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Computationele biologie (2024/2025: periode 3)
Cursusdoel
Leerdoelen
Computational Biology uses computer modeling to investigate biological problems. The course teaches a variety of modeling techniques and techniques to analyse the model behaviour. Moreover, biological theory obtained by computational modeling is examined.
Vaardigheden
Computational biology is a discipline by itself. Nevertheless interfaces with many different parts within biology, as well as computer science.
Computational Biology uses computer modeling to investigate biological problems. The course teaches a variety of modeling techniques and techniques to analyse the model behaviour. Moreover, biological theory obtained by computational modeling is examined.
Vaardigheden
Computational biology is a discipline by itself. Nevertheless interfaces with many different parts within biology, as well as computer science.
| Skills | Part of the course? | Explicitely examined? |
| Writing | ||
| Presenting | x | x |
| Data handling | X | |
| Practical research skills | X | |
| General research skills | ||
| Co-operation | X | |
| Critical thinking | x | X |
| Career orientation | ||
| Interdisciplinarity |
Vakinhoudelijk
Ingangseisen
Mandatory prerequisite knowledge of Quantitative Biology and Genomics. It is strongly recommended to do course Biological Modeling (year 2) beforehand. Students with similar knowledge can be accepted too. For students outside of the UU Biology programme, please contact the coordinator to discuss your pre-knowledge level.
Studie-interesserichting
The Computational Biology course is a core course of the studypath Theoretical Biology and Bioinformatics. Moreover, the course offers you strong theoretical support in the Molecular and Ecological directions.
Taal
This course is entirely in English
Inhoud
During the course, the emphasis will be on composing exact models, based on specific hypotheses. The models are analysed, the results yielding insights in the original biological system. The models that are studied address fundamental questions from a variety of biological fields, among which:
Evolutionary dynamics
Developmental dynamics (from genes to organisms) (plant and animal models will be used)
Network dynamics)
BehaviourBehavior
(Spatial) pattern formation and emergent properties are common themes emphasized in all these areas and the related general theory is introduced as a separate module.
A number of different model formalisms are used, namely:
Analysis tools include bifurcation analysis, sensitivity analysis, and various pattern analysis techniques.
Werkvormen
A typical day starts with lectures, followed by computational modelling exercises, including a mini project, about which a report is to be written. Literature will be handed out related to the computer exercises , and at the end of the course, literature seminars are given by the students.
Toetsing
To pass this course, a minimum of 5,5 is mandatory. The student's final mark is based on primarily the written exam; and rounded off based on the literature seminar and the mini project report.
Studiemateriaal
Mandatory prerequisite knowledge of Quantitative Biology and Genomics. It is strongly recommended to do course Biological Modeling (year 2) beforehand. Students with similar knowledge can be accepted too. For students outside of the UU Biology programme, please contact the coordinator to discuss your pre-knowledge level.
Studie-interesserichting
The Computational Biology course is a core course of the studypath Theoretical Biology and Bioinformatics. Moreover, the course offers you strong theoretical support in the Molecular and Ecological directions.
Taal
This course is entirely in English
Inhoud
During the course, the emphasis will be on composing exact models, based on specific hypotheses. The models are analysed, the results yielding insights in the original biological system. The models that are studied address fundamental questions from a variety of biological fields, among which:
Evolutionary dynamics
- Eco-evolutionary dynamics and spatial pattern formation,
- Host-pathogen co-evolution,
- Genome evolution, e.g. Interaction between gene regulation and evolution,
- Evolution of complexity, robustness and evolvability.
Developmental dynamics (from genes to organisms) (plant and animal models will be used)
- Pattern formation,
- Cell differentiation,
- Morphogenesis and mechanical interactions between cells,
- EVO-DEVO (evolution of development).
Network dynamics)
- Gene regulation and metabolic networks,
- RNA interference.
BehaviourBehavior
- Behavioral self-structuring through local interactions,
- Interface between learning and evolution.
(Spatial) pattern formation and emergent properties are common themes emphasized in all these areas and the related general theory is introduced as a separate module.
A number of different model formalisms are used, namely:
- Non-linear differential/difference equations (ODE and maps),
- Reaction Diffusion Systems (PDE),
- Cellular automata machines,
- Event based models,
- Individually oriented models,
- Evolutionary computation,
- Hybrid models using several combinations of the above formalisms.
Analysis tools include bifurcation analysis, sensitivity analysis, and various pattern analysis techniques.
Werkvormen
A typical day starts with lectures, followed by computational modelling exercises, including a mini project, about which a report is to be written. Literature will be handed out related to the computer exercises , and at the end of the course, literature seminars are given by the students.
Toetsing
To pass this course, a minimum of 5,5 is mandatory. The student's final mark is based on primarily the written exam; and rounded off based on the literature seminar and the mini project report.
Studiemateriaal
- course manual, sheets and literature
- LINUX software on the computers
Werkvormen
Computerpracticum
Hoorcollege
Werkcollege
Hoorcollege
Werkcollege
Toetsing
Eindresultaat
Verplicht | Weging 100% | ECTS 7,5
Ingangseisen en voorkennis
Ingangseisen
Je moet inschreven staan voor een van de volgende opleidingen:
- Scheikunde
- Biologie
- Molecular and Biophysical Life Sciences
Voorkennis
Verplichte voorkennis zijn de eerstejaars cursussen Genomica, Kwantitatieve Biologie (Systeembiologie) & de niveau 2 cursus Biologische modellering. Sterk aanbevolen wordt om voorafgaand aan de cursus de niveau 2 cursus Data Science te volgen. Studenten met vergelijkbare kennis kunnen ook toegelaten worden. Voor studenten van buiten biologie; Neem contact op met de cursuscoordinator om de voorkennis te bespreken.
Voertalen
- Engels
Cursusmomenten
Gerelateerde studies
- Biologie vanaf 2017-2018
- Biologie vanaf 2020-2021
- Biologie voor 2017-2018
- Molecular and Biophysical Life Sciences vanaf 2021-22
- Molecular Life Sciences Biologie
- Molecular Life Sciences Scheikunde
- Wiskunde en toepassingen vanaf 2019-2020
- Wiskunde en toepassingen vanaf 2022-2023
- Wiskunde en toepassingen vanaf 2024-2025
Tentamens
Er is geen tentamenrooster beschikbaar voor deze cursus
Verplicht materiaal
-
SOFTWARELinux software
Aanbevolen materiaal
-
HANDLEIDINGPracticum manuals, sheets en literature
Coördinator
| prof. dr. P. Hogeweg | P.Hogeweg@uu.nl |
Docenten
| prof. dr. P. Hogeweg | P.Hogeweg@uu.nl |
Inschrijving
Deze cursus is open voor bijvakkers. Controleer wel of er aanvullende ingangseisen gelden.
Inschrijving
Van maandag 4 november 2024 tot en met vrijdag 22 november 2024
Na-inschrijving
Van maandag 20 januari 2025 tot en met dinsdag 21 januari 2025
Inschrijving niet geopend
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