Statistics, Probability and Applications in Bioinformatics

Are you interested in a scientific career as a woman in bioinformatics? You have questions and worries regarding how to get there?

The online lecture series "Women in Bioinformatics" provides the answers. Successful female scientists present their research, their career path and answer your questions.

Registration is now open for the talk by Prof. Dr. Alice McHardy on 10.05.22, 14:30-16:00 (CEST). Prof. Dr. McHardy holds a diploma in biochemistry and a doctoral degree in bioinformatics, both from Bielefeld University in Germany. From 2005 to 2007 she first was a postdoc and then a permanent staff member in the Bioinformatics and Pattern Discovery Group at the IBM T.J. Watson Research Center in Yorktown Heights, USA. She then became the head of the independent research group for Computational Genomics and Epidemiology at the Max Planck Institute for Computer Science in Saarbrücken. In 2010, she was appointed Chair of Algorithmic Bioinformatics at Heinrich Heine University in Düsseldorf. In 2014, she became head of the Department of Computational Biology of Infection Research at the Helmholtz Centre for Infection Research in Braunschweig and was appointed as a full professor at TU Braunschweig.

Registration is also still possible for the next talk by Prof. Dr. Olga Kalinina on 22.03.22, 16:30-18:00 (CET). Prof. Dr. Kalinina is professor for Drug Bioinformatics at the Helmholtz Institute for Pharmaceutical Research Saarland (HIPS). She received a M.Sc. degree with distinction in mathematics from the Moscow State University in 2003 and a Ph.D. from the Engelhardt Institute for Molecular Biology of the Russian Academy of Sciences in 2007. She continued her research in bioinformatics as a postdoctoral fellow at the European Laboratory for Molecular Biology, for which she was awarded an EMBO Long Term Fellowship from the European Molecular Biology Organization, and later at the University of Heidelberg, working with Prof. Dr. Robert B. Russell (2007-2011). In 2012, she established her independent junior group at the Max Planck Institute for Informatics in the Department for Computational Biology and Applied Algorithmics lead by Prof. Dr. Dr. Thomas Lengauer, where she was researching resistance mechanisms in human viruses until 2018.

Participation is free but registration is required for every talk. Details can be found at: https://www.bio.ifi.lmu.de/women-in-bioinformatics. Please note that the time of the lecture may vary.

For further updates on upcoming talks please register for our Newsletter (https://lists.lrz.de/mailman/listinfo/wbioinformatics) or follow us on Twitter (https://twitter.com/WBioinformatics).

Note: This lecture series is open to women only!

Update on the SPAB re-exam

The re-exam will be on March 28 + 29 (Mon/Tue).
A poll for time slots is now open. The link is available for registered participants of the course in the Materials section.
Note that we will check your qualification and will remove you if you have not qualified to take the exam.

Official registration in LSF will be opened next week.

Please make sure you do both: get a time slot and register in LSF if you want to participate in the re-exam.

Have a nice vacation if you can under the current circumstances

Sven

As announced in the last lecture, I will be answering your questions today from 14:00 - 15:00 or as long as there are questions. This is to answer questions that require discussion and cannot be easily asked on the forum. (In general, the forum is preferable, so everyone gets to read questions and answers.) If you want to ask something today, please use the normal lecture link at 14:00. That's in 1 hour.

Dear all,

many of you have registered for the exam in the LSF. Great. If you haven't, the exam number is 10159.

Please don't forget to also ask me for a time slot on either Thursday (preferred) or on Friday (almost booked out) if you have not done so.
(If you have asked and did not get a reply, your email probably got lost, so please write again!).

If at all possible, please take a spot on Thursday the 17th.

The exam will be done on zoom by default.
If for any reason you prefer an exam on campus (e.g. unreliable internet connection, etc), please let me know. It can be arranged under some conditions.
If you cannot be in Saarbrücken, obviously zoom is the only option.
A link will be sent out early next week to those who are registered.

 

Note: These talks are specially for women in bioinformatics. Male students cannot register!

Are you interested in a scientific career as a woman in bioinformatics? You have questions and worries regarding how to get there?

The online lecture series "Women in Bioinformatics" provides the answers. Successful female scientists present their research, their career path and answer your questions.

Registration is now open for the talk by Prof. Dr. Olga Kalinina on 22.03.22, 16:30-18:00. Prof. Dr. Kalinina is professor for Drug Bioinformatics at the Helmholtz Institute for Pharmaceutical Research Saarland (HIPS). She received a M.Sc. degree with distinction in mathematics from the Moscow State University in 2003 and a Ph.D. from the Engelhardt Institute for Molecular Biology of the Russian Academy of Sciences in 2007. She continued her research in bioinformatics as a postdoctoral fellow at the European Laboratory for Molecular Biology, for which she was awarded an EMBO Long Term Fellowship from the European Molecular Biology Organization, and later at the University of Heidelberg, working with Prof. Dr. Robert B. Russell (2007-2011). In 2012, she established her independent junior group at the Max Planck Institute for Informatics in the Department for Computational Biology and Applied Algorithmics lead by Prof. Dr. Dr. Thomas Lengauer, where she was researching resistance mechanisms in human viruses until 2018.

Registration is also still possible for the next talk by Prof. Dr. Caroline Friedel on 15.02.22, 16:30-18:00. Prof. Friedel is professor for Bioinformatics at the Institute of Informatics at the Ludwig-Maximilians-Universität München. Her research focus is on development of analysis methods for large-scale sequencing data, integrated multi-omics data analysis and virus-host transcriptomics with a particular focus on DNA viruses.

Participation is free but registration is required for every talk. Details can be found at: https://www.bio.ifi.lmu.de/women-in-bioinformatics. Please note that the time of the lecture may vary.

For further updates on upcoming talks please register for our Newsletter (https://lists.lrz.de/mailman/listinfo/wbioinformatics) or follow us on Twitter (https://twitter.com/WBioinformatics).
 

-- 
Prof. Dr. Caroline Friedel
Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 4. Stock, Büro 402
80333 München
E-Mail: Caroline.Friedel@bio.ifi.lmu.de

We have just added evaluation links to the Materials section.

Please evaluate the course until 03-Feb-2022, and please do so separately for the lecture and the tutorial (there are two separate links!).

Some of you also asked how many exercise sheets there will be, and the answer is 13.
This week we will publish sheet #12, and next week there will be a last exercise sheet #13.

We hope that this information helps you with planning.

Dear all, the first set of exam dates (oral exam, ~30 minutes) has now been determined: Feb 17+18.
You can already register in the LSF for these dates, but note that your registration is invalid if you do not qualify in the end.
(Remember: To qualify, you need >= 50% of theory points AND >= 50% of programming points.)
You can un-register from the exam till one week before the exam date (Feb 11). After that, if you do not take the exam, it will count as failed.

A second set of exam dates will be shortly before the start of the summer semester (dates to be determined; you can offer proposals).

Also, PDFs and videos of recent lectures, as well as assignment 10 (due in one week) are now online.

 

Dear all, the deadline for assignment 8 has been extended till Sunday evening, in case you don't want to go on holidays any time soon.

By all means, if you are ready, submit tonight. But if you need more time, feel free to extend your work over the weekend.

If questions arise, please use the forum instead of personal emails.

Thank you and have a nice break!

Dear all,

we have so far covered discrete probability theory and important computational aspects.

We still need to go on a bit with theory (until the holidays perhaps) and learn some basics of statistics, in particular foundations of test theory and estimation theory. To do this properly, we need to use continuous distributions (in addition to discrete ones).

So the plan for next week is continuous distributions and introduction to testing (which I already somewhat did today). We will use differential gene expression analysis and differential methylation analysis as typical examples from "omics" to highlight the challenges. After the holidays, we will look into even more applications, and at the same time introduce more powerful models and procedures.

I hope that this gives you some orientation.

Slides for this week (Lectures 13 and 14, one common PDF) and videos are online, as well as the new assignment sheet from today, due in one week on December 9. This one is more programming-heavy, but not too difficult. Keep up the good work!

If you would like to expand your experience in coding, you can do the "advent of code" challenges. Every day in December (1 to 25), you receive a two-part problem embedded in a story. Given some (individualized) input file, you have to compute a solution of the problem. It starts out quite simple, and the first few problems can always be solved with a few lines of code. Later, it becomes more and more challenging. The first part of the problem on any day is usually simpler than the second part, which is only unlocked after you have solved the first part.

Best of all: it's free (but you can make a donation to the maintainer/inventor if you want to, or buy merchandise).

The website is her: https://adventofcode.com/2021

Note: The coding challenges are typically not related to this course (i.e., there are almost never any probability-related tasks), but it is good coding experience in general!

Have fun!

Dear all,

unfortunately, due to illness, today's online tutorial could not take part. Jens will discuss the past solutions next time.

Given the changes in university regulations, we are thinking about going fully online, i.e., also holding the Thursday tutorial online. On the other hand, the exchange works much better in an on-campus tutorial. Therefore:

all of you who are currently visiting the on-campus tutorial, please inform myself or Jens Zentgraf (ideally both of us) if you would like to continue on-campus. If nobody wants to come to the on-campus tutorial, it will become an online tutorial from this week on!

Thank you!

As I am travelling this Thursday, there is only a (short) pre-recorded lecture. I re-explain càdlàg functions and show again how to to logarithmic addition, with an example. Then I showcase the PCR app (runs with streamlit locally in your browser), which turned out to still have some bugs. In the downloadable code, these bugs are fixed, so you can now play with it and, if you like, work on the bonus task of Assignment 06 (due December 2), which is also now online.

Dear all,

we had an error in assignment 5 task 1: The entries of the random matrix were given as +1 or -1, but they should be + or - 1 / sqrt(d).  The sheet has been updated last Friday. But if you solved the problem with the original formulation (+-1), this is also fine. You can simply re-scale the solution accordingly.

To give you some background, this type of "random projection" is important in practice. By multiplying with a random matrix of a well-chosen type (such as in this task), you can project points from n-dimensional space into d-dimensional space (where d is much smaller than n) and approximately keep lengths and distances unchanged (in expectation).

Dear all,

with sick kids, I will not be able to come to the university today (Thursday Nov 18) to give the lecture live. I have therefore recorded it now, so it is available for viewing in the cloud (see Materials, Lecture 10 Video). I will extend the lecture later by a presentation of a small app to investigate the PCR distribution.

Next Monday, we will start a new topic (on "numerical probability"). Next Thursday, there will be no lecture because Lecture 10 got quite long, and there will be the additional app video (which you could watch next Thursday during the lecture time).

Some not so good news: With increasing numbers of infections, the 3G policy will be more heavily enforced. on campus with an increased number of random and non-random checks of vaccination status. You need your "3G proof" at all times on campus or you may get in trouble. Please remember that, especially if you come to an on-campus tutorial. Stay healthy by solving probability paradoxes!

This week, we finished discussing discrete probability distributions and introduced conditional probabilities and independence.

Please check out the visualization app for discrete distributions (Materials for Lecture 05). Download the code, take a look, and install the requirements, as shown in Assignment 03. If you can, get some extra programming points by extending the app with the finite (n-element) Zipf distribution.

Bayes' Theorem today is an extremely important piece of knowledge. Be sure to understand how to apply it, e.g., to the rare disease example.

Dear all,

the system has made an automatic tutorial assignment. Please note: You can come to the other tutorial as well. The assignment is non-binding.

In fact, please do the following: Come to the online tutorial if you can (Tue at 10, after the lecture, different zoom link!).
If not, please come to the Thursday (14ct) on-campus tutorial.

If neither option works for you, please send an email to Jens Zentgraf with all your available time slots.