The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.

SUMMARY: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The 'Guided Solution Finder' which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades ('tasks'), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided. AVAILABILITY: The HNB portal is available at http://www.hnbioinfo.de

BioSim--a new qualitative simulation environment for molecular biology.

Traditionally, biochemical systems are modelled using kinetics and differential equations in a quantitative simulator. However, for many biological processes detailed quantitative information is not available, only qualitative or fuzzy statements about the nature of interactions. In a previous paper we have shown the applicability of qualitative reasoning methods for molecular biological regulatory processes. Now, we present a newly developed simulation environment, BioSim, that is written in Prolog using constraint logic programming techniques. The simulator combines the basic ideas of two main approaches to qualitative reasoning and integrates the contents of a molecular biology knowledge base, EcoCyc. We show that qualitative reasoning can be combined with automatic transformation of contents of genomic databases into simulation models to give an interactive modelling system that reasons about the relations and interactions of biological entities. This is demonstrated on the glycolytic pathway.

Design and implementation of a qualitative simulation model of lambda phage infection.

MOTIVATION: Molecular biology databases hold a large number of empirical facts about many different aspects of biological entities. That data is static in the sense that one cannot ask a database 'What effect has protein A on gene B?' or 'Do gene A and gene B interact, and if so, how?'. Those questions require an explicit model of the target organism. Traditionally, biochemical systems are modelled using kinetics and differential equations in a quantitative simulator. For many biological processes however, detailed quantitative information is not available, only qualitative or fuzzy statements about the nature of interactions. RESULTS: We designed and implemented a qualitative simulation model of lambda phage growth control in Escherichia coli based on the existing simulation environment QSim. Qualitative reasoning can serve as the basis for automatic transformation of contents of genomic databases into interactive modelling systems that can reason about the relations and interactions of biological entities.