Course material for the Algorithms for sequence-based bioinformatics course (CS4255) at TU Delft
The first lecture will take place on November 12. In the first lecture we will go over some logistics, including project planning and assignment, and setting the exam appointment. Attendance during the first lecture (and all others) is highly recommended.
The exercise session scheduled for November 11 will not take place. ** The lecture of December 17 has been postponed **
For location, check this page before lecture.
| Start | Topic |
|---|---|
| Monday, 11 November 2019 8:45 | Cancelled |
| Tuesday, 12 November 2019 13:45 | Chapter 1 |
| Thursday, 14 November 2019 13:45 | Chapter 2 |
| Monday, 18 November 2019 8:45 | Exercises chapters 1 & 2 |
| Tuesday, 19 November 2019 13:45 | Chapter 3 |
| Thursday, 21 November 2019 13:45 | backup slot |
| Monday, 25 November 2019 8:45 | Exercises. ch 3 |
| Tuesday, 26 November 2019 13:45 | Chapter 5 |
| Thursday, 28 November 2019 13:45 | backup slot |
| Monday, 2 December 2019 8:45 | Exercises. ch. 5 |
| Tuesday, 3 December 2019 13:45 | Chapter 6 |
| Thursday, 5 December 2019 13:45 | backup slot |
| Monday, 9 December 2019 8:45 | Exercises. ch. 6 |
| Tuesday, 10 December 2019 13:45 | Chapter 7 |
| Thursday, 12 December 2019 13:45 | backup slot |
| Monday, 16 December 2019 8:45 | Exercises. ch. 7 |
| Tuesday, 17 December 2019 13:45 | postponed |
| Thursday, 19 December 2019 13:45 | backup slot |
| Monday, 6 January 2020 8:45 | Exercises. ch. 9 |
| Tuesday, 7 January 2020 13:45 | Chapter 9 |
| Thursday, 9 January 2020 13:45 | Chapter 10 |
| Monday, 13 January 2020 8:45 | Exercises. ch. 10 |
| Tuesday, 14 January 2020 13:45 | backup slot |
| Thursday, 16 January 2020 13:45 | backup slot |
| Friday, 17 January | Project deadline |
| Tuesday, 28 January | Exam see BrightSpace for times |
You need to bring your own laptop.
Requirements:
Desired (but not required):
In this course we will cover Chapters 1,2,3,5,6,7,9,10 from the book “Bioinformatics Algorithms - an active learning approach”. Having the related chapters at hand during the programming exercises will prove very helpful.
Corresponding slide material is available on Brightspace.
Exercises are hosted on Rosalind. You first need to enroll in the course.
After you have enrolled in the course, you can also directly access it. Each Monday you will be working on the exercises of the lectures from the previous week (Tuesday and Thursday).
You should select one research papers out of the list below to implement in your project:
Your project grade will be the 40% of your final grade. You are expected to submit your project by January 17.
You are required to submit your scripts to the shared Dropbox folder of this course. Your submission must include:
Exam grade will make up the 60% of your final grade.