(in Polish) Modelowanie i Bioinformatyka Strukturalna 1400-MBS
The following topics will be covered in this class:
● Python programming basics, basic libraries (Pandas, Seaborn, Numpy, BioPython), visualization and processing of large amounts of data
● Homology, analogy and coevolution in the context of protein sequences and structures, concepts of protein families and domains and how to classify them
● Sequence and structure databases (AFDB, ECOD, UniProt), accessing databases from within Python
● Sequence methods (HHsuite, HMMER, MMseqs2, CCmpred), homology detection, function determination and protein classification
● Structural methods (AlphaFold, FoldSeek, PyMol), modelling of oligomers, protein-protein interactions and fibre structures
● Embeddings and language models and tools based on them, such as pLM-BLAST and tSNE/UMAP visualisation techniques
● Carry out your own experiment based on the knowledge gained. Design from a pool of available designs or self-invented.
|
Term 2024Z:
None |
Type of course
Course coordinators
Learning outcomes
KNOWLEDGE
Has elementary knowledge in the field of bioinformatics and understands its relationships and dependencies with other natural disciplines (K_W01).
Demonstrates knowledge of the basics of bioinformatics, conceptual categories and terminology and the development of research methods in this field (K_W02).
Uses mathematical tools to describe biological phenomena (K_W03).
Knows basic bioinformatics techniques and tools used to study natural phenomena (K_W04).
Has knowledge of computer techniques and uses computer tools to retrieve information (K_W08).
SKILLS
Applies techniques specific to bioinformatics (K_U01).
Is able to read with understanding professional literature on bioinformatics in English (K_U02).
Is able to use available sources of information (K_U03).
Applies mathematical and statistical methods at a basic level to describe phenomena and analyse data in bioinformatics (K_U05).
SOCIAL COMPETENCES
Develops an attitude of acceptance of mathematical and statistical methods used in bioinformatics (K_K02).
Demonstrates responsibility for his/her own work and equipment entrusted to him/her, and respects his/her own work and that of others (K_K03).
Understands the need to communicate new developments in bioinformatics to the public and is able to do so in an understandable way (K_K06).
Assessment criteria
Realisation of an individual project
Bibliography
1. Polański J, Bąk A. Podstawy chemoinformatyki leków. Wydawnictwo Uniwersytetu Śląskiego, Katowice 2018
2. Xiong J. Podstawy bioinformatyki. Wydawnictwa Uniwersytetu Warszawskiego, Warszawa 2009
Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: