Dec 29 | Protein Structure Prediction and Engineering | |
| 14 | Jan 05 | Biology of Diseases and Personalized Medicine | |
| 15 | Jan 12 | Project Presentations |
Course Policies¶
Assignments¶
There will be approximately ten quizes and assignments, consisting of programming problems and explorations of biological questions through computational approaches. Assignments will be submitted through Jupyter Notebook at the course page.
The Jupyter notebook files (named as studentid.ipynb) prepared for the assignments should be uploaded to the folder of the given week in the Google Drive folder of the course (CENG4525_Introduction_to_Bioinformatics).
Computing¶
Computing can be done on the Google Colab or your own computer's Jupyter Notebook. We will be using the Jupyter Notebook system with Python 3.
Exams¶
There will be two gradings in the course, one mid-semester and the other during finals period. The grading will cover quizes, homeworks, project proposals and project presentation. Quizes and assignments will be open-book and open-notes.
Grading¶
Final grades will be determined according to the following weightings:
10% Quizes
30% Assignments
10% Project Proposal
50% Group Project
Late assignments will incur a 10% penalty per day unless arrangements are made for an extension at least 24 hours prior to the due date. Extensions will only be granted in the case of verifiable medical excuses or other similarly dire circumstances. All exams and projects are required; failure to complete any component will result in failure in the course.
Group project¶
During the second half of the semester, students will work in small (2-3 person) groups on an independent programming project that explores an area of biology through computation. Topics may include simulations of genetic regulatory systems, modeling of evolutionary dynamics or epidemiology, bioinformatics data analysis, or any other topic of interest in biology. Groups will present their work in an oral presentation to the class, and through a Jupyter notebook that clearly describes both the biological questions being addressed and the computational approaches taken.