Claudia Täubner

Improving literature preselection by searching for images

In this paper we present a picture search engine for life science literature and show how it can be used to improve literature preselection. This preselection is needed as a way to compensate for the vast amounts of literature that are available. While searching for DNA binding sites for example, we wanted to add the results of specific experiments (DNAse I footprint and EMSA) to our database. The preselection via abstract search was very unspecific (150 000 hits), but by looking for paper with images concerning the experiments, we could improve precision immensely. They are displayed like hits in a search engine, allowing easy and quick quality assessment without having to read through the whole paper. The images are found by their annotation in the paper: the figure caption. To identify that, we analyse the layout of the paper: the position of the image and the surrounding text.

Discrete Modelling of the Ethylene-Pathway

Arabidopsis thaliana is a small flowering plant that is widely used as a model organism in plant biology. We describe here the Ethylene-Response Pathway (Ethylene- Pathway) whose is belong to the signal transduction pathways. The knowledge of the signaling pathways are still incomplete and discrete modelling has been shown to help a better understanding of the underlying mechanisms. In this paper we provide a brief introduction to the Ethylene- Pathway and describe two approaches - UML-Statecharts and Life Sequence Charts (LSC) - in discrete modelling of the signaling pathway.

Signal Transduction Pathways as Concurrent Reactive Systems: A Modeling and Simulation Approach Using LSCs and the Play-Engine

Signal transduction pathways describe how cells respond to extracellular signals which are received by receptors at the cell membrane and usually transferred into the nucleus. In this paper we present our approach to model these signal transduction pathways as concurrent reactive systems by means of Life Sequence Charts and to simulate them using the Play-Engine tool. This aspect is part of a bigger approach, where we provide an extendable system to generate models of signal transduction pathways in different modeling languages and to simulate these models with the corresponding simulation tools.