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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===Rozvrh===
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===Schedule===
* Prednáška: štvrtok 15:40-17:10 F1-328
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* Lecture: Thursday 15:40-17:10 C
* Cvičenie (pre inf): štvrtok 14:00-15:30 F1-328
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* Tutorial for computer science (BIN, INF, mINF, mAIN): Thursday 14:00-15:30 C
* Cvičenie (pre biol): štvrtok 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
  
===Vyučujúci===
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===Instructors===
 
* [http://compbio.fmph.uniba.sk/~bbrejova/ doc. Mgr. Broňa Brejová, PhD.] M-163
 
* [http://compbio.fmph.uniba.sk/~bbrejova/ doc. Mgr. Broňa Brejová, PhD.] M-163
 
* [http://compbio.fmph.uniba.sk/~tvinar/ doc. Mgr. Tomáš Vinař, PhD.] M-163
 
* [http://compbio.fmph.uniba.sk/~tvinar/ doc. Mgr. Tomáš Vinař, PhD.] M-163
 
* [http://new.dcs.fmph.uniba.sk/index.php/Zamestnanci?_method=detail&_key=alias&alias=AskarGafurov Mgr. Askar Gafurov] M-25
 
* [http://new.dcs.fmph.uniba.sk/index.php/Zamestnanci?_method=detail&_key=alias&alias=AskarGafurov Mgr. Askar Gafurov] M-25
* Konzultácie po dohode emailom
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* Consultations can be arranged by e-mail
  
===Ciele predmetu===
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===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.
  
===Stručná osnova===
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===Brief syllabus===
Základné pojmy z molekulárnej biológie, algoritmov a strojového učenia. Sekvenovanie a zostavovanie genómov. Hľadanie génov. Zarovnávanie sekvencií. Evolučné modely a fylogenetické stromy. Komparatívne metódy. Štruktúra RNA. Hľadanie motívov a analýza expresie génov. Štruktúra a funkcia proteínov. Úvod do populačnej genetiky. Vybrané aktuálne témy.
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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.
  
===Literatúra===
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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.
  
Mnohé základné pojmy budú preberané podľa kníh:
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===Literature===
  
* Durbin, Eddy, Krogh, Mitchison: Biological sequence analysis. Cambridge University Press 1998.
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Many basic concepts can be found in the following textbooks:
:: K dispozícii v knižnici FMFI k prezenčnému používaniu, signatúra I-INF-D-21
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* Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008.
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:: K dispozícii v knižnici FMFI k prezenčnému používaniu, signatúra I-INF-Z-2
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Tieto budú doplnené poznatkami z odborných článkov a ďalšej literatúry.
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* '''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
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* '''ZB''': Zvelebil, Baum: Understanding Bioinformatics. Taylor & Francis 2008. Can be studied in the FMFI  library under code I-INF-Z-2
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The course material also draws on scientific literature and other materials.

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.