Topic outline
 
Algebraic and Discrete Methods in Biology (326.300, SS 2007)

Time:
Thursday, 13:45-15:15
Place: HS12 (except March 29), BA 9907 (on March 29)
Start: March 8

Applications of symbolic (algebraic, logic, discrete) methods to biological problems attracts growing interest. Some of the examples are applications of Groebner bases in the reverse engineering of gene regulatory networks from experimental data; modeling and analysis of signal transduction and metabolic networks in mammalian cells using rewriting logic; modeling biochemical regulatory networks as boolean networks; applications of hybrid automata and cylindrical algebraic decomposition in systems biology; using temporal logics to formalize a set of biological properties such as reachability, checkpoints, stability or oscillations; application of difference equations in population dynamics, constraint solving techniques in molecular biology, etc.

The course gives an overview of some of the methods from computer algebra and computational logic that can be (potentially) applied to biological problems. In particular, techniques and tools from automated reasoning, polynomial algebra, algorithmic combinatorics, formal methods will be discussed.

To take part in the course, you have to enrol in the KUSSS system. If you also login in Moodle and register as a course participant, you will receive per email all messages posted in the News forum.

Forum News forum
 
2
Groebner Basen in Systembiologie
Wolfgang Windsteiger

In dieser Einfuehrung werden wir Anwendungen von Groebner Basen (GB) in der Systembiologie als Ausgangspunkt fuer die Beschaeftigung mit Groebner Basen nehmen. Kurz die Theorie der GB, multivariate Polynome, Polynom Reduktion, etc. Anwendungen im speziellen auf das Loesen polynomialer Gleichungssysteme. Wir werden auch die Grundform des GB-Algorithmus behandeln und damit die einfuehrenden Beispiele loesen.
Resource Unterlagen zu Groebner Basen

5
Applications of Rewriting Logic in Biology
Temur Kutsia
Resource Slides

6
Biological Systems as Concurrent Processes
Wolfgang Schreiner

A particular strand of research in systems biology is based on the observation that there are certain similarities between concurrent and mobile software systems and biological systems on the cellular and molecular level. Correspondingly, concepts and techniques developed for the formal specification and verification of concurrent systems have been applied to biological systems, in particular the specification of properties in the language of temporal logic and the verification of such properties by automatic model checking. We will give an overview on recent work in this direction.

Introduction (4 on 1)
Part 1: Modeling and Simulating (4 on 1)
Part 2: Specifying and Verifying (4 on 1)

Resource BioSPi project
Resource Stochastic Pi-Machine (SPiM)
Resource Probabilistic Symbolic Model Checker (PRISM)
Resource Computational Systems Biology
Resource Regev et al: "Representation and simulation of biochemical processes using the pi-calculus process algebra"
Resource Heat et al: "Probabilistic model checking of complex biological pathways"

7
Exam
Another exam will take place on Wednesday, November 7 2007, 8:30-10:00 in K 034D. To take part, register in the KUSSS system for the exam. No materials are allowed, bring your student id with you.

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