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

Introduction · Rules · Tasks and dates · Materials · Moodle · Discussion
Quizzes can be found in Moodle.
Homework assignments and journal club papers can be found in Tasks and dates.
Groups for journal club have each their own channel in MS Teams.


Rules: Rozdiel medzi revíziami

Z MBI
Prejsť na: navigácia, hľadanie
(Journal club)
Riadok 1: Riadok 1:
 
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==Courses==
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* Course 1-BIN-301 is for computer-science related programs, namely BIN, INF, mINF, mAIN, DAV (shortly denoted computer science)
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* Course 2-AIN-501 is for students from Faculty of Natural Sciences and physics (shortly biology)
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==Grading==
 
==Grading==
  
Riadok 5: Riadok 10:
 
* Journal club 10%
 
* Journal club 10%
 
* Quizzes 10% (each week 1%)
 
* Quizzes 10% (each week 1%)
* Final exam 50%
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* For computer science: final exam 50%
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* For biology: project 50%
  
 
To pass the course, you need to satisfy both requirements below (otherwise Fx grade will be assigned):
 
To pass the course, you need to satisfy both requirements below (otherwise Fx grade will be assigned):
 
* overall at least 50% of points
 
* overall at least 50% of points
* at least 50% of points from the final exam
+
* at least 50% of points from the final exam / project
  
 
Final grade: A: 90+, B: 80+, C: 70+, D: 60+, E: 50+
 
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).
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Homeworks may contain separate versions of some questions, one for computer science students and one for biologists.
  
 
==Journal club==
 
==Journal club==
Riadok 43: Riadok 49:
 
==Exam==
 
==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.
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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 cheat 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.
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==Project==
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* Project topic will be chosen during the semester by November 3.
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* We recommend starting working on the project during the semester and consult any questions during tutorials for biologists.
 +
* The final report will be due during the exam period, followed by a short personal meeting with discussion of the project.
  
 
==Academic integrity==
 
==Academic integrity==
Riadok 53: Riadok 65:
 
During exams, do not use unauthorized aids and do not communicate with persons other than the instructors.
 
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.
+
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. Similarly for project reports.
  
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.
+
When cheating or plagiarism is detected, we will normally assign a grade of 0 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.

Verzia zo dňa a času 10:02, 21. september 2022


Courses

  • Course 1-BIN-301 is for computer-science related programs, namely BIN, INF, mINF, mAIN, DAV (shortly denoted computer science)
  • Course 2-AIN-501 is for students from Faculty of Natural Sciences and physics (shortly biology)

Grading

  • 3 homework assignments 30% (10% each)
  • Journal club 10%
  • Quizzes 10% (each week 1%)
  • For computer science: final exam 50%
  • For biology: project 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 / project

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

Homeworks may contain separate versions of some questions, one for computer science students and one for biologists.

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 cheat 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.

Project

  • Project topic will be chosen during the semester by November 3.
  • We recommend starting working on the project during the semester and consult any questions during tutorials for biologists.
  • The final report will be due during the exam period, followed by a short personal meeting with discussion of the project.

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. Similarly for project reports.

When cheating or plagiarism is detected, we will normally assign a grade of 0 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.