Volume 48, Issue 3

Information technology is an important part within the highly interdisciplinary scientific field of systems biology. In this paper we are presenting an overview over systems biology, focusing on the information technological aspects, current developments, and future challenges.

Numerous software platforms in Computational Systems Biology have been developed in the past decade. Each program has its own strengths but their functionality often overlaps significantly. In this article, we review numerous aspects related to the functionality and infrastructure of existing platforms in the context of a selected set of tools. We discuss the biological problems that can be solved with these tools and point out directions for future research in the field.

The creation of models for heterogeneous and complex cellular networks is a central goal of Systems Biology. When modeling a biological network, one may wish to account for certain aspects in detail, while a bird's eye perspective would seem more appropriate for other parts. Multi-level models combine such overview and detail representations. We illustrate multi-level modeling with gene regulation of the Tryptophan operon in E. coli. We review three discrete event modeling formalisms and discuss model design therein: DEVS, STATECHARTS, and stochastic π-CALCULUS. This introductory presentation already reveals some of their respective virtues and shortcomings.

Chemical organization theory has been proposed to provide a new perspective to study complex dynamical reaction networks. It decomposes a reaction network into overlapping sub-networks called organizations. An organization is an algebraically closed and self-maintaining set of molecular species. The set of organizations form a hierarchical “organizational structure”, which is here a lattice. In order to evaluate the usefulness of this approach we apply the theory to five models of immune response to HIV infection. We found four different lattices of organizations, which can be used as a first classification of the models. Furthermore, each organization found can be assigned to a functional state of the system. And finally, the lattice of organizations can be used to explain a treatment strategy on a more abstract level, i. e., as a movement from one organization into another.

Ciliates have developed a puzzling genomic organization. Genes are broken into many pieces in the micronucleus, separated by non-coding sequences, and sometimes also shuffled and inverted. During sexual reproduction, all pieces are precisely assembled in the orthodox order to yield the transcriptionally active macronuclear genes. We give in this paper a brief survey of the genome structure in stichotrichous ciliates and present two molecular models proposed for gene assembly. We then establish a set of invariants for gene assembly. We prove that in any model based on the paradigm of pointer-directed assembly, the set of molecules excised during the assembly of a given gene, the linearity of the assembled gene, and its IES context are all uniquely defined by the micronuclear structure of the gene and thus, are invariants of the gene assembly process.

The immune system is an impressive information processing system with many appealing properties for solving problems. Artificial immune systems are a paradigm inspired by the immune system and are used for solving computational and information processing problems. In this paper, we outline two different immune-inspired approaches typically used for IT-security problems. Specifically, we present one of the first proposed immune inspired approaches for network intrusion detection, this is then complimented with an overview of recent investigations on the latest immunological theories and how they may be exploited in IT-security. We then present an artificial immune system concept for database security which encompasses issues such as confidentiality of database information and prevention of privacy-preserving data mining.

Zusammenfassung Der Feldafinger Kreis wurde durch eine Initiative von Repräsentanten der deutschen Wissenschaftsorganisationen und dem Bundesverband der deutschen Industrie (BDI) im August 2001 gegründet. Er hat sich zum Ziel gesetzt, den Dialog zwischen Wissenschaft und Wirtschaft auf dem Gebiet ‚Forschung für die Internetgesellschaft‘ zu intensivieren, die Internetforschung in Deutschland zu stimulieren und Impulse zu geben zur besseren Nutzung der Innovationspotenziale, die das Internet bietet.

Zusammenfassung Effizienz und Dienstgüte sind zwei sehr wichtige Eigenschaften von IP Netzwerken. Aus der Sicht eines Internet Netzwerkbetreibers (engl.: Internet Service Provider, ISP) untersuchen wir in dieser Arbeit, wie man die Effizienz und Dienstgüte verbessern kann. Hierzu betrachten wir die Netzwerkarchitektur, die Interkonnektion und die Verkehrs- und Netzwerkanpassungsmaßnahmen (engl.: network & traffic engineering).