1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2022/23

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Introduction: Rozdiel medzi revíziami

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===Rozvrh===
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__NOTOC__
* Prednáška: štvrtok 15:40-17:10 F1-328
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* Cvičenie (pre inf): štvrtok 14:00-15:30 F1-328
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===Schedule===
* Cvičenie (pre biol): štvrtok 17:20-18:50 F1-328 (druhá polovica občas v F1-248)
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* Lecture: Thursday 15:40-17:10 F1-108
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* Tutorial for computer science (BIN, INF, mINF, mAIN, DAV): Thursday 14:00-15:30 F1-108
===Prednášajúci===
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* Tutorial for biologists (PriFUK, physics): Thursday 17:20-18:50 C, M-217
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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/ Mgr. Tomáš Vinař, PhD.] M-163
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* [http://new.dcs.fmph.uniba.sk/index.php/Zamestnanci?_method=detail&_key=alias&alias=AskarGafurov Mgr. Askar Gafurov, PhD.] M-25
* Konzultácie po dohode emailom
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* [http://compbio.fmph.uniba.sk/~tvinar/ doc. Mgr. Tomáš Vinař, PhD.] M-163
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* Consultations can be arranged by e-mail
===Ciele predmetu===
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===Course objectives===
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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.
  
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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* Everyone: Overview of basic methods for analysis of biological sequences and other data sets in molecular biology.
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* CS: Algorithms and data structures, machine learning, probability. How to develop mathematical abstractions for real-world problems.
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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.
  
* Pre všetkých: podať prehľad základných metód používaných na výpočtovú analýzu biologických sekvencií a ďalších dát v molekulárnej biológii.
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===Brief syllabus===
* 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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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.
* Pre biológov: pochopiť matematické modely tvoriace základ populárnych bioinformatických nástrojov, naučiť sa tieto nástroje používať a interpretovať ich výsledky.  
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===Stručná osnova===
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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.
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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'''Literatúra'''
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===Literature===
  
Mnohé základné pojmy budú preberané podľa kníh:
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Many basic concepts can be found in the following textbooks:
  
* Durbin, Eddy, Krogh, Mitchison: Biological sequence analysis. Cambridge University Press 1998.
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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  
:: K dispozícii v knižnici FMFI k prezenčnému používaniu, signatúra 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
* 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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The course material also draws on scientific literature and other materials.

Aktuálna revízia z 14:43, 21. september 2022

Schedule

  • Lecture: Thursday 15:40-17:10 F1-108
  • Tutorial for computer science (BIN, INF, mINF, mAIN, DAV): Thursday 14:00-15:30 F1-108
  • 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.