FACULTY OF ENGINEERING
Department of Genetics and Bioengineering
GBE 411 | Course Introduction and Application Information
| Course Name |
Design and Analysis in Bioengineering
|
|
Code
|
Semester
|
Theory
(hour/week) |
Application/Lab
(hour/week) |
Local Credits
|
ECTS
|
|
GBE 411
|
Fall/Spring
|
2
|
2
|
3
|
5
|
| Prerequisites |
None
|
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| Course Language |
English
|
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| Course Type |
Elective
|
|||||
| Course Level |
First Cycle
|
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| Mode of Delivery | - | |||||
| Teaching Methods and Techniques of the Course | - | |||||
| Course Coordinator | ||||||
| Course Lecturer(s) | ||||||
| Assistant(s) | ||||||
| Course Objectives | The aim of this course is to teach design and analysis strategies of bioengineered molecular diagnostics and medicinal biomolecules together with their bioprocess production pipeline. |
| Learning Outcomes |
The students who succeeded in this course;
|
| Course Description | Design and analysis of bioengineered molecular diagnostics and medicinal biomolecules as well as their production pipeline with a computational and simulation-based approach will be given. Following detailed explanations on molecular diagnostics design and drug simulation modelling with relevant examples, final steps of biological drug and diagnostics production in a factory setting will be covered. A platform where students will be able to use their knowledge and skills will be introduced via project homeworks. |
|
|
Core Courses | |
| Major Area Courses |
X
|
|
| Supportive Courses | ||
| Media and Management Skills Courses | ||
| Transferable Skill Courses |
WEEKLY SUBJECTS AND RELATED PREPARATION STUDIES
| Week | Subjects | Related Preparation |
| 1 | Design and analysis of a diagnostic test | • Chapter 4 and 5. Tietz Textbook of Clinical Chemistry and Molecular Diagnostics (6th edition). Rifai, Horvath, Wittwer. Elsevier, 2018 • How to evaluate a diagnostic test. Leeflang and Allerberger. Clin Microbiol Infect. 2019;25(1):54-59 • Designing studies for diagnostic tests. Bakke. Clin Respir J. 2008;2 Suppl 1:72-5. • Characteristics of good diagnostic studies. Mol et al. Semin Reprod Med. 2003;21(1):17-25. |
| 2 | Design, limitations and applications of Biosensors | • Blueprints for biosensors: Designs,Limitations and Applications. Carpenter et al. Genes (Basel). 2018; 9(8): 375. |
| 3 | Design and analysis of immunoassays | • Chapter 23. Tietz Textbook of Clinical Chemistry and Molecular Diagnostics (6th edition). Rifai, Horvath, Wittwer. Elsevier, 2018 • Designing paper-based immunoassays for biomedical applications. Hristov et al. Sensors (Basel). 2019; 19(3): 554. |
| 4 | Design and analysis of nucleic acid tests | • Guidance on the development and validation of diagnostic tests that depend on nucleic acid amplification and detection. Saunders et al. J Clin Virol. 2013; 56(3):260-70. |
| 5 | System miniaturization | • Chapter 24. Tietz Textbook of Clinical Chemistry and Molecular Diagnostics (6th edition). Rifai, Horvath, Wittwer. Elsevier, 2018 • Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: a review. Ahmad and Hashsham. Anal Chim Acta. 2012 Jul 6;733:1-15. • Miniaturized immunoassays: moving beyond the microplate. Vercht and Bakhtiar. Bioanalysis. 2012 Jan;4(2):177-88. • Bioengineering methods for analysis of cells in vitro. Underhill et al. Annu Rev Cell Dev Biol. 2012;28:385-410. |
| 6 | Designing biodrugs with molecular docking | • Chapter 3. Computational Drug Discovery and Design. Springer Protocols, Humana Press, 2018. Gore and Jagtap. • Molecular Docking and structure-based drug design strategies. Ferreira et al. Molecules. 2015; 22;20(7):13384-421. |
| 7 | Simulation of biomolecular dynamics | • Chapter 6 and 13. Computational Drug Discovery and Design. Springer Protocols, Humana Press, 2018. Gore and Jagtap. • Bridging molecular docking to molecular dynamics in Exploring ligand-protein recognition process: An overview. Salmaso and Moro. Front Pharmacol. 2018 Aug 22;9:923 |
| 8 | Review and Midterm Exam | |
| 9 | Bioprocess optimization and experimental design | • Experimental design methods for bioengineering applications. Gundogdu et al. Crit Rev Biotechnol. 2016;36(2):368-88. • Bioprocess Engineering Principles (2nd Edition),Doran P, Academic Press, 2012 |
| 10 | Bioprocess optimization and experimental design | • Model-assisted design of experiments as a concept for knowledge-based bioprocess development. Moller et al. Bioprocess Biosyst Eng. 2019 May;42(5):867-882. • Bioprocess Engineering Principles (2nd Edition),Doran P, Academic Press, 2012 |
| 11 | Bioreactor design | • Chapter 14. Bioprocess Engineering Principles (2nd Edition),Doran P, Academic Press, 2012 |
| 12 | Bioreactor design | • Chapter 14. Bioprocess Engineering Principles (2nd Edition),Doran P, Academic Press, 2012 |
| 13 | Downstream processing design and analysis | • Downstream Processing Technologies/Capturing and Final Purification : Opportunities for Innovation, Change, and Improvement. A Review of Downstream Processing Developments in Protein Purification. Singh and Herzer. Adv Biochem Eng Biotechnol. 2018;165:115-178. |
| 14 | Feasibility Analysis | • Integrated continuous bioprocessing: Economic, operational, and environmental feasibility for clinical and commercial antibody manufacture. Pollock et al. Biotechnol Prog. 2017 ; 33(4): 854–866. |
| 15 | Review of the semester | |
| 16 | Final Exam |
| Course Notes/Textbooks |
|
| Suggested Readings/Materials | • How to evaluate a diagnostic test. Leeflang and Allerberger. Clin Microbiol Infect. 2019;25(1):54-59
• Designing studies for diagnostic tests. Bakke. Clin Respir J. 2008;2 Suppl 1:72-5.
• Characteristics of good diagnostic studies. Mol et al. Semin Reprod Med. 2003;21(1):17-25.
• Blueprints for biosensors: Designs,Limitations and Applications. Carpenter et al. Genes (Basel). 2018; 9(8): 375.
• Designing paper-based immunoassays for biomedical applications. Hristov et al. Sensors (Basel). 2019; 19(3): 554.
• Guidance on the development and validation of diagnostic tests that depend on nucleic acid amplification and detection. Saunders et al. J Clin Virol. 2013; 56(3):260-70.
• Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: a review. Ahmad and Hashsham. Anal Chim Acta. 2012 Jul 6;733:1-15.
• Miniaturized immunoassays: moving beyond the microplate. Vercht and Bakhtiar. Bioanalysis. 2012 Jan;4(2):177-88.
• Bioengineering methods for analysis of cells in vitro. Underhill et al. Annu Rev Cell Dev Biol. 2012;28:385-410..
• Molecular Docking and structure-based drug design strategies. Ferreira et al. Molecules. 2015; 22;20(7):13384-421.
• Bridging molecular docking to molecular dynamics in Exploring ligand-protein recognition process: An overview. Salmaso and Moro. Front Pharmacol. 2018
• Experimental design methods for bioengineering applications. Gundogdu et al. Crit Rev Biotechnol. 2016;36(2):368-88.
• Model-assisted design of experiments as a concept for knowledge-based bioprocess development. Moller et al. Bioprocess Biosyst Eng. 2019 May;42(5):867-882.
• Downstream Processing Technologies/Capturing and Final Purification : Opportunities for Innovation, Change, and Improvement. A Review of Downstream Processing Developments in Protein Purification. Singh and Herzer. Adv Biochem Eng Biotechnol. 2018;165:115-178.
• Integrated continuous bioprocessing: Economic, operational, and environmental feasibility for clinical and commercial antibody manufacture. Pollock et al. Biotechnol Prog. 2017 ; 33(4): 854–866.
• Heller et al. Annu Rev Anal Chem (Palo Alto Calif). 2018; 12;11(1):79-100.
|
EVALUATION SYSTEM
| Semester Activities | Number | Weigthing |
| Participation | ||
| Laboratory / Application | ||
| Field Work | ||
| Quizzes / Studio Critiques | ||
| Portfolio | ||
| Homework / Assignments | ||
| Presentation / Jury |
2
|
20
|
| Project |
2
|
40
|
| Seminar / Workshop | ||
| Oral Exams | ||
| Midterm |
1
|
15
|
| Final Exam |
1
|
25
|
| Total |
| Weighting of Semester Activities on the Final Grade |
5
|
75
|
| Weighting of End-of-Semester Activities on the Final Grade |
1
|
25
|
| Total |
ECTS / WORKLOAD TABLE
| Semester Activities | Number | Duration (Hours) | Workload |
|---|---|---|---|
| Theoretical Course Hours (Including exam week: 16 x total hours) |
16
|
2
|
32
|
| Laboratory / Application Hours (Including exam week: '.16.' x total hours) |
16
|
2
|
32
|
| Study Hours Out of Class |
16
|
1
|
16
|
| Field Work |
0
|
||
| Quizzes / Studio Critiques |
0
|
||
| Portfolio |
0
|
||
| Homework / Assignments |
0
|
||
| Presentation / Jury |
2
|
3
|
6
|
| Project |
2
|
14
|
28
|
| Seminar / Workshop |
0
|
||
| Oral Exam |
0
|
||
| Midterms |
1
|
16
|
16
|
| Final Exam |
1
|
20
|
20
|
| Total |
150
|
COURSE LEARNING OUTCOMES AND PROGRAM QUALIFICATIONS RELATIONSHIP
|
#
|
Program Competencies/Outcomes |
* Contribution Level
|
||||
|
1
|
2
|
3
|
4
|
5
|
||
| 1 | To have adequate knowledge in Mathematics, Science and Genetics and Bioengineering; to be able to use theoretical and applied information in these areas on complex engineering problems. |
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| 2 | To be able to identify, define, formulate, and solve complex Genetics and Bioengineering problems; to be able to select and apply proper analysis and modeling methods for this purpose. |
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| 3 | To be able to design a complex system, process, device or product under realistic constraints and conditions, in such a way as to meet the requirements; to be able to apply modern design methods for this purpose. |
X | ||||
| 4 | To be able to devise, select, and use modern techniques and tools needed for analysis and solution of complex problems in Genetics and Bioengineering applications; to be able to use information technologies effectively. |
X | ||||
| 5 | To be able to design and conduct experiments, gather data, analyze and interpret results for investigating complex engineering problems or Genetics and Bioengineering research topics. |
X | ||||
| 6 | To be able to work efficiently in Genetics and Bioengineering disciplinary and multi-disciplinary teams; to be able to work individually. |
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| 7 | To be able to communicate effectively in Turkish, both orally and in writing; to be able to author and comprehend written reports, to be able to prepare design and implementation reports, to present effectively, to be able to give and receive clear and comprehensible instructions. |
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| 8 | To have knowledge about global and social impact of Genetics and Bioengineering practices on health, environment, and safety; to have knowledge about contemporary issues as they pertain to engineering; to be aware of the legal ramifications of Genetics and Bioengineering solutions. |
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| 9 | To be aware of ethical behavior, professional and ethical responsibility; to have knowledge about standards utilized in Genetics and Bioengineering applications. |
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| 10 | To have knowledge about industrial practices such as project management, risk management, and change management; to have awareness of entrepreneurship and innovation; to have knowledge about sustainable development. |
X | ||||
| 11 | To be able to collect data in the area of Genetics and Bioengineering, and to be able to communicate with colleagues in a foreign language. |
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| 12 | To be able to speak a second foreign language at a medium level of fluency efficiently. |
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| 13 | To recognize the need for lifelong learning; to be able to access information, to be able to stay current with developments in science and technology; to be able to relate the knowledge accumulated throughout the human history to Genetics and Bioengineering. |
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*1 Lowest, 2 Low, 3 Average, 4 High, 5 Highest
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