A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

Object-oriented Tools for Distributed Computing

Distributed computing systems are proliferating, owing to the availability of powerful, affordable microcomputers and inexpensive communication networks. A critical problem in developing such systems is getting application programs to interact with one another across a computer network. Remote interprogram connectivity is particularly challenging across heterogeneous environments, where applications run on different kinds of computers and operating systems. NetWorks! (trademark) is an innovative software product that provides an object-oriented messaging solution to these problems. This paper describes the design and functionality of NetWorks! and illustrates how it is being used to build complex distributed applications for NASA and in the commercial sector

Towards an aspect weaving BPEL engine

This position paper proposes the use of dynamic aspects and the visitor design pattern to obtain a highly configurable and extensible BPEL engine. Using these two techniques, the core of this infrastructural software can be customised to meet new requirements and add features such as debugging, execution monitoring, or changing to another Web Service selection policy. Additionally, it can easily be extended to cope with customer-specific BPEL extensions. We propose the use of dynamic aspects not only on the engine itself but also on the workflow in order to tackle the problems of Web Service hot deployment and hot fixes to long running processes. In this way, composing aWeb Service "on-the-fly" means weaving its choreography interface into the workflow

SPIN-ning Software Architectures: A Method for Exploring Complex Systems

When designing complex software systems that provide multiple non-functional properties, it is usual to try to reuse (and finally compose) simpler existing designs, which deal with each of these properties in solitude. The paper describes a method for automatically and quickly identifying all the different ways one can compose such designs, with the aid of a model checke

Separating Agent-Functioning and Inter-Agent Coordination by Activated Modules: The DECOMAS Architecture

The embedding of self-organizing inter-agent processes in distributed software applications enables the decentralized coordination system elements, solely based on concerted, localized interactions. The separation and encapsulation of the activities that are conceptually related to the coordination, is a crucial concern for systematic development practices in order to prepare the reuse and systematic integration of coordination processes in software systems. Here, we discuss a programming model that is based on the externalization of processes prescriptions and their embedding in Multi-Agent Systems (MAS). One fundamental design concern for a corresponding execution middleware is the minimal-invasive augmentation of the activities that affect coordination. This design challenge is approached by the activation of agent modules. Modules are converted to software elements that reason about and modify their host agent. We discuss and formalize this extension within the context of a generic coordination architecture and exemplify the proposed programming model with the decentralized management of (web) service infrastructures