Jörg Ackermann

DNA library design for molecular computation.

A novel approach to designing a DNA library for molecular computation is presented. The method is employed for encoding binary information in DNA molecules. It aims to achieve a practical discrimination between perfectly matched DNA oligomers and those with mismatches in a large pool of different molecules. The approach takes into account the ability of DNA strands to hybridize in complex structures like hairpins, internal loops, or bulge loops and computes the stability of the hybrids formed based on thermodynamic data. A dynamic programming algorithm is applied to calculate the partition function for the ensemble of structures, which play a role in the hybridization reaction. The applicability of the method is demonstrated by the design of a twelve-bit DNA library. The library is constructed and experimentally tested using molecular biology tools. The results show a high level of specific hybridization achieved for all library words under identical conditions. The method is also applicable for the design of primers for PCR, DNA sequences for isothermal amplification reactions, and capture probes in DNA-chip arrays. The library could be applied for integrated DNA computing of twelve-bit instances of NP-complete combinatorial problems by multi-step DNA selection in microflow reactors.

A library of OCL specification patterns for behavioral specification of software components

One important aspect in building trusted information systems is the precise specification of systems and system parts. This applies even more for information systems built from COTS components. To specify behavioral aspects of software components the UML Object Constraint Language (OCL) is well suited. One current problem in component specifications comes from the fact that editing OCL constraints manually is time consuming and error-prone. To simplify constraint definition we propose to use specification patterns for which OCL constraints can be generated automatically. In this paper we outline this solution proposal and present a library of reusable OCL specification patterns.

Using a Specification Data Model for Specification of Black-Box Software Components.

Compositional plug-and-play-like reuse of black-box components requires sophisticated techniques to specify components. In the past little attention has been paid to the use of a conceptual data model to guide behavioral specification of components. In this paper we show how specifications are limited if no such data model is used and overcome these limitations by introducing the concept of a component specification data model. Additionally we propose a solution on how to obtain interface specification data models that are integrated and consistent with the component specification data model.

On the specification of parameterizable business components

To build enterprise applications out of software components promises more flexible and adaptable information systems. In practice it turns out that the business components to be used must be themselves adaptable. Parameterization is an adaptation technique which is well-suited for adaptation on business level. Successful reuse of business components requires techniques to specify the components. In this paper we discuss how the parameterization properties of a component can be included in its specification - this includes parameters themselves and their effect on the components functionality.