Computational Biology (ENS 210)

2022 Fall
Faculty of Engineering and Natural Sciences
Engineering Sciences(ENS)
Ogün Adebali,
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IF100 MATH101
Formal lecture,On-line task/distance,Laboratory
Interactive,Learner centered,Discussion based learning,Project based learning,Guided discovery
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1. Basic Concepts of Molecular Biology; Life, Proteins, Nucleic acids. 2. The Mechanisms of Molecular Genetics; Genes and the Genetic Code, Transcription, Translation and Protein Synthesis, junk DNA and Reading frames,Chromosomes 3. How the Genome is Studied; Maps and Sequences, Specific Techniques 4. The Human Genome Project 5. Molecular Biology Databases on the Web 6. Strings, Graphs and Algorithms 7. Sequence Alignment Algorithms; Global, Semiglobal, and Local Alignment 8. Multiple Sequence Alignment; Star alignment, Tree alignment 9. Database Search; PAM, BLOSSUM matrices, BLAST, FASTA 10. Quantitative and Probabilistic Pattern Matching 11. Protein Ligand Docking 12. Bio-ethics Also part of the "core course" pools for the BIO and CS degree program.


To supply the students with the foundations in Computational Biology.


  • To have basic knowledge of molecular biology genetics and biochemistry
  • To learn PYTHON and at to be able write PYTHON programs for basic computational biology problems.
  • To gain basic knowledge of the sequence alignment, database search , clustering, and profile algorithms in computational biology.
  • To learn ways to model biological problems and analyticla methodsfor solving problems in biology and medicine.
  • To learn to design an implement an algorithm and analyze the results of their algorithm that they developed as a team.


1. Understand the world, their country, their society, as well as themselves and have awareness of ethical problems, social rights, values and responsibility to the self and to others. 1

2. Understand different disciplines from natural and social sciences to mathematics and art, and develop interdisciplinary approaches in thinking and practice. 4

3. Think critically, follow innovations and developments in science and technology, demonstrate personal and organizational entrepreneurship and engage in life-long learning in various subjects; have the ability to continue to educate him/herself. 5

4. Communicate effectively in Turkish and English by oral, written, graphical and technological means. 4

5. Take individual and team responsibility, function effectively and respectively as an individual and a member or a leader of a team; and have the skills to work effectively in multi-disciplinary teams. 4

1. Possess sufficient knowledge of mathematics, science and program-specific engineering topics; use theoretical and applied knowledge of these areas in complex engineering problems. 4

2. Identify, define, formulate and solve complex engineering problems; choose and apply suitable analysis and modeling methods for this purpose. 4

3. Develop, choose and use modern techniques and tools that are needed for analysis and solution of complex problems faced in engineering applications; possess knowledge of standards used in engineering applications; use information technologies effectively. 4

4. Have the ability to design a complex system, process, instrument or a product under realistic constraints and conditions, with the goal of fulfilling specified needs; apply modern design techniques for this purpose. 4

5. Design and conduct experiments, collect data, analyze and interpret the results to investigate complex engineering problems or program-specific research areas. 4

6. Possess knowledge of business practices such as project management, risk management and change management; awareness on innovation; knowledge of sustainable development. 4

7. Possess knowledge of impact of engineering solutions in a global, economic, environmental, health and societal context; knowledge of contemporary issues; awareness on legal outcomes of engineering solutions; knowledge of behavior according to ethical principles, understanding of professional and ethical responsibility. 4

8. Have the ability to write effective reports and comprehend written reports, prepare design and production reports, make effective presentations, and give and receive clear and intelligible instructions. 4

1. Comprehend key concepts in biology and physiology, with emphasis on molecular genetics, biochemistry and molecular and cell biology as well as advanced mathematics and statistics. 5

2. Develop conceptual background for interfacing of biology with engineering for a professional awareness of contemporary biological research questions and the experimental and theoretical methods used to address them. 5

1. Design, implement, test, and evaluate a computer system, component, or algorithm to meet desired needs and to solve a computational problem. 5

2. Demonstrate knowledge of discrete mathematics and data structures. 4

3. Demonstrate knowledge of probability and statistics, including applications appropriate to computer science and engineering. 5

1. Use mathematics (including derivative and integral calculations, probability and statistics, differential equations, linear algebra, complex variables and discrete mathematics), basic sciences, computer and programming, and electronics engineering knowledge to (a) Design and analyze complex electronic circuits, instruments, software and electronics systems with hardware/software or (b) Design and analyze communication networks and systems, signal processing algorithms or software

1. Applying fundamental and advanced knowledge of natural sciences as well as engineering principles to develop and design new materials and establish the relation between internal structure and physical properties using experimental, computational and theoretical tools. 3

2. Merging the existing knowledge on physical properties, design limits and fabrication methods in materials selection for a particular application or to resolve material performance related problems. 3

3. Predicting and understanding the behavior of a material under use in a specific environment knowing the internal structure or vice versa. 1

1. Formulate and analyze problems in complex manufacturing and service systems by comprehending and applying the basic tools of industrial engineering such as modeling and optimization, stochastics, statistics. 4

2. Design and develop appropriate analytical solution strategies for problems in integrated production and service systems involving human capital, materials, information, equipment, and energy. 2

3. Implement solution strategies on a computer platform for decision-support purposes by employing effective computational and experimental tools. 4


  Percentage (%)
Final 25
Midterm 50
Other 25



Python textbook:
> Martin Jones, Python for Biologists,
Supporting reading material:
> Donald Forsdyke, Evolutionary Bioinformatics, 3rd ed., Springer 2015. (Chs: 2, 4, 7, and 12.)
> Stephen D. Bentley and Julian Parkhill, Comparative Genomic Structure of Prokaryotes, Annual Reviews of Genetics, 38:771-791 (2004).
> John Lightfield, Noah R. Fram, Bert Ely, Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage, PLoS ONE, 6:e17677 (2011).
> Karen E. Nelson et al., Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima, Nature, 399: 323-329 (1999).
> Carl R. Woese and George E. Fox, Phylogenetic structure of the prokaryotic domain: The primary kingdoms, Proc. Natl. Acad. Sci. USA, 74: 5088-5090 (1977).
> Nick Lane, Power, Sex, Suicide: Mitochondria and the Meaning of Life, Oxford University Press, 2005. (Introduction, Chs. 1 and 7.)
> Nick Lane, The Vital Question: Energy, Evolution, and the Origins of Complex Life, Norton & Company, 2015. (Introduction and beginning of Ch. 4.)