Komplexpraktikum/Project in SS 2005


The topics of this Komplexprakticum will be in the following areas:
- Term rewriting,
- Molecular computing,
- Logical reasoning.

Initial meeting
takes place on April 8th, Room 151, 13:00-14:00. Attending the initial meeting is mandatory for participation in the praktikum/project.
People who want to participate in the praktikum/project, but have serious reasons to not attend the initial meeting, please send an email until April 7th.

Position in curriculum
- Diplomstudiengang Informatik (Diplom- und Bakkalaureatsabschlu▀), ab 5. Semester ;Wahlpflichtveranstaltung (-/-/4)
- Course of studies Computation Logic; project (12 credits)

Prerequisites
for computer scientists: Pflichtvorlesung "Grundlagen der Theoretischen Informatik"

Organisation
- An initial meeting is held at the beginning of the semester (see above). In this meeting, a brief presentation of the available topics will be given. Students then have the opportunity to choose a topic to work on.
- Each student is assigned a tutor, depending on the topic chosen. During the semester, there will be regular meetings of the student and his tutor.
- The results of the praktikum/project will be presented at the end of the semester in a talk given by the student.

Language
The language of the initial meeting is English. Concerning the final presentations, students may choose to present their work in German or in English.

Participants Duties
The participants are expected to read the relevant literature, and to discuss it with their tutor in order to become acquainted with the topic chosen. The required implementation work should be carried out in a structured way, and has to be documented appropriately. If a topic is shared by two or more participants, acquiring team-working skills is another goal of the project. The results of the project have to be described in a project paper (~15 pages) and presented in a 30 minutes talk at the end of the semester.

It is also the duty of the participants to reserve enough time for performing the project. The sharp deadline for finishing the project is the beginning of the following semester, i.e. the allowed time for the project is one semester plus the following semester break. Failure to finish the project in time will result in no credits to be given. It is the obligation of the participant to start the project in time, and to make appointments with the supervisor for regular meetings during the semester.

Topics
When choosing a topic, please take into account the knowledge you have already acquired. For example, if you'd like to do a project concerning knowledge representation, you are expected to have successfully attended the lecture "Logic-based knowledge representation" before starting the project.

(1) Implementation of Tools for the Term Rewriting lecture.

The project consists of finding appropriate tools which can help in learning concepts presented in the Term Rewriting lecture and installing them (under supervision). The main systems designed for the problems in term rewriting can be found at http://rewriting.loria.fr.

A student will have to choose appropriate systems, get to know their functionality and design a common interface. The main problems which should be possible to solve with the help of the existing tools are:

  • with a TRS and a term as an input, output a normal form of the term or a set of its normal forms;
  • with a TRS as an input, decide its termination using the orders known from the lecture (lpo, polynomial order);
  • with an equational theory as an input, perform its completion.

Since different systems may have different input/output formats, the decision should be made on one such format, which is then translated depending on which system is going to be used to solve a specific problem. A short manual should be written describing how to use the tools for term rewriting, i.e. how to write correct input, how to trigger a desirable action and what is the form of the output.

Literature:
  • Database of Rewriting Systems, http://rewriting.loria.fr/
  • Franz Baader, Tobias Nipkow. Term Rewriting and All That, Cambridge University Press, 1998.

Prerequisites: Lecture "Term Rewriting Systems"

Tutor: Dr. Barbara Morawska,



(2) Molecular Computing

Molecular Computing, known also under the name Biological Computing (computing in test tubes), is a new computation paradigm that employs DNA molecule manipulation to solve mathematical problems. Some aspects such as the high data density allow one to achieve parallel reactions in a test tube. Many computationally complete models of biological computers are developed and many experiments are executed e.g. DNA Haskell. As a special programming language DNA Haskell supports the construction of DNA algorithms which should be executed in labs via molecular biological techniques. Experimental studies on Molecular Computing are prepared on the basis of these algorithms.

Objective of the Komplexpraktikum are:

  • Execution and checking all examples described in the book "Rechnen mit DNA - Eine Einführung in Theorie und Praxis", chapter 3 - main chapter about molecular biological operations. (Book is written in German.)
  • Implementation of special sequences consisting of different kinds of molecular biological operations.
  • Reparation of DNA strands after each operation execution in the sense of a compact description in the data structure.

Literature:
  • Th. Hinze, M. Sturm. "Rechnen mit DNA - Eine Einführung in Theorie und Praxis". Oldenbourg Wissenschaftsverlag München, 2004.

Prerequisites: Some knowledge of functional programming (Haskell, Hugs) and some understanding of concepts in biology and genetics would be helpful.

Tutor: Dr.-Ing. Monika Sturm,



(3) The emptiness problem for alternating automata

Two-way Alternating automata (2ATAs) on infinite trees are an elegant approach to deciding satisfiability in a broad range of logics. For many such applications in logic, it is important that the emptiness problem of 2ATAs can be checked in deterministic exponential time. Unfortunately, this result is scattered across several papers, and a clear and straight- forward presentation is missing. The goal of this project is to locate and read the relevant literature, and to produce a direct and self-contained proof of the fact that the emptiness problem for 2ATAs is in ExpTime.

Note that this is a theoretical project: it does not involve implementation, but requires the participants to prove some theoretical results.

Literature: will be provided.
Prerequisites: The lecture "Automata and Logic".

Tutor: Dr. Carsten Lutz,


Barbara Morawska