1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2021/22

Introduction · Rules · Tasks and dates · Materials · Moodle · Discussion
Cvičenia vo štvrtok o 14:00 sú určené pre študentov BIN, INF, mINF, mAIN, DAV. Cvičenia vo štvrtok o 17:20 sú pre študentov z PriFUK a z fyzikálnych odborov. Obidvoje cvičenia sa budú konať už v prvom týždni semestra.


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===Schedule===
 
===Schedule===
 
* Lecture: Thursday 15:40-17:10 C
 
* Lecture: Thursday 15:40-17:10 C
* Tutorial for computer science (BIN, INF, mINT, mAIN): Thursday 14:00-15:30 C
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* Tutorial for computer science (BIN, INF, mINF, mAIN): Thursday 14:00-15:30 C
* Tutorial for biologists (PriFUK, physics): Thursday 17:20-18:50 F1-328, M-217
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* Tutorial for biologists (PriFUK, physics): Thursday 17:20-18:50 C, M-217
  
 
===Instructors===
 
===Instructors===
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===Course objectives===
 
===Course objectives===
  
Tento predmet je určený pre študentov informatických aj biologických odborov. Prednášky budú spoločné pre všetkých, cvičenia budú zvlášť pre informatikov a biológov a poskytnú potrebné doplňujúce informácie.
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This course is targeted at students of both computer science and life science study programs. Lectures will be together for both groups. Tutorials are held separately for CS and biology students.  
  
* Pre všetkých: podať prehľad základných metód používaných na výpočtovú analýzu biologických sekvencií a ďalších dát v molekulárnej biológii.
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* Everyone: Overview of basic methods for analysis of biological sequences and other data sets in molecular biology.
* Pre informatikov: prehĺbiť/získať znalosti z algoritmov a dátových štruktúr, strojového učenia a pravdepodobnosti. Na príkladoch z biológie ukázať, ako prejsť od problému v reálnom svete k matematickej abstrakcii.
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* CS: Algorithms and data structures, machine learning, probability. How to develop mathematical abstractions for real-world problems.
* Pre biológov: pochopiť matematické modely tvoriace základ populárnych bioinformatických nástrojov, naučiť sa tieto nástroje používať a interpretovať ich výsledky.  
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* Biology: Mathematical models at the core of popular bioinformatics tools, how to use tools, interpretation of their results.
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* Everyone: Experience with interdisciplinary collaboration.
  
 
===Brief syllabus===
 
===Brief syllabus===

Verzia zo dňa a času 08:01, 20. október 2021

Schedule

  • Lecture: Thursday 15:40-17:10 C
  • Tutorial for computer science (BIN, INF, mINF, mAIN): Thursday 14:00-15:30 C
  • Tutorial for biologists (PriFUK, physics): Thursday 17:20-18:50 C, M-217

Instructors

Course objectives

This course is targeted at students of both computer science and life science study programs. Lectures will be together for both groups. Tutorials are held separately for CS and biology students.

  • Everyone: Overview of basic methods for analysis of biological sequences and other data sets in molecular biology.
  • CS: Algorithms and data structures, machine learning, probability. How to develop mathematical abstractions for real-world problems.
  • Biology: Mathematical models at the core of popular bioinformatics tools, how to use tools, interpretation of their results.
  • Everyone: Experience with interdisciplinary collaboration.

Brief syllabus

Basic concepts from molecular biology, algorithms and machine learning. Sequencing and assembling genomes. Gene finding. Sequence alignment. Evolutionary models and phylogenetic trees. Comparative genomics. RNA structure. Motif finding and gene expression analysis. Protein structure and function. Selected current topics.

Students of computer science programs will focus on computer science methods and mathematical modeling of the covered problems. Life science students will focus on understanding and correct application of these methods on real data.

Literature

Many basic concepts can be found in the following textbooks:

  • DEKM: Durbin, Eddy, Krogh, Mitchison: Biological sequence analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press 1998. Can be studied in the FMFI library under code I-INF-D-21
  • ZB: Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008. Can be studied in the FMFI library under code I-INF-Z-2

The course material also draws on scientific literature and other materials.