Using registries to integrate bioinformatics tools and services into workbench environments

The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand increasingly usable and integrated ways to access and analyse data, especially within convenient, integrated “workbench” environments. Resource descriptions are the core element of registry and workbench systems, which are used to both help the user find and comprehend available software tools, data resources, and Web Services, and to localise, execute and combine them. The descriptions are, however, hard and expensive to create and maintain, because they are volatile and require an exhaustive knowledge of the described resource, its applicability to biological research, and the data model and syntax used to describe it. We present here the Workbench Integration Enabler, a software component that will ease the integration of bioinformatics resources in a workbench environment, using their description provided by the existing ELIXIR Tools and Data Services Registry

Higher-Order Process Modeling: Product-Lining, Variability Modeling and Beyond

We present a graphical and dynamic framework for binding and execution of business) process models. It is tailored to integrate 1) ad hoc processes modeled graphically, 2) third party services discovered in the (Inter)net, and 3) (dynamically) synthesized process chains that solve situation-specific tasks, with the synthesis taking place not only at design time, but also at runtime. Key to our approach is the introduction of type-safe stacked second-order execution contexts that allow for higher-order process modeling. Tamed by our underlying strict service-oriented notion of abstraction, this approach is tailored also to be used by application experts with little technical knowledge: users can select, modify, construct and then pass (component) processes during process execution as if they were data. We illustrate the impact and essence of our framework along a concrete, realistic (business) process modeling scenario: the development of Springer's browser-based Online Conference Service (OCS). The most advanced feature of our new framework allows one to combine online synthesis with the integration of the synthesized process into the running application. This ability leads to a particularly flexible way of implementing self-adaption, and to a particularly concise and powerful way of achieving variability not only at design time, but also at runtime.Comment: In Proceedings Festschrift for Dave Schmidt, arXiv:1309.455