Christmas Greetings

Merry Christmas to all Followers and Readers of this blog.

“It is good to be children sometimes, and never better than at Christmas, when its mighty Founder was a child Himself.” - Charles Dickens

Bachelor Computational Informatics - Changes

There will be some changes to the curriculum of the Bachelor CI which will take effect in the winter term 2011/12:

Semester 1:

•  Machine-based Programming (instead of Computer Architecture); this will be a laboratory.

Semester 3:

• Computer Engineering and Hardware Lab (instead of Introduction to Security  and Databases)

Semester 5/6:

• Introduction to Security and Databases (instead of Web Engineering and Compiler Construction).

The courses Computer Architecture, Web Engineering, and Compiler Construction will become Compulsory Electives.

Discrete Mathematics I - Lecture 9

Heute ging es abschließend um Zählkoeffizienten für Variationen inklusive ihrer Typisierung, Permutationen, geordnete und ungeordnete Zahlpartitionen sowie Mengenpartitionen.
Damit ist das Kapitel über Kombinatorik beendet.

Computational Biology - Lecture 9

Today, the basics of Groebner bases were presented including test of ideal membership, uniqueness of division, existence of Groebner bases, and Hilbert's basis theorem.

Introduction to Bioinformatics - Lecture 9

Today, we resumed with additive-tree methods for the construction of phylogenetic trees. As an example, the UPGMA method was provided and a genetic algorithm for searching the space of trees with a constant number of leaves.

Living as Machine?

This is the title of the new book of Klaus Mainzer (Mentis Verlag, Paderborn, 2010, 274 p.) that I got the other day. Mainzer's view is that of a unified theory of complex dynamical systems which is based on the assumption that all dynamic processes can be described by a computer program. This view embraces systems biology, artificial intelligence, and cyber physical systems. At the end, humans will be able to communicate with thinking machines and will merge into a single super-organism.

Discrete Mathematics I - Lecture 8

Die Themen der heutigen Vorlesung:

• Prinzip der Inklusion-Exklusion,
• Darstellung von Abbildungen durch Wörter,
• Kombinationen, Binomialkoeffizient,
• Repetitionen,
• Variationen.

Computational Biology - Lecture 8

Today, we will present basics of computational commutative algebra:

• polynomial rings in several unknowns,
• term orders (plex, grlex, grevlex),
• Dickson's Lemma,
• division algorithm.

Introduction to Bioinformatics - Lecture 8

Today, we will firstly consider the maximum likelihood method for the reconstruction of phylogenies. For this, we will introduce evolutionary models. Such a model is based on a rooted tree and a rate matrix which specifies the substitution matrices along the branches of the tree. Then we will introduce the likelihood of the tree and discuss the problem of optimizing the branch lengths.

Secondly, we will study distance based methods. The goal is to construct the most additive tree from a given set of evolutionary distances. We will use linear programming to tackle this problem. An example involving four species will be given.

Discrete Mathematics I - Lecture 7

In der heutigen Vorlesung wurden zuerst abzählbare und überabzählbare Mengen behandelt:

• Menge der ganzen Zahlen,
• Menge der rationalen Zahlen (erste Cantorsche Diagonalisierungsmethode),
• Menge der Algorithmen,
• Menge der reellen Zahlen (zweite Cantorsche Diagonalisierungsmethode),
• Potenzmenge der natürlichen Zahlen.

Die Kontinuumshypothese sowe Abstufungen im Unendlichen wurden diskutiert.

Anschließend ging es um elementare Zählprinzipien:

• Gleichheitsprinzip,
• Additionsprinzip,
• Prinzip der doppelten Abzählung.

Computational Biology - Lecture 7

Today, we will consider the expectation-maximization (EM)  algorithm which can be used to provide maximum-likelihood estimates of the parameters in a statistical model with hidden variables, like the hidden Markov model (HMM). As an example, the EM algorithm is going to be applied to the casino model.

Finally, an HMM for CpG islands in human genomes will be discussed.

Introduction to Bioinformatics - Lecture 7

Today, we will start with the basics on phylogenetics:

• Distance and character data, basic assumptions.
• Number of labeled binary trees with fixed number of leaves - rooted or non-rooted.
• Small parsimony methods: weighted (Sankoff) and unweighted (Fitch).

MentorIng Meeting

The next MentorIng meeting will be on Friday, December 17, from 12:15 to 1:15 in room SBS95-3032. There are actually some new developments concerning the course of studies in CI (computer architecture, technical informatics).
Punsch, orange juice, and cookies will be served.