E7441: Scientific computing in biology and
biomedicine
Overview
Vlad Popovici, Ph.D.
RECETOX
Bibliography:
KONG Q., SIAUW T., BAYEN A. (2020). Python programming and
numerical methods. Academic Press. ISBN: 9780128195499
HEATH M.T. (2002). Scientific Computing. An introductory survey.
McGraw-Hill, 2nd edition. ISBN: 0-07-239910-4 Good accompanying
materials at https://heath.cs.illinois.edu/scicomp/notes/index.html,
including slides and demos! Used as basis for the first part of the
course.
KEPNER J. (2009). Parallel Matlab for Multicore and Multinode
Computers. SIAM Publishing. ISBN: 978-0-898716-73-3
GENTLE J.E. (2005). Elements of Computational Statistics. Springer.
ISBN:978-0387954899
Vlad Popovici, Ph.D. (RECETOX) E7441: Scientific computing in biology and biomedicine 2 / 6
Computing environments for the course:
Python 3, https://www.python.org - with NumPy and SciPy packages
recommended: JupyterLab for exercises
suggestion: install Python and related packages using a distribution
like Anaconda or Mamba for easier integration of dependencies
R, http://www.r-project.org - "environment for statistical computing
and graphics"
WARNING: Some pieces of code shown during the course may not
represent the optimal implementation in the given language. They are
merely a device for demonstrating some principles.
Vlad Popovici, Ph.D. (RECETOX) E7441: Scientific computing in biology and biomedicine 3 / 6
Overview of the topics:
1 Introduction to scientific computing
2 Systems of linear equations: square and non-square
3 Basic methods for non-linear equations and optmization
4 Stochastic methods (touching upon optimization as well)
5 Basic concepts of parallel computing (in Python)
6 Examples of implementations of various fundamental methods in
statistics and machine learning
Vlad Popovici, Ph.D. (RECETOX) E7441: Scientific computing in biology and biomedicine 4 / 6
Organization:
combined theoretical presentation and practical work
4 homeworks and 1 project (i.e. a more consistent homework)
Project presentations: May 12th, 2025
Deadline for sending in the homeworks (via email): May 12th, 2025
Delivery of homeworks and project presentations are required for
qualifying for the exam. No homeworks and/or project = no exam
Final mark: 50% homework and project + 50% exam
Vlad Popovici, Ph.D. (RECETOX) E7441: Scientific computing in biology and biomedicine 5 / 6
Questions?
Vlad Popovici, Ph.D. (RECETOX) E7441: Scientific computing in biology and biomedicine 6 / 6