Course objectives:
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There are three major goals: 1. Familiarize students with the fundamental cellular components and their functions, e.g., the structure of DNA, RNA, and proteins, and interplay in the central dogma of molecular biology. 2. Introduce some standard quantitative models of biological systems and their relation to first principles. 3. Introduce relevant analysis and identification techniques and familiarize students with their value.
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Requirements on student
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The course is evaluated on a pass/fail bases. To pass, students must attend and participate in the lectures. At the end of the semester, students are also required to present a cellular subsystem model that they developed during the course.
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Content
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Biology (4 lectures): Introduction, central dogma of molecular biology, regulation mechanisms and signal transduction, and other mechanisms.
Modeling (5 lectures): The fundamental stochastic model, deterministic models of chemical reaction networks, other deterministic approximations, analysis, and common motifs.
Identification (3 lectures): Identification strategy, structural identification, identification of kinetics, and parameter estimation.
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Activities
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Fields of study
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Guarantors and lecturers
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Literature
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Recommended:
Gerald Karp. Cell and Molecular Biology: Concepts and Experiments. Wiley, 2007. ISBN 978-0-470-04217-5.
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Recommended:
Zoltan Szallasi, Jorg Stelling, and Vipul Periwal. System Modeling in Cellular BIology: From concepts to nuts and bolts. The MIT Press, 2006. ISBN 0-262-19548-8.
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On-line library catalogues
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Time requirements
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All forms of study
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Activities
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Time requirements for activity [h]
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Presentation preparation (report in a foreign language) (10-15)
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15
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Contact hours
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39
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Practical training (number of hours)
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39
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Individual project (40)
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39
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Total
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132
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Prerequisites
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Knowledge - students are expected to possess the following knowledge before the course commences to finish it successfully: |
student nemá žádné znalosti |
student má alespoň střední znalosti anglického jazyka |
Skills - students are expected to possess the following skills before the course commences to finish it successfully: |
student má základní počítačové dovednosti |
student umí komunikovat písemně a verbálně v anglickém jazyce |
Competences - students are expected to possess the following competences before the course commences to finish it successfully: |
N/A |
N/A |
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Learning outcomes
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Knowledge - knowledge resulting from the course: |
student je seznámen s koncepty biochemických reakcí |
student je seznámen s prvky genetických sítí |
student je seznámem s motify genetických sítí |
student rozumí princpům robustnosti ve vybraných biochemických systémech |
Skills - skills resulting from the course: |
student umí schematicky popsat biochemický buněčný systém |
student umí sestavit systém diferenciálních rovnic pro biochemické sítě pomocí Guldberg Waage zákonu |
student umí zjednodušit biochemický systém rozdělením časových řádů |
student umí parametrizovat biochemické reakce pomocí Miechalis-Menten konstant |
student umí popsat genetické regulační sítě pomocí principů kooperativity |
student umí realizovat daný biochemický systém v softwarovém nástroji založeným na biochemických pravidlech |
student umí iterativně naladit dynamické chování biochemického systému pomocí parametrizovaných motifů |
student umí prezentovat svojí práci v anglickém jazyce |
Competences - competences resulting from the course: |
N/A |
N/A |
N/A |
N/A |
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Assessment methods
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Knowledge - knowledge achieved by taking this course are verified by the following means: |
Skills demonstration during practicum |
Skills - skills achieved by taking this course are verified by the following means: |
Project |
Individual presentation at a seminar |
Competences - competence achieved by taking this course are verified by the following means: |
Skills demonstration during practicum |
Individual presentation at a seminar |
Seminar work |
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Teaching methods
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Knowledge - the following training methods are used to achieve the required knowledge: |
Lecture |
Practicum |
Multimedia supported teaching |
Textual studies |
Collaborative instruction |
Self-study of literature |
One-to-One tutorial |
Discussion |
Skills - the following training methods are used to achieve the required skills: |
Lecture |
Practicum |
Multimedia supported teaching |
Textual studies |
Collaborative instruction |
Self-study of literature |
One-to-One tutorial |
Discussion |
Competences - the following training methods are used to achieve the required competences: |
Lecture |
Practicum |
Multimedia supported teaching |
Textual studies |
Collaborative instruction |
Self-study of literature |
One-to-One tutorial |
Discussion |
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