This is the main course page for Introduction to Bioinformatics (KB7004).
The course is taught by lectures, bioinformatics labs, programming exercises, an oral presentation and discussions.
Here follows some practical instructions:
Lectures
All lectures by Arne Elofsson are pre-recorded and available online. Also, for many topics there might exist more pedagogic lectures online. For these lectures it is recommended that the students tches the videos as well as read the material in advance. Some part of the assigned time for the lecture will then be used to discuss and explain the content in more depth.
Additional slides (and in some case videos) from other lectures will be put in the website after some lectures.
Requirements
Presence on exams and presentations (see below) is mandatory.
To pass the course you need to be pass the following moments:
- A written exam showing your understanding of bioinformatics tools.
- A number of bioinformatics labs performed individually
- A number of programming exercise performed individually
- One presentation of a scientific article, performed together with another student.
Book and reading instructions
Arne Elofsson’s lectures are primarily based on freely available material see links for each lecture in the schedule.
Samuel Flores’s lectures make heavy use of the book: “Understanding bioinformatics” by Zvelebil and Baum, ISBN: 9780815340249 .
The book can be bought from many online resellers and is normally delivered within a day or two.
For a review of protein and nucleic acid structure we also recommend Liljas et al, Textbook of Structural Biology, ISBN: 978-981-277-208-4 .. a couple of very useful chapters are available online for free from World Scientific.
Programming tutorials
Online tutorials for programming in python is available online.
We do really recommend the book “Practical computing for Biologists” by Haddock and Dunn, ISBN: 978-0878933914
Examination
To pass the course you need to pass the exam, pass all labs and make a presentation of a paper. The grades will be based 100% on the written exam as long as the labs are passed in time. However, if you have not passed the assignments in time the highest grade you can achieve is an E, see below. To pass the course you need to have at least 50% in total and all labs need to be passed.
Presentation
At the first discussion you will be assigned a partner and a scientific paper for the two of you. You should read and understand the paper. This paper should then be presented at the oral-presentation towards the end of the course to. You need to be present at all presentations. If you fail to be present you need to write a 1000 word summary of your paper.
General information
Reporting
All reporting are made through email to the email address present on the lab webpage. The answers should be submitted as a PDF attachment.
If your answers are satisfactory, you will receive a mail in return saying that you passed the practical in question, otherwise you will receive a mail stating which answers require more work. You need then to resubmit your report, clearly indicating the corrections you made to those questions.
Originality
You may work together in small groups, but every student must write his/her own report. You may not copy each other’s reports. To do so, or to make a copy, then change a few words, will be considered cheating. The purpose of the course is to ensure that, after having gone through it, every student will possess the necessary skills to work independently with these tools in later courses.
Please note that all lab reports are checked for plagiarism, so you cannot copy text from anywhere. Failing these tests might result in disciplinary punishments.
In order to help you with that you should go through the tutorial that you find using the following link:
http://www.ub.gu.se/skriva/plagiering/
It contains information on plagiarism and how to avoid it. If you have questions please contact your teacher.
Deadlines
The lab reports are a training to write scientific texts and an important part of the course. To pass you need to provide a final version of the lab report within 7 days after the lab. You have one chance to submit a preliminary version and receive feedback on it (not mandatory). The preliminary version needs to be submitted within 72 hours of the lab and feedback will be provided at the latest 24 hours before the deadline of the assignment. If the final report it not submitted in time or it contains an error you will get an Fx on the lab course. This means that you have to submit an updated lab report within 7 days after the exam and that the highest grade you can get is an E on the entire course. If this does not occur you will have to re-register for the course next time it is given (normally next year) and complete the missing parts that year and you can still not receive a grade higher than E. So in short this is the rules for the lab reports.
- 0-0 Lab
- 0-3 days after the lab – Preliminary version
- 3-6 days after the lab – Feedback
- 7 days after the lab – Final version
The lab report must be complete upon submission, i.e. you have to provide an answer to each question. The assistant has the right to return / not approve the submission if it is not complete. Linguistic accuracy is a must.
Returns should get back to s within a week after you have received it. The submission of returns must be a version where all comments appear. All comments should be considered carefully or else it does not count as a return. A maximum of 1 return is allowed. The second return means that you have to re-register for the course next time it is given (normally next year) and complete the lab then.
Complete reports in time for all bioinformatics and programming labs are compulsory.
Grading
The timing of the practical reports will be used in grading, as follows: To pass you need to provide a final version of the lab report within 7 days after the lab. You have a chance but it is not mandatory to submit a preliminary version and receive feedback on it. The preliminary version needs to be submitted within 72 hours of the lab and feedback will be provided at the latest 24 hours before the deadline of the assignment. If the final report it not submitted in time or it contains an error you will get an Fx on the lab course. This means that you have to submit an updated lab report within 7 days after the exam and that you will receive an E on the entire course. If this does not occur you will have to re-register for the course next time it is given (normally next year) and complete the missing parts that year and you can still not receive a grade higher than E.
Paper presentations
In addition to the practicals, the course involves the completion of a paper presentation.
Old exams
Two examples of questions from old exams can be found here (click download):
Contact
by email.
Email list: kb7004-vt2017@googlegroups.com
Schedule