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Modeling of Biological Processes

Code:

BINF029

Sigla:

MPB

Áreas Científicas
Classificação	Área Científica
OFICIAL	Biotecnologia

Ocorrência: 2019/2020 - 1S

Ativa?	Yes
Unidade Responsável:	Biotecnologia
Curso/CE Responsável:	Undergraduate in Bioinformatics

Ciclos de Estudo/Cursos

Sigla	Nº de Estudantes	Plano de Estudos	Anos Curriculares	Créditos UCN	Créditos ECTS	Horas de Contacto	Horas Totais
BINF	18	Study Plan	3	-	5	60	135

Língua de trabalho

Portuguese

Objetivos

This UC goal is to provide students with the mathematical skills to model and simulate biological/biochemical systems from a kinetic/metabolic perspective. This stems from the biochemical systems theory, in which biochemical systems can be modelled using differential equations, encompassing not only kinetics and flows but also regulation processes and compartmentation. This UC also includes models of pharmacokinetic origin.

Resultados de aprendizagem e competências

.

Modo de trabalho

Presencial

Programa

1. Modelling enzymatic reactions: enzyme kinetics; mechanisms of activation and inhibition; mathematical modelling of one enzyme systems – mass action laws, power laws and Henri-Michaelis-Menten law
2. Modelling metabolic networks I: using mass action laws and power laws to describe a 1-compartment metabolic system; system analysis under the framework of metabolic control analysis
3. Modelling metabolic networks II: understanding parallel alternative pathways and what triggers switching among them
4. Modelling metabolic networks III: the role of genes, single gene, probabilistic prokaryotic gene and eukaryotic cis-regulatory control modelling
5. Modelling metabolic networks IV: the case of drugs
6. Modelling compartments I: flow between compartments; transporters
7. Modelling compartments II: a basic overview of the cell as a multitude of communicating compartments; inter-compartment signaling as an approach to extracellular modelling
8. Modelling compartments III: pharmacokinetics

Bibliografia Obrigatória

Fell, D.; Understanding the Control of Metabolism (Frontiers in Metabolism), Portland Press. ISBN: 978-1- 855-78047-7
Bower, J.M., Bolouri, H. (eds.); Computational Modeling of Genetic and Biochemical Networks, Bradford Book. ISBN: 978-0-262-52423-0
Britton, N.F.; Essential Mathematical Biology, Springer. ISBN: 978-1-852-33536-6
Peters, S.A.; Physiologically-Based Pharmacokinetic (PBPK) Modeling and Simulations: Principles, Methods, and Applications in the Pharmaceutical Industry Hardcover, Wiley. ISBN: 978-0-470-48406-7

Métodos de ensino e atividades de aprendizagem

Demonstrative lectures and exercises that will be focused on show-casing in a large number of simple examples the various mathematical models that arise in this area

Software

Optflux (www.optflux.org/)
Copasi (http://copasi.org/)
CellDesigner (http://www.celldesigner.org/)
JWS online (http://jjj.biochem.sun.ac.za/)
COBRA (https://opencobra.github.io/)

Tipo de avaliação

Distributed evaluation with final exam

Componentes de Avaliação

Designation	Peso (%)
Teste	70,00
Trabalho escrito	30,00
Total:	100,00

Componentes de Ocupação

Designation	Tempo (Horas)
Apresentação/discussão de um trabalho científico	0,50
Estudo autónomo	40,00
Frequência das aulas	60,00
Trabalho escrito	34,50
Total:	135,00

Obtenção de frequência

Not applicable