Rules

Grading

• Homeworks: 45%
• Project proposal: 5%
• Project: 40%
• Oral exam: 10%

Grades:

• A: 90 and more, B: 80...89, C: 70...79, D: 60...69, E: 50...59, FX: less than 50%

You will get Fx if your oral exam is not satisfactory, even if you have sufficient points from other activities.

Course format

• Every Thursday three-hour class, we start with a short lecture. Then you start solving assigned tasks, which you complete as a homework assignment.
• We highly recommend doing the homework during class, as we can help you as needed. We really encourage you to ask questions during this time. At other times, ask your questions via email, but you may have to wait longer for the answer.
• If you attend the whole 3-hour class, you are allowed to work on the homework in a pair with one of your classmates. You can then also finish the homework together after the class and submit just one homework listing both your names.
  • During work, occasionally exchange roles (driver who is typing the program or commands and navigator who is advising the driver). Both students should completely understand all parts of the submitted homework.
  • If you do not attend the class (or only a part of it), you have to do the homework individually.
• Some weeks will have a separate material for Bioinformatics program and separately for others. If you would like to do a homework other than the one intended for you, you must obtain a prior consent of the instructors.
• You will submit a project during the exam period. Afterwards there will be an oral exam concentrating on the project and submitted homework.
• You will have an account on a Linux server dedicated to this course. Use this account only for the purposes of this course and try not to overload the server so that it serves all students. Any attempts to disrupt the operation of the server will be considered a serious violation of the course rules.

Homework

• The deadline for each homework is 9:00 of the day of the next lecture, i.e. usually almost one week from when the homework was published.
• You can work on your homework on any computer, preferably under Linux. However, the submitted code or commands should be executable on the course server, so do not use special software or settings on your computer.
• The homework is submitted by copying the required files to the required directory on the server. Details will be specified in the assignment.
• Follow any filenames specified in the assignment and use reasonable filenames for additional files.
• Make sure the submitted source code is easy to read (indentation, reasonable variable names, comments as needed)

Protocols

• Usually, a document called a protocol will be a required part of the homework.
• Write the protocol in txt format and name the file protocol.txt (copy it to the upload directory)
• The protocol can be in Slovak or English.
• If you write with diacritics, use UTF8 encoding, but feel free to omit diacritics in protocols.
• In most homeworks, you get a protocol outline, follow it and do not change our headings.

Self-assessment

• At the top of the protocol, fill in the names of the authors of the homework. This is very important if you work in a pair.
• Below fill in a self-assessment which for every task should contain one of the following codes.
  • Use code DONE if you think the task is completely and correctly solved.
  • Use code PART if you have completed only a part of the task. After the code briefly state, which part was completed and potentially if you had problem with something.
  • Use code UNSURE, if you have completed the task but are not sure about something. Again briefly explain what are you unsure of.
  • Use code NOTHING, if you have not even started to do the task.
• Your self-assessment will guide us in grading. Tasks marked as DONE will be checked briefly, but we will try to give you feedback to tasks marked UNSURE or PART, particularly if you note down what was causing you problems.
• Try to fill in self-assessment the best you can. It can influence your grade.

Protocol contents

• Unless specified otherwise, the protocol should contain the following information:
  • List of submitted files: usually already filled in, add any other files you submit with a brief explanation of their meaning.
  • The sequence of commands used, or other steps you took to get the results. Include commands to process data and run your or other programs. It is not necessary to specify commands related to the programming itself (starting the editor, setting file permissions), copying the files to the server, etc. For more complex commands, also provide brief comments explaining the purpose of a particular command or group of commands.
  • Observations the results required by the tasks and any discussion of these results.
  • Resources: websites and other sources that you used to solve the task. You do not have to list the course website and resources recommended directly in the assignment.

Overall, the protocol should allow the reader to understand your files and also, in case of interest, to perform the same calculations as you used to obtain the result. You do not have write to a formal text, only clear and brief notes.

Project

The aim of the project is to extend your skills on a data processing project. Your task is to obtain data, analyze this data with some techniques from the lectures and display the results in graphs and tables.

• In about two thirds of the semester, you will submit a short project proposal
• A deadline for submitting the project (including the written report) will be during the exam period
• You can also do projects in pairs, but then we require a larger project and each member should be primarily responsible for a certain part of the project

More detailed information on projects is on a separate page.

Oral exam

• During the oral exam, we will give you our feedback to your project and ask related questions.
• We can also ask you about some of the homeworks you have submitted during the semester.
• You should be able to explain your code and do small modifications in it.

Details:

• Before the exam we will publish preliminary time schedule.
• Please come to the computer room where the exam takes place at the indicated time, start one of the computers and open your project in a form in which you can modify it. You may also use your computer if you prefer.
• One of us will talk with you and assign you a small task related to your project or homeworks.
• You will have time to work on this task. You may use course website and internet resources, such as documentation and existing discussions. You may not communicate with other people or use AI tools during the oral exam.
• Please leave any resources you used open in the browser.

Academic integrity

• You are allowed to talk to classmates and other people about homework and projects and general strategies to solve them. However, the code, the results obtained, and the text you submit must be your own work. It is forbidden to show your code or texts to the classmates.

• When working on the homework and the project, we expect you to use Internet resources, especially various manuals and discussion forums on the used technologies. However, do not try to find ready-made solutions to the given tasks. List all resources used in a homework or a project.

• Do not use AI chatbots or AI code generation in your editor (such as Github copilot and similar) for solving homeworks (you do not learn anything that way!). Some use of AI code generation is permitted on the final projects, see project rules.

• If we find cases of plagiarism or unauthorized aids, all participating students will receive zero points for the relevant homework or project (including the students who provided their solutions to others to copy). Violations of academic integrity will be also referred to the faculty disciplinary committee.

Sharing materials

Assignments and materials for the course are freely available on this webpage. However, do not publish or otherwise share your homework solutions as they closely follow the outline given by us. You can publish your projects if you wish, as long as it does not conflict with your agreement with the provider of your data.