CS-E5875 - High-Throughput Bioinformatics D, 27.10.2020-14.12.2020
This course space end date is set to 14.12.2020 Search Courses: CS-E5875
Topic outline
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Exercise sessions
The weekly exercise sessions will be held on Fridays (30.10.2020 - 4.12.2020) at 14.15 - 16.00 on Zoom (the link can be found below)
There will also be an exercise helpline session on Zoom on Tuesdays at 15.00 - 16.00, starting from week 45.
During the first three weeks, we will work on exercises from different topics each week. During the last three weeks, we will work on the project, which will be divided into three parts. The project instructions will be published on week 46 at the latest.
Exercise session instructions:
-Install the latest version of Zoom (version 5.3.1 or later). We will use features that are only available in the latest version!
-Join Slack (the link can be found below).
-The exercise sessions will be organized like this:- The TAs go through the solution to last week’s exercise (exercise sessions 2-4).
- The TAs go through the current week’s exercise and give hints. Feel free to ask if there is anything unclear in the exercise.
- Everyone starts working on the exercise on their own. If you want to work in small groups or as a pair to solve the exercises, join an unoccupied breakout room where you can discuss in private.
- If you need help from the TAs, join an unoccupied breakout room (if you are not in one already). Go to Slack channel queue and write a comment in the queue thread. The comment should include your breakout room number. TAs go through the thread in the order of the comments and join your breakout room to help you. After getting help you may leave the breakout room. If you need help again, repeat the steps above.
- The exercise session ends at 16:00, after which the TAs will stop going through the help queue. If you need help after this, you can ask questions in Slack or join the exercise helpline session on Tuesdays at 15:00-16:00.
Instructions for the first three weeks
The exercise instructions of each week (during the first three weeks) is published on Thursday at the latest. You will have time till the following week’s Friday 12.00 (noon) to submit your solutions via MyCourses. The solutions to the previous week's exercise will be presented in the beginning of the exercise session. You are expected to submit a report in the PDF format (max. 5 pages) along with a separate folder containing your Jupyter notebook or R script (.ipynb or .R file format). Submitting just your notebook/R script is not enough! In the report you should explain the steps of your analysis, show the implementation when needed, include plots and results and discuss the results you obtained. You may use the notebook templates as a base for your report if you wish. The maximum number of points you can get from each exercise is 5. You will need at least 5 points from the exercises to pass the course.
We recommend that you revise the lecture slides that cover the exercise topic and read through the exercise problems before each exercise session!
Project work instructions
The project will be published on week 46 at the latest. Maximum number of points you can get from the project is 15. Please reserve enough time for working on the project! There will be some tasks that take a lot of computation time. The deadline for returning your report is 18.12.2020 by 12:00 (noon).
Jupyterhub environment
The course has a Jupyterhub environment where all the R packages and bioinformatics tools needed in the course are available. We encourage you to use Jupyterhub already starting from the first exercise in order to get used to it before the project work begins. The needed data and code templates for the project will be available through Jupyterhub. Jupyterhub can be accessed from https://jupyter.cs.aalto.fi. Please see the page https://scicomp.aalto.fi/aalto/jupyterhub/ for more information and FAQ. If you encounter problems (please check the FAQ page first!) with Jupyterhub, please contact the TAs on Slack.
Slack
The course will have a Slack environment for discussion and asking questions. The invitation link to Slack can be found below. The TAs will be following the discussion and answering your questions on weekdays. Feel free to help each other and discuss the assignments there, but sharing answers and codes between students is prohibited! Always ask your question in the appropriate channel, do not private message the TAs! If TAs need to see your code to answer your question, they can ask you to send a private message.
Plagiarism is STRICTLY PROHIBITED!
In the past, a few students have been caught uploading exercise solutions from the CS courses (including this one) to GitHub or other public repositories. Those repositories have been taken down now. Uploading exercise sessions to public repositories or sharing among students is strictly prohibited! Presenting other students’ solutions (from this year or previous years) as your own will be considered as PLAGIARISM. Aalto University has a strict code of conduct regarding plagiarism and other misconducts (such as uploading solutions to public repositories).
“Section 40 Academic consequences for violation against Code of Academic Integrity
A study attainment may be left ungraded, if the student is deemed to have violated the Code of Academic Integrity while completing it. Students violating the Code of Academic Integrity may be subject to disciplinary action on the grounds set forth in the Universities Act.”
Please read more about Aalto University’s code of conduct in the link below:
To ensure that your work is not plagiarised, we would require you to write the following sentence at the end of each report in admittance of doing no plagiarism or other misconducts:
“I hereby certify that this report and the attached documents are a product of my own work and not copied or otherwise plagiarised from the work of another student. I also certify that the solutions of this assignment have not been and will not be submitted to any public repositories.”
By copy-pasting this text to the end of each report, you are attesting to performing no misconduct. A report will not be graded without this statement as it will be understood to be plagiarised. If the claims are found to be false (i.e. you are caught plagiarising or uploading solutions to a public repository despite of certifying otherwise), appropriate disciplinary action will be taken against the student by the University authorities.