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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* Prednáška: štvrtok 15:40-17:10 F1-328
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===Schedule===
* Cvičenie (pre inf): štvrtok 14:00-15:30 F1-328
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* Lecture: Thursday 15:40-17:10 C
* Cvičenie (pre biol): štvrtok 17:20-18:50 M-217
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* Tutorial for computer science (BIN, INF, mINF, mAIN): Thursday 14:00-15:30 C
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* Tutorial for biologists (PriFUK, physics): Thursday 17:20-18:50 C, M-217
  
===Prednášajúci===
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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://compbio.fmph.uniba.sk/~tvinar/ doc. Mgr. Tomáš Vinař, PhD.] M-163
* Konzultácie po dohode emailom
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* [http://new.dcs.fmph.uniba.sk/index.php/Zamestnanci?_method=detail&_key=alias&alias=AskarGafurov Mgr. Askar Gafurov] M-25
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* Consultations can be arranged by e-mail
===Ciele predmetu===
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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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===Course objectives===
  
* Pre všetkých: podať prehľad základných metód používaných na výpočtovú analýzu biologických sekvencií a ďalších dát v molekulárnej biológii.
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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 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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* 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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* Everyone: Overview of basic methods for analysis of biological sequences and other data sets in molecular biology. 
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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* 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.
  
===Literatúra===
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===Brief syllabus===
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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.
  
Mnohé základné pojmy budú preberané podľa kníh:
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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.
  
* Durbin, Eddy, Krogh, Mitchison: Biological sequence analysis. Cambridge University Press 1998.
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===Literature===
:: 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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Many basic concepts can be found in the following textbooks:
  
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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
<script>(function(d, s, id) {
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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
  var js, fjs = d.getElementsByTagName(s)[0];
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  if (d.getElementById(id)) return;
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The course material also draws on scientific literature and other materials.
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<div class="fb-page" data-href="https://www.facebook.com/Computational-Biology-at-Comenius-University-in-Bratislava-1186005448094730/" data-tabs="timeline" data-height="600" data-small-header="true" data-adapt-container-width="true" data-hide-cover="false" data-show-facepile="false"></div>
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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.