Alignment-free Sequence Analysis with Python

Dear all,

the missing files from the last lecture have been uploaded.

Please remember your projects. The deadline can be moved if needed. In principle, I need to review the work in a timely manner so we can conduct exams before the 30.09. in principle (end of semester). However, it can also be moved into October, but must be finished before the start of the new lecture period. So I'm asking you to send me your project work as soon as it is finished, but in one month (15.09.) at the latest. Exam dates will be made on an individual basis. The exam will discuss the project (for a few minutes) but then ask about the theory (hashes, filters, some Python).

Hello,

I have completed the project assignment based on your preferences. Please read it in the description of the project slides in the Materials section. Please let me know if something is wrong. Next week, I will add slides about possible data to work on. I would like have short individual meetings about each project to discuss specifics.

Hello,

I have finally uploaded some project proposals. Please find them in the Materials section and have a look. Please send me your preferred project (rahmann@cs) within one week (till Monday, June 19, 23:59). If you have a different idea, you can also do something else (within the general context of the lecture). In that case, please write a short sketch of your idea, also till Monday evening.

Furthermore, the slide sets have been updated, including a preview of the next lecture (on 23.06.)

Hello everyone,

hope you are enjoying a long weekend with tomorrow's holiday. In the meantime, we have updated the slides on Bloom filters and uploaded the slides on XOR filters, which you can find in the Materials section.

Please remember to complete the practice assignment on computing the FPR of blocked Bloom filters by Friday 02.06. Everything you need (formulas) are on the Bloom filter slides; you just have to put it together and run it for some values of h and c.

To clarify a question that came up: These assignments are, in a sense, optional, i.e. there is no punishment for not doing them. The requirement for passing the course is doing a project (to be discussed on Friday 02.06.) and then passing an exam on the course material and your project. However!, doing these assignments will help your understanding of the material (I hope) and give you some more programming practice before things get busy.

Friday 02.06. is also the day of the next lecture, where we complete the XOR filters (I had planned on completing them last time) and then talk about hashing more generally, e.g., what are good and simple hash functions; what are good collision resolution strategies? I will present project ideas, and you are also welcome to propose your own ideas.

After that lecture there will be a longer break and the following lecture will be on 23.06. During this time between lectures, you should start project work.

Good afternoon,

the slides of today's lecture (and some more) are now online, as well as assignment 3 which asks you to visualize the false positive rate of standard vs. blocked Bloom filters. It is due in 2 weeks (on 02.06.).

As for the updated schedule, the plan is to move ahead with the posted schedule on the main page (except that the 12.05. was moved to 19.05.). This means, the next lecture will already be next week (26.05.) and then one more the week after (02.06.). We will continue a bit on Bloom filters (especially their use as k-mer filters!), and then move to hashing, so we can implement key-value stores for k-mers and associated information.

Good morning,

unfortunately, due to personal reasons, I have to cancel the lecture today. It will be moved to next week. I am really sorry for the inconvenience. The topic is "Bloom Filters", an important basic data structure, with many variations that make it work much better in practice.

An updated schedule will be posted later today.

Sven Rahmann

Hello everyone,

after today's lecture, you are well prepared for a first practice assignment: to write your intbitarray.py implementation, which will allow you to create an array of integers of any bit-width 1 <= w <= 64, without wasting any bits.

Please carefully review the bitarray lecture before you start with the assignment. It is due in 2 weeks from today.

Happy coding!

Good morning,

Wednesday is our tutorial day; the E2.1 Computer Pool has been reserved for this course from 14 - 18.

However, due to another start-of-semester-kickoff meeting, the tutorial will start 15:00 today!

As you currently do not have a project assignment, we will use this week to make sure everyone has a good setup, mainly: shell, conda, git. Please make sure you do the setup this week, as we cannot repeat the same instructions every week after.

 

Hello,

in our first lecture, we discussed that the focus of the course is on project work using jit-compiled Python for implementing an alignment-free sequence analysis project. I presented a simple example how compilation speeds up Python code, and in particular explained the advantages of late compilation. The example can be found in the Materials section (after registration), together with the slide set.

There are no video recordings of this lecture.