SubjectsSubjects(version: 855)
Course, academic year 2019/2020
Methods and applications in computational cell biology and biophysics - MC260P117
Title: Methods and applications in computational cell biology and biophysics
Czech title: Výpočetní metody v buněčné biologii a biofyzice
Guaranteed by: Department of Physical and Macromolecular Chemistry (31-260)
Faculty: Faculty of Science
Actual: from 2019 to 2019
Semester: summer
E-Credits: 3
Examination process: summer s.:combined
Hours per week, examination: summer s.:2/0 Ex [hours/week]
Capacity: unlimited
Min. number of students: 3
State of the course: taught
Language: English
Guarantor: prof. Mgr. Pavel Jungwirth, CSc., DSc.
Teacher(s): Lukasz Cwiklik, Ph.D., D.Sc. (Tech.)
prof. Mgr. Pavel Jungwirth, CSc., DSc.
Hector Martinez-Seara, Dr.
Opinion survey results   Examination dates   Schedule   
Annotation -
Last update: doc. RNDr. Iva Zusková, CSc. (02.05.2017)
The studies of biologically relevant systems are increasingly relying on computational methods. The lecture aims
at familiarizing students with different computational methods that can be used to tackle biological and biophysical
problems. We will provide a solid background for choosing appropriate computational techniques based on
scenarios of realistic biological problem. For this, we will provide a comprehensive overview of commonly used
computational tools and their underlying theoretical basis. The lecture will emphasize the strengths and drawbacks
of the presented approaches.
Literature -
Last update: doc. RNDr. Iva Zusková, CSc. (02.05.2017)
l Glaser, Ronald. Biophysics (5h ed), Heidelberg: Spriger-Verlag, 2001. Print

l Cotterill, Rodney. Biophysics: And introduction, Chichester: Wiley, 2002.Print

l Leach, Andrew R. Molecular Modelling: Principles and Applications (2nd Edition), Harlow: Pearson Education Limited, 2001. Print

l Bishop, Christopher M. Pattern recognition and machine learning, Singapore: Springer, 2006. Print

Requirements to the exam
Last update: doc. RNDr. Iva Zusková, CSc. (02.05.2017)
Examination Requirements
An oral exam covering the topics of the syllabus with the emphasis in the applicability of computational methods and their drawbacks. Two compulsory case study student projects covering one computational technique and one application to modeling of an experiment.

Syllabus -
Last update: doc. RNDr. Iva Zusková, CSc. (02.05.2017)
l Overview of computational strategies applied to cell and macromolecular imaging (4 lectures)

 Introduction to pattern and morphology recognition (½ lecture)

(cases studies in cell confocal imaging and CRYOEM image sorting approaches)

 Image manipulation methods (½ lecture)

(benefits and drawbacks of image manipulation, filtering techniques, and pixel normalization)

 Concepts of probability theory applied to pattern recognition (1 lectures)

(probability densities, expectations and covariances, Bayesian probabilities, the Gaussian distribution, curve fitting, and Bayesian curve fitting)

 Choosing an appropriate model for a given biological system and phenomenon (½ lecture)

(minimizing the number of model parameters, Markov state models, finite elements, and Voronoi tessellation)

 Decision theory as methodology behind pattern and morphology recognition techniques (1 lectures)

(minimizing the misclassification rate, minimizing the expected loss, the reject option, inference and decision, and loss functions for regression)

 Machine learning applied to image recognition (½ lecture)

l Data mining and high-throughput data analysis (1 lecture)

 Introduction and methods

(case study on DNA search patterns; Association Analysis for Large-Scale Gene Set Data)

l Overview of computational methods in biological problems: from atomistic to macroscopic approaches (6 lectures)

 Modeling biosystems at atomistic resolution (2 lecture)

(choosing an appropriate molecular-level approach: quantum mechanics, molecular dynamics, Monte Carlo, and QM/MM)

 Modeling of mesoscopic and macroscopic biological systems (2 lectures)

(mean field models; thermodynamic and kinetic models)

 Network analysis and kinetics in biosystems (2 lectures)

(signaling, transport, and biochemical cycles)

l Software and computational tools in computational biology (3 lectures)

 General programming platforms optimal for biological problems (½ lecture)

(Python, R, and Matlab/Octave)

 Image processing software (1 lecture)

(ImageJ, and matplotlib)

 Choosing a proper software for a particular computational biological problem (½ lecture)

(computational strategies in connection with limitations of the theory and methods behind)

 Machine learning (1 lecture)

(TensorFlow, and scikit-learn)

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