Teaching

From Bioinformatics Group

Contents

Infrastructure

Hardware

We administer three Dell-based computer laboratories. Demanding computations are performed on a small MPI-ready Opteron-based cluster. A separate MOSIX cluster is at hand for students learning techniques of molecular simulation.

Software

As an e-learning and communication platform we extensively use Pegaz [Platforma zdalnego nauczania moodle na Uniwersytecie Jagiellońskim] and the Blackboard systems [Krakowski Kampus Wirtualny].

Paperware

Irena Roterman and Leszek Konieczny published a book "Strategia działania organizmu żywego" (Strategy of functioning of a living organism) that is an introductory handbook in the field of systems biology.


Courses

Courses for students of comp-sci and physics

Courses primarily for the students of computer science but all students with some computer skills are more than welcomed to join

  • Systems biology - to view an organism as an integrated and interacting network of genes, proteins and biochemical reactions which give rise to life.
  • Bioinformatics - to provide an introduction to interdisciplinary problems and algorithmic methods of the field.
  • Genomics - to learn how to tackle computationally information inscribed in whole genomes in order to reason about gene functions and related disorders.
  • Proteomics - to give computational insight into the astounding world of molecules that are vital for all processes of life.
  • Computer-Aided Drug Design - to understand how the computational design is used to eventually create new medicines.
  • Quantum Chemistry - to show how to determine computationally chemical properties of small molecules.
  • Biometrics - to learn how to capture individual features of human body and build reliable classifiers using the machine learning approach.

Courses for students of medicine

  • Biochemistry - a series of molecular modelling classes.
  • Computer Science for Medicine.
  • Biostatistics.
  • Biostatistics workshops.

Student projects

Following projects were realized by students attending Bioinformatics Courses

  • Protein-ligand complex description contacts maps and simple consensus classification of complexes [CMapper]
  • Ligand Database some major and minor changes of Ligand Databse (under construction) [LiganDB]
  • Barrels in protein structure detection and classification of barrels or barrel-like structures [GetBarrel]

Theses

If you are looking for a thesis topic in the field of bioinformatics or related, please perform a search in the [database].

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