Content according to Studienordnung

Es werden vertieft Themen aus folgenden Gebieten behandelt:

• Verfahren für exaktes und approximatives Suchen in Strings, Filter und Stringindices sowie Alignments von RNA, DNA und Proteinsequenzen
• Algorithmen zum Finden regulatorischer und codierender Signale in Gensequenzen
• Verfahren zur Vorhersage molekularer Evolution auf Sequenzebene, vergleichende Genomik
• Algorithmen zur Auswertung von Gen- und Proteinexpressionsexperimenten
• Struktur und Aufbau molekularbiologischer Datenbanken sowie Verbinden verschiedener Datenquellen

Die veranschlagten Zeiten:

Vorlesungsteil	veranschlagte Zeit (h)
Präsenz Vorlesung	45
Vor- und Nachbereitung Vorlesung	90
Präsenz Übung	15
Bearbeitung der Übungsaufgaben	30
Präsenz Praktikum	30
Eigenarbeit Praktikum	60
Prüfungsvorbereitung und Prüfung	30

General setup of lecture

We will try out a new, more project based format for this lecture. That means we will deviate from the usual format:

• blackboard lecture
• exercises
• practical programming

and will integrate all that in a more project oriented, collaborative lecture.

We have three them complexes which encompass basically all of the content mentioned in the Studienordnung:

1. Algorithms for next generation sequencing data
2. Algorithms for comparative genomics
3. Algorithms and mathematical models for protein expression analysis

We will work out the specific content using a project for each of the topics.

Each student will work on one project, but participate in all lectures. The projects can be proposed by the students out of the the three complexes (one each). You are free to follow your interest. However, I will require a (small) number of subjects that we will cover in any case and which should be incorporated into your projects. That will be subject to negotiation during the project proposal phase of the lecture. I propose three possible projects, which you can choose and will offer background reading for them. The details are not specified and subject to your inquisitive minds.

Phases of lecture

As you can see below we will have three phases of the lecture. In each phase we will cycle through the three projects. That means that a group has a higher workload within a week presenting material, taking lead roles in discussion, explaining to other groups.

Proposal phase

In the proposal phase a group of students will work out a project plan about the topic for which I will give the theme and initial pointers to literature and scripts. This project plan should include

1. A rough sketch of the analysis problem of the project.
2. A list of algorithmic problems and statistical/mathematical models connected with the project (embedded in the sketch)
3. A proposal of each member of the group for a practical task within a project (worth 60 hours of programming)

More specifically. Read the overview paper and and at least read over the additional literature. We have an algorithm lecture. Try to factor out the algorithmic problems connected with the project. Problems you do not know a solution yet, and problems you do know a solution.

This project proposal will be discussed in the first week. The outcome of this discussion is:

1. a more detailed project plan
2. a plan for in-depth lectures during lecture phase (including core lectures)
3. a practical programming project for each member of the team

Lecture phase

After the proposal phase for each project, we will cycle through the three projects in the following mode (three sessions per week).

Session 1

the team introduces in-depth a topic that was agreed on in the planning phase (this is carefully prepared with the help of instructors). Feedback is given and points collected that should be emphasized, and worked through (in the sense of a traditional Übung).

Session 2

The mentioned points, exercises from Session 1 are talked through.

Session 3

Here we might have special skill lessons (e.g. scientific writing), or use the time with instructors to work on practical assignments, or preparation of next weeks lecture.

Be prepared to work an additional 10-11 hours a week on the lecture (on average), in your project's week this will be more, otherwise it might be less. During the lecture phase you will prepare a project report (probably in in LaTeX) which will serve as a script and is relevant for the examination. The group will organize this work itself if possible with the help of the instructors.

Presentation and feedback phase

In the last two weeks the projects present an overview of their project in the light of the new knowledge acquired. Each project team will also produce a script of their project which will be the basis of the examination. Both, script and presentation will be discussed, feedback and improvement suggestions will be given (the improvements have to be worked in).