Biomathematics Models

Code:

M4043

Acronym:

M4043

Keywords
Classification	Keyword
OFICIAL	Mathematics

Instance: 2016/2017 - 1S

Active?	Yes
Web Page:	http://cmup.fc.up.pt/cmup/biomodels/
Responsible unit:	Department of Mathematics
Course/CS Responsible:	Master in Mathematical Engineering

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
M:ENM	4	Official Study Plan since 2013-2014	1	-	6	56	162
M:M	1	Plano de Estudos do M:Matemática	1	-	6	56	162
			2

Teaching language

Suitable for English-speaking students

Objectives

This course aims to give an overview of the various methods of mathematical modeling in Systems Biology.

The systems approach to biology is a new methodological paradigm that transformed research in biology in the 21st century. The key idea is that we can study the interactions of all components of a biological system to reveal their emergent properties. Recently won a new impact, mainly due to the remarkable progress of experimental and computational methods (Bioinformatics), ever more ingenious and powerful. It is supported accumulated in biological knowledge, more detailed, the creation of new experimental techniques in genomics and proteomics, new technologies to make extensive measurements DNA sequence, expression and regulation of genes, protein-protein interactions, modeling tradition math biological processes and the exponential growth of Bioinformatics (as a prerequisite for the construction of huge databases and analysis of large-scale systems).

Biology has become increasingly multidisciplinary with biologists, computer scientists, engineers, mathematicians, physicists and doctors, to join efforts to develop high-efficiency technologies and computational and mathematical tools, guided by current needs of biology and medicine.

Learning outcomes and competences

It is intended that the students acquire skills in construction and analysis of models in biological systems.
At the end of this course, students should be able to:
1) mathematically represent the properties and dynamics of biological systems, explaining precisely the assumptions and simplifications used
2) take advantage of different areas of mathematics to create and analyze models
3) use the computer as a working tool in the creation and analysis models

Working method

Presencial

Pre-requirements (prior knowledge) and co-requirements (common knowledge)

Program

1. Introduction to Mathematical Modeling, Systems Biology and Synthetic Biology.


2. Static Network Models, Network Biology. Design of Biological Networks. Motifs.


3. The Mathematics of Biological Systems. Modeling of Chemical Reaction Networks. Biochemical Kinetics. Stochastic algorithms (Gillespie type).


4. Parameter Estimation.


5. Gene Regulatory Networks. Signal Transduction Pathways. Boolean Networks.


6. Protein Systems. PPI Networks


7. Metabolic Networks. Stoichiometric Network Analysis. Metabolic Pathway Analysis. Constraint-Based Modeling --Metabolic Flux Analysis.


8. Integrative Analysis of Genome, Protein, and Metabolite Data.


9. Systems Biology in Medicine and Drug Development.


10. Emerging Topics in Systems Biology.

Mandatory literature

Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald; Systems Biology: A Textbook, Wiley-Blackwell, 2016. ISBN: 978-3-527-33636-4

Complementary Bibliography

Eberhard Voit; A First Course in Systems Biology, Garland Science, Taylor & Francis Group, 2012. ISBN: 9780815344674
Brian Ingalls; Mathematical Modeling in Systems Biology: An Introduction, MIT Press, 2013. ISBN: 0262018888

Comments from the literature

Teaching methods and learning activities

Lectures with exposure of concepts
Solving exercises
Practical classes with computer simulation models

Evaluation Type

Distributed evaluation without final exam

Assessment Components

designation	Weight (%)
Participação presencial	60,00
Trabalho escrito	10,00
Trabalho prático ou de projeto	30,00
Total:	100,00

Eligibility for exams

Calculation formula of final grade

Students will be approved provided they obtain a grade equal to or greater than 10 points in continuous assessment, including resolution of the exercises and presentation Article / class - students should individually present a lecture on an integrated subject within the discipline, submit an article in the area; the choice of subject or article shall be made with the help of teachers.

Examinations or Special Assignments

Presentation article / class: students should individually present a lecture on an integrated subject within the discipline, submit an article in the area; the choice of subject or article shall be made with the help of teachers

Internship work/project

Special assessment (TE, DA, ...)

Classification improvement

Observations