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Code ENS 210
Term 201801
Title Computational Biology
Faculty Faculty of Engineering and Natural Sciences
Subject Engineering Sciences(ENS)
SU Credit 3
ECTS Credit 6.00 / 6.00 ECTS (for students admitted in the 2013-14 Academic Year or following years)
Instructor(s) Ogun Adebali -oadebali@sabanciuniv.edu,
Language of Instruction English
Level of Course Undergraduate
Type of Course Click here to view.
Prerequisites
(only for SU students)
MATH101 CS201
Mode of Delivery Formal lecture,On-line task/distance,Laboratory
Planned Learning Activities Interactive,Learner centered,Discussion based learning,Project based learning,Guided discovery
Content

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.

Objective

To supply the students with the foundations in Computational Biology.

Learning Outcome

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.

Programme Outcomes
 
Common Outcomes For All Programs
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. 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
Common Outcomes ForFaculty of Eng. & Natural Sci.
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 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 Knowledge of business practices such as project management, risk management and change management; awareness on innovation; knowledge of sustainable development. 4
7 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; understanding of professional and ethical responsibility. 4
Computer Science and Engineering Program Outcomes Core Electives
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
Molecular Biology, Genetics and Bioengineering Program Outcomes Core Electives
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
Industrial Engineering Program Outcomes Area Electives
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
Electronics Engineering Program Outcomes Area Electives
1 Use mathematics (including derivative and integral calculations, probability and statistics), basic sciences, computer and programming, and electronics engineering knowledge to design and analyze complex electronic circuits, instruments, software and electronics systems with hardware/software. 4
2 Analyze and design communication networks and systems, signal processing algorithms or software using advanced knowledge on differential equations, linear algebra, complex variables and discrete mathematics. 3
Materials Science and Nano Engineering Program Outcomes Area Electives
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
Assessment Methods and Criteria
  Percentage (%)
Final 25
Midterm 50
Other 25
Recommended or Required Reading
Readings

Python textbook:
> Martin Jones, Python for Biologists, http://pythonforbiologists.com
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.)