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

Introduction · Rules · Tasks and dates · Materials · Moodle · Discussion
Exam rules, example questions and syllabus
Groups for journal club have each their own channel in MS Teams.


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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 60%
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* Quizzes 10% (each week 1%)
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* Final exam 50%
  
Na úspešné absolvovanie predmetu je potrebné splniť dve podmienky:
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To pass the course, you need to satisfy both requirements below (otherwise Fx grade will be assigned):
* celkovo aspoň 50% bodov
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* overall at least 50% of points
* aspoň polovicu bodov zo skúšky
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* at least 50% of points from the final exam
  
Hodnotenie: A: 90+, B: 80+, C: 70+, D: 60+, E: 50+
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Final grade: A: 90+, B: 80+, C: 70+, D: 60+, E: 50+
  
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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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.
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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.
* V prípade potreby sa skupina stretne aj viackrát, alebo ďalej komunikuje elektronicky. V prípade otázok k článku si môžete celá skupina alebo jej niektorí členovia dohodnúť aj konzultácie s vyučujúcimi.  
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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.
* Skupinka spíše správu, v ktorej vlastnými slovami vysvetlí hlavné metódy a výsledky článku a ďalšie potrebné pojmy tak, aby bol text zrozumiteľný pre študentov tohto predmetu (informatikov aj biológov).
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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).
  
Podrobnosti k stretnutiu skupiny pre journal club
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Details for the journal club group meeting
* Nezabudnite, že pred prvým stretnutím má mať každý už prečítaný článok
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* Remember that everyone should read the article before the first meeting
* Prvé stretnutie by sa malo konať najneskôr 24.11. a miesto stretnutia by malo byť na FMFI prípadne na PriFUK. Pokúste sa vybrať čas vhodný pre všetkých členov skupiny, pričom na dohadovanie času odporúčame použiť napr. službu doodle.com alebo diskusiu na Facebookovej skupine predmetu.
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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.
* Zvolený čas a miesto prvého stretnutia zverejnite na Facebookovej skupine predmetu najneskôr 2 dni pred stretnutím.  
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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.
* Po prvom stretnutí zástupca skupiny pošle krátku správu B.Brejovej, v ktorej uvedie, kto sa stretnutia zúčastnil, kto sa ospravedlnil a kto sa prípadne skupine neozval a aký bol záver stretnutia - či má skupina problémy s niektorými časťami článku, či sa plánuje stretnúť znovu, či potrebuje konzultáciu s vyučujúcimi a pod.
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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.  
* Ak sa stretnutie neuskutoční podľa týchto pravidiel, môže to ovplyvniť známku zo záverečnej správy.
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* Failure to hold the first meeting according to these rules may affect the grade of the final report.
  
Rady a pokyny k správe zo journal clubu
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Advice and instructions for the written report from the journal club
* V správe vlastnými slovami opíšte hlavné metódy a výsledky článku
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* In the report, describe the main methods and results of the article in your own words
* Správa by mala byť pochopiteľná pre študentov tohto predmetu (informatikov aj biológov), vysvetlite preto aj potrebné pojmy, ktoré v článku vysvetlené nie sú
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* 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
* V správe nemusíte pokryť celý obsah článku a naopak, môžete využiť aj iné zdroje
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* You do not have to cover the entire content of the article in the report and, conversely, you can use other resources
* Skúste do textu vložiť vlastný pohľad na tému
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* Try to express your own view of the topic, do not strictly follow the text of the article
* Odporúčaný rozsah je cca 1-2 strany na osobu. Správa by však mala tvoriť jeden ucelený text, preto si dobre dohodnite, kto o čom a ako bude písať a nechajte si čas na úpravy celkového textu.
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* 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.
* 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 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.
  
==Skúška==
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==Exam==
  
Skúška je písomná v trvaní 2-3 hodiny. Obsah upresníme neskôr. Na skúšku si môžete priniesť "ťahák" - 2 listy A4 popísaných čímkoľvek, čo uznáte za vhodné.
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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.
  
==Opisovanie==
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==Academic integrity==
  
Opisovanie domácich úloh a opisovanie na skúškach je vážnym porušením akademickej integrity.
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Cheating and plagiarism on homeworks and exams is a serious violation of academic integrity.  
  
Opisovanie domácich úloh 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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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.
  
V správe zo journal clubu 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 vytvorte vlastné alebo pri prevzatých obrázkoch uveďte zdroj, z ktorého pochádzajú.
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During exams, do not use unauthorized aids and do not communicate with persons other than the instructors.
  
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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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.
  
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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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.

Aktuálna revízia z 12:39, 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.