Thomas Bode

Adapters, shims, and glue---service interoperability for in silico experiments

MOTIVATION Computationally, in silico experiments in biology are workflows describing the collaboration of people, data and methods. The Grid and Web services are proposed to be the next generation infrastructure supporting the deployment of bioinformatics workflows. But the growing number of autonomous and heterogeneous services pose challenges to the used middleware w.r.t. composition, i.e. discovery and interoperability of services required within in silico experiments. In the IRIS project, we handle the problem of service interoperability by a semi-automatic procedure for identifying and placing customizable adapters into workflows built by service composition. RESULTS We show the effectiveness and robustness of the software-aided composition procedure by a case study in the field of life science. In this study we combine different database services with different analysis services with the objective of discovering required adapters. Our experiments show that we can identify relevant adapters with high precision and recall.

First Experiences with GEOSTORE, an Information System for Geologically Defined Geometries

Since the beginning of 1993 our group is a member of the SFB “Interactions of Continental Substance-Systems and their Modelling” 1. In this interdisciplinary project about 20 groups of the University of Bonn, mainly geoscientists, are participating. To provide the SFB with database technology as soon as possible, we decided to develop GEOSTORE, a first prototype system which is restricted on the management of geologically defined geometries such as 3D-points and triangulated 3D-surfaces of geological layers and faults. The functionality of GEOSTORE includes the management of three dimensional geological surfaces, the checking of spatial integrity constraints, the 2D-visualization of the examinated area in the Lower Rhine Embayment and a 2D-visualization of horizontal and vertical intersections with 3D-faces. GEOSTORE has first been realized on top of a relational DBMS and secondly on top of an ODBMS. For the 3D-visualization of the geological layers and faults a coupling with GEOCON, a 3D-construction and modelling tool for geological surfaces, is realized via remote procedure call.

The Story of the GeoToolKit—An Object-Oriented Geodatabase Kernel System

The quickly increasing number of spatio-temporal applications in fields like environmental monitoring, geology and mobile communication is a new challenge to the development of geodatabases. However, the query functionality of todays geo-information systems is still limited to the thematic attributes of spatial objects and to spatial 2-D objects. This article reports on GeoToolKit, an object-oriented geo-database kernel system developed at Bonn University to support 3-D/4-D geological applications. GeoToolKit is not a GIS-in-a-box package, but rather a library of C ++ classes that allows the incorporation of spatio-temporal functionality within an application. Being a component toolkit, it encourages the development and deployment of re-usable and open software. The history, concepts and implementation of GeoToolKit are discussed in detail. Performance tests underline the practicability of the concepts. Extensions to and experiences with GeoToolKit applications like GeoStore, GeoWeb and WellStore are presented. Finally, we give an outlook on our future research introducing GeoToolKit as a 3-D/4-D database component within a network of distributed and mobile geo-information services.

A Library Application on Top of an RDBMS: Performance Aspects

Applications which require a combination of structured data with unstructured text fields are becoming of increasing practical interest. But whereas structured data are usually stored in a relational database, large text collections are maintained by proprietary text or information retrieval systems. The synthesis of both areas is still a topic of intensive research. We describe one such application, namely maintaining library catalogues, and study the efficiency of two implementation alternatives both based on RDBMS technology. In the first alternative word occurrence information is encoded using bitlists. The other chooses a direct implementation within the relational model. Performance tests are done which are based on real world data and real world user transactions. They demonstrate that the problem of the bitlist implementation is caused by conversions which are necessary to combine them with structured data. In contrast, our direct implementation benefits from todays sophisticated RDBMS technology and performs promisingly well.

Maintaining library catalogues with an RDBMS : A performance study

Applications which require a combination of structured data with unstructured text elds are becoming of increasing practical interest. But whereas structured data are usually stored in a relational database, large text collections are maintained by proprietary text or information retrieval systems. The synthesis of both areas is still a topic of intensive research. We describe one such application, namely maintaining library catalogues, and study the eeciency of two implementation alternatives both based on RDBMS technology. In the rst alternative word occurrence information is encoded using bitlists. The other chooses a direct implementation within the relational model. Performance tests are done which are based on real world data and real world user transactions. They demonstrate that the problem of the bitlist implementation is caused by conversions which are necessary to combine them with struc-tured data. In contrast, our direct implementation beneets from todays sophisticated RDBMS technology and performs promisingly well.

Coupling the Complex-Relational Data Base CoReDB with the Object Management System OMS

The CoReDB/OMS approach consequently integrates mechanisms to handle very large logic programs in a data base system.