Course syllabus

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Welcome to the MVE510 - Introduction to bioinformatics. This is the course home page and contains all the information you need to participate and complete the course.

 

Instructions and rules for the Easter re-exam on Wednesday April 8, 14.00-18.00 (the second bullet point updated 09.47 2020-04-03)

In order to take the exam, you must:

  • Be registered for the exam
  • During the entire examination period be connected to the Zoom meeting https://chalmers.zoom.us/j/4193728773 with the video turned on with you in the picture. You must have your real name stated in the meeting so that the examiner sees this. You should have the microphone turned on at the Zoom meeting and the sound muted unless asked to turn it on. The zoom meeting will be recorded to check the conduct of the student during the exam if necessary. The recording is deleted when the results are reported in Ladok. You can connect from computer or phone. For technical problems, contact the examiner by telephone.
  • Have an id next to you during the entire exam period, which is displayed at the start of the exam, during the exam, and scanned together with the solutions. To check identity etc. you will be moved to a "breakout room" in Zoom so you only need to show this to the exam guard.

All aids are allowed, but it is absolutely forbidden to communicate with anyone else during the exam period except the examiner and the guard. Therefore, it is prohibited to:

  • use all kinds of headphones or earphones
  • communicate orally or in writing with persons other than the examiner and the guard
  • be in a room with more than one person present, or in a room adjacent to another person's room unless the door between these rooms is closed. If this is not possible due to quarantine or other circumstances, you must notify the examiner in advance what other people will be present. Under no circumstances are more than one person taking an exam allowed to have direct contact with each other.

Upon submission of the exam, you will certify in writing that you have followed these rules. Any suspicion of violating any of these rules will be reported.

Procedures for the exam

  • The Zoom meeting will be open at least 15 minutes before the exam starts so you can join in time.
  • The exam questions are published on Canvas at the start of the exam.
  • You will be invited to a breakout room in Zoom for identity verification, etc. at the start of the exam and on one or a few occasions during the exam. You will then be asked to put on your speaker and / or to share your screen and to show one of your ongoing solutions.
  • If you have questions for the examiner or exam guard during the exam, you can write this in the chat in Zoom by choosing to write only to him.
  • If you need to go to the toilet, do so quickly and notify the exam guard when you go and when you come back through a direct message in the chat in Zoom.
  • The exam time is 4 hours (4 * 3/2 hours for those who are entitled to extended time).
  • At the end of the exam, start scanning your solutions immediately. It is not allowed to continue working with the solutions after the end of time. You have a maximum of 30 minutes to scan and submit the solutions. Delayed submission will only be approved if it is due to technical problems, e.g. the pressure on Canvas will be intense so you may have to try more than once to upload. If you are using the phone for scanning, use a document scanning app (free apps that can be used are CamScanner and Genius skanning / Genius scan available for both Android and iOS). The solutions must be submitted as a single pdf file. Test the app you intend to use before the exam so you know how to scan a number of sheets into a single PDF file. As a "cover page" to the solutions, you should scan your credentials together with a declaration that you have followed the rules of not communicating with anyone during the exam period.
  • The exam is submitted via an "Assignment" in Canvas.
  • After submitting the solutions in Canvas, you should remain in Zoom until the examiner announces that the exam is over. You may be asked to individually answer simple questions about some of your solutions. If you choose to submit your solutions before the end of time, you must notify the exam guard so that you can answer any control questions directly and then leave Zoom.

Before the exam, you who will be taking the exam should to avoid extra stress as far as possible:

  • Familiarize yourself with Zoom and make sure you understand how the program works so that you can follow the rules above.
  • If you plan to use the phone to scan the solutions, download a document scanning app and familiarize yourself with it so you know how to scan a number of sheets into a single pdf file.
  • Prepare a cover page that says "I assure that I did the exam on my own without getting help from any other person and that I formulated all the solutions myself" along with a signature. Leave space where you can place your id when scanning this cover page as part of your solutions.

 

Teachers

Erik Kristiansson, examiner, course administrator, lecturer

Juan Salvador Inda Diaz, computer exercise assistant

David Lund, computer exercise assistant

 

Student representatives

Adrià Amell Tosas (MPENM)
Drilon Haxhijaj (MPBIO) 
Erik Johansson (MPENM)
Moa Lord (MPBIO)
Yili Padilla Flores (MPBIO)

 

Course aims, plan and schedule

Syllabus with course aim

Course schedule

Course plan (updated 2019-12-04)

 

Course material

Please refer to the course plan for lecture-by-lecture reading instructions.

Lecture notes

Papers 

The following scientific papers are a part of the literature of this course. 

Extra exercises

Optional course book

Xinkun Wang, Next-Generation Sequencing Data Analysis, CRC Press, ISBN 9781482217889. A few copies are available at Cremona. The course covers chapters 2-5, 7-9, and 13. 

 

Computer exercises

The course contains four compulsory computer exercises. Computer exercise 1 is examined at the scheduled exercise. Computer exercise 2, 3 and 4 should be handed in as written reports. The computer exercises should be made in groups of maximum two persons.

 

 

Guidelines for writing and submitting reports

The reports submitted as a group (of maximum two persons) through the Canvas course page. The report should be either in PDF or WORD-format. All of the code necessary should be included in the end of the report as an Appendix. Please double check that the sumibbted code works as intended. Don't forget to add the names and Swedish social security number for all persons in the group at the front page. You only need to submit one report per group.

The reports should contain answers to all the questions posed in the exercise sheet. The answers should almost always have some motivation, meaning that even though the question could be answered with a yes or a no, we require a motivation why. Example question: "Do you see any differences?" Describe the observed differences (if the answer is yes), and not only a yes or a no. When you have been asked to generate a figure, this figure should be included in the report. The reports do not need an introduction, method, results, or discussion section, but should include some information about what has been done. Example: “When doing the quality assessment using fastqc, we saw that…”.

Good luck!

 

Exam

  • 16 January 2020

Previous exams

 

Examination
This  course is examined based on,

  • Written exam: 08:30 on January 16, 2020. This gives you 5 hp and determines your grade in the course.
  • Four compulsory computer exercises. When you have passed all four of them you earn 2.5 hp. Computer exercise 1 is examined at the scheduled exercises. Computer exercise 2, 3 and 4 require a lab report, specified in these guidelines. After the first submission, the report can either pass or require revision to correct for errors and misinterpretations.

 

Course summary:

Date Details Due