1-BIN-301, 2-AIN-501 Methods in Bioinformatics, 2023/24

Introduction · Rules · Tasks and dates · Materials · Moodle
Quizzes can be found in Moodle.
Homework assignments and journal club papers can be found in Tasks and dates.
Exam rules, example questions and syllabus
Groups for journal club have each their own group in Moodle.


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==Hodnotenie==
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==Grading==
  
* 3 domáce úlohy 30% (10% každá)
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* 3 homework assignments 30% (10% each)
 
* Journal club 10%
 
* Journal club 10%
* Skúška alebo projekt 60%
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* Quizzes 10% (each week 1%)
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* Final exam 50%
  
Hodnotenie: A: 90+, B: 80+, C: 70+, D: 60+, E: 50+
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To pass the course, you need to satisfy both requirements below (otherwise Fx grade will be assigned):
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* overall at least 50% of points
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* at least 50% of points from the final exam
  
Domáce úlohy a skúška môžu obsahovať dve verzie niektorých otázok, jednu určenú pre biológov (resp. iných študentov prírodovedných odborov) a jednu pre študentov informatických odborov.
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Final grade: A: 90+, B: 80+, C: 70+, D: 60+, E: 50+
  
Namiesto skúšky môžete odovzdať projekt, ak ho máte vopred schválený od vyučujúcich. Doktorandi musia robiť projekt.
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Homeworks and exams may contain separate versions of some questions, one for computer science students (namely, BIN, INF, mINF, mAIN students) and one for biologists (more precisely, students for Faculty of Natural Sciences and physics students).
  
 
==Journal club==
 
==Journal club==
  
Journal club sa robí v skupinách, pričom každá skupina má za úlohu naštudovať a spísať vlastnými slovami jeden článok z odbornej literatúry.
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Journal club is a group activity, where each groups studies one scientific paper and rewrites it in their own words.
  
* Každý študent si z ponúknutého zoznamu vyberie tri články, ktoré ho najviac zaujali.
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* Each student will select from the provided list the three articles that are of highest interest to him/her.
* Podľa týchto preferencií vyučujúci rozdelia študentov do skupín. Každá skupina bude čítať iný článok.
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* According to these preferences, instructors will divide the students into groups. Each group will read a different article.
* Každý študent si najskôr sám prečíta pridelený článok.
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* Each student first reads the assigned article individually.
* Potom sa stretne celá skupina, prediskutuje článok a pokúsi sa vysvetliť si navzájom nejasné časti, prípadne zohnať chýbajúce informácie v literatúre. V prípade záujmu sa na takomto stretnutí môžu zúčastniť vyučujúci a pomôcť zodpovedať prípadné otázky.
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* Then the whole group meets, discusses the article and tries to clarify any questions or to find missing information in the literature.
* Skupinka spíše správu, v ktorej vlastnými slovami vysvetlí hlavné metódy a výsledky článku a ďalšie potrebné pojmy tak, aby správa bola pochopiteľná pre študentov biológie aj informatiky.
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* If needed, the group meets several times or continues to communicate electronically. In case of questions about the article, the whole group or some of its members can also arrange consultations with the instructors.
* V správe je potrebné vymenovať členov skupiny, ktorí sa na jej práci reálne podieľali. Študenti, ktorí v tomto zozname nebudú uvedení, nezískajú za správu body.  
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* The group writes a report, in which they explain in their own words the main methods and results of the article and other necessary concepts so that the text is understandable to students of this course (both computer scientists and biologists).
  
==Skúška==
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Details for the journal club group meeting
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* Remember that everyone should read the article before the first meeting
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* The first meeting should take place no later than November 23. The meeting can be online or in person. Online meetings should be on MS Teams, in person meetings should be at FMFI or PriFUK. Try to choose a time suitable for all members of the group. We will create a channel for each group on MS Teams which can be used for any discussions and for the meeting itself.
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* Post the chosen time and place of the first meeting on MS Teams General channel no later than 1 day before the meeting.
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* After the first meeting, one representative of the group will post a short summary to the group channel on MS Teams stating who attended the meeting, who apologized and who did not respond to the group and what was the outcome of the meeting - whether the group had problems with some parts of the article, whether it plans to meet again, whether they need a consultation with the instructors, etc. You do not need to report subsequent meetings, unless you need help.
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* Failure to hold the first meeting according to these rules may affect the grade of the final report.
  
Skúška je písomná v trvaní 2-3 hodiny. Obsah upresníme neskôr. Na skúšku si môžete priniest "ťahák" - 2 listy A4 popísaných čímkoľvek, čo uznáte za vhodné.
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Advice and instructions for the written report from the journal club
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* In the report, describe the main methods and results of the article in your own words
 +
* The report should be understandable for students of this course (both computer scientists and biologists), so explain the necessary terms that are not explained in the article
 +
* You do not have to cover the entire content of the article in the report and, conversely, you can use other resources
 +
* Try to express your own view of the topic, do not strictly follow the text of the article
 +
* The recommended length is about 1-2 pages per person. However, the report should form one coherent text, so agree well on the outline and division of work and spend some time at the end on combining and editing individual contributions into a coherent report.
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* The report should list the members of the group who have actively participated in its work. Students who are not on this list will receive zero points for the report.
  
==Projekt==
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==Exam==
  
* Projekt je pre magisterských a bakalárskych študentov nepovinný, pričom nahrádza skúšku. Doktorandskí študenti robia projekt povinne.
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The exam is primarily in a written form and takes 2-3 hours. The content will be specified later. You can bring a chat sheet - 2 pages of A4 paper with arbitrary content (handwritten or printed). If the exam will take place online, it will be followed by an oral exam to verify that you understand the course material tested in the written exam.
* Môže sa týkať témy vašej bakalárskej/diplomovej/dizertačnej práce, malo by však ísť o ucelený celok, na ktorom ste ešte doteraz nepracovali.
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* Projekt je možné robiť aj v skupinách, avšak náročnosť a rozsah by mali stúpať s počtom členov skupiny.
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* Projekt môže obsahovať napríklad analýzu nových dát existujúcimi programami, experimentálne porovnanie viacerých programov na reálnych alebo simulovaných dátach, modifikácie v existujúcich programoch, teoretickú analýzu modelov alebo algoritmov, programovanie nových nástrojov, alebo prehľad niekoľkých súvisiacich článkov z odbornej literatúry.
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* Navrhovanú tému projektu je potrebné mať schválenú najneskôr do konca semestra od vyučujúcich, ale čím skôr tým lepšie pre vás. Pošlite stručný popis navrhovaného projektu e-mailom a dohodnite si aj osobné stretnutie.
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* Projekt treba odovzdať písomne a príslušné súbory (dáta, program a pod.) elektronicky. Niekoľko dní po odovdzaní projektu sa koná ústna skúška, na ktorej sa diskutuje o detailoch projektu. Pri skupinových projektoch má každý člen skúšku osobitne.  
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Podrobnejšie pokyny k projektom nájdete na [[Pokyny k projektom|zvláštnej stránke]].
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==Academic integrity==
  
==Opisovanie==
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Cheating and plagiarism on homeworks and exams is a serious violation of academic integrity.
  
Opisovanie domácich úloh, projektov a opisovanie na skúškach je vážnym porušením akademickej integrity.
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On homeworks, you are '''not allowed''' to copy other person's work (eg from a classmate, from the Internet, or from scientific literature) and submit it as your own. You are also not allowed to let another person to copy your solution. We allow and encourage discussion among students about individual homework tasks. However, the solutions you submit must be your own work written in your own words. To avoid unnecessary problems, do not take notes during group discussions about homework and wait at least three hours after such a discussion before writing the solution to be submitted.
  
Opisovanie domácich úloh a projektov zahŕňa opísanie práce inej osoby (napr. od spolužiaka, z internetu, alebo z odbornej literatúry) a jej odovzdanie pod vlastným menom, umožnenie inej osobe opísať vlastné riešenia, ale aj spoluprácu pri riešení nad rámec povolený prednášajúcimi predmetu. Opisovanie na skúške zahŕňa použitie nepovolených pomôcok, ale aj nepovolenú komunikáciu s inými osobami počas skúšky.
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During exams, do not use unauthorized aids and do not communicate with persons other than the instructors.
  
V správe zo journal clubu a v projekte musíte citovať všetku použitú literatúru. Zapíšte získané poznatky vlastnými slovami. Nekopírujte z literatúry a iných zdrojov celé vety (výnimkou môžu byť len krátke priame citáty s uvedením zdroja). Obrázky pokiaľ možno vytvorte vlastné, alebo ak to nie je možné, uveďte pri prevzatých obrázkoch zdroj, z ktorého pochádzajú.
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In the report from the journal club, you must cite all used literature. Express the knowledge you have gained on the topic in your own words. Do not copy or mechanically translate entire sentences from the paper and other sources (except for short direct quotes indicating the source). Create your own images or specify the source of the downloaded images used in the report.
  
Pri zistení opisovania budeme štandardne prideľovať známku -100% za príslušnú časť práce, s minimálnym znížením výslednej známky o jeden stupeň; v prípade opisovania na skúške automatická strata termínu a zníženie výslednej známky o dva stupne. Obzvlášť hrubé porušenia akademickej integrity budú postúpené na riešenie dekanovi fakulty.
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When cheating or plagiarism is detected, we will normally assign a grade of -100% for the relevant part of the work, with a minimum reduction of the final grade by one letter. Cheating on the exam will result in the FX grade for the exam. Particularly serious violations of academic integrity will be referred to the dean of the faculty.
 
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U domácich úloh povoľujeme a podporujeme diskusiu medzi študentami o jednotlivých príkladoch. Riešenia ktoré odovzdáte, však musia byť vašou vlastnou prácou napísanou vašimi vlastnými slovami. Aby ste sa vyhli zbytočným problémom, nerobte si pri skupinových diskusiách o domácich úlohách poznámky a so spisovaním materiálu určeného na odovzdanie počkajte aspoň tri hodiny po takejto diskusii.
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Verzia zo dňa a času 11:39, 21. október 2021

Grading

  • 3 homework assignments 30% (10% each)
  • Journal club 10%
  • Quizzes 10% (each week 1%)
  • Final exam 50%

To pass the course, you need to satisfy both requirements below (otherwise Fx grade will be assigned):

  • overall at least 50% of points
  • at least 50% of points from the final exam

Final grade: A: 90+, B: 80+, C: 70+, D: 60+, E: 50+

Homeworks and exams may contain separate versions of some questions, one for computer science students (namely, BIN, INF, mINF, mAIN students) and one for biologists (more precisely, students for Faculty of Natural Sciences and physics students).

Journal club

Journal club is a group activity, where each groups studies one scientific paper and rewrites it in their own words.

  • Each student will select from the provided list the three articles that are of highest interest to him/her.
  • According to these preferences, instructors will divide the students into groups. Each group will read a different article.
  • Each student first reads the assigned article individually.
  • Then the whole group meets, discusses the article and tries to clarify any questions or to find missing information in the literature.
  • If needed, the group meets several times or continues to communicate electronically. In case of questions about the article, the whole group or some of its members can also arrange consultations with the instructors.
  • The group writes a report, in which they explain in their own words the main methods and results of the article and other necessary concepts so that the text is understandable to students of this course (both computer scientists and biologists).

Details for the journal club group meeting

  • Remember that everyone should read the article before the first meeting
  • The first meeting should take place no later than November 23. The meeting can be online or in person. Online meetings should be on MS Teams, in person meetings should be at FMFI or PriFUK. Try to choose a time suitable for all members of the group. We will create a channel for each group on MS Teams which can be used for any discussions and for the meeting itself.
  • Post the chosen time and place of the first meeting on MS Teams General channel no later than 1 day before the meeting.
  • After the first meeting, one representative of the group will post a short summary to the group channel on MS Teams stating who attended the meeting, who apologized and who did not respond to the group and what was the outcome of the meeting - whether the group had problems with some parts of the article, whether it plans to meet again, whether they need a consultation with the instructors, etc. You do not need to report subsequent meetings, unless you need help.
  • Failure to hold the first meeting according to these rules may affect the grade of the final report.

Advice and instructions for the written report from the journal club

  • In the report, describe the main methods and results of the article in your own words
  • The report should be understandable for students of this course (both computer scientists and biologists), so explain the necessary terms that are not explained in the article
  • You do not have to cover the entire content of the article in the report and, conversely, you can use other resources
  • Try to express your own view of the topic, do not strictly follow the text of the article
  • The recommended length is about 1-2 pages per person. However, the report should form one coherent text, so agree well on the outline and division of work and spend some time at the end on combining and editing individual contributions into a coherent report.
  • The report should list the members of the group who have actively participated in its work. Students who are not on this list will receive zero points for the report.

Exam

The exam is primarily in a written form and takes 2-3 hours. The content will be specified later. You can bring a chat sheet - 2 pages of A4 paper with arbitrary content (handwritten or printed). If the exam will take place online, it will be followed by an oral exam to verify that you understand the course material tested in the written exam.

Academic integrity

Cheating and plagiarism on homeworks and exams is a serious violation of academic integrity.

On homeworks, you are not allowed to copy other person's work (eg from a classmate, from the Internet, or from scientific literature) and submit it as your own. You are also not allowed to let another person to copy your solution. We allow and encourage discussion among students about individual homework tasks. However, the solutions you submit must be your own work written in your own words. To avoid unnecessary problems, do not take notes during group discussions about homework and wait at least three hours after such a discussion before writing the solution to be submitted.

During exams, do not use unauthorized aids and do not communicate with persons other than the instructors.

In the report from the journal club, you must cite all used literature. Express the knowledge you have gained on the topic in your own words. Do not copy or mechanically translate entire sentences from the paper and other sources (except for short direct quotes indicating the source). Create your own images or specify the source of the downloaded images used in the report.

When cheating or plagiarism is detected, we will normally assign a grade of -100% for the relevant part of the work, with a minimum reduction of the final grade by one letter. Cheating on the exam will result in the FX grade for the exam. Particularly serious violations of academic integrity will be referred to the dean of the faculty.