Component-Based Model-Driven Software Development

Model-driven software development (MDSD) and component-based software development are both paradigms for reducing complexity and for increasing abstraction and reuse in software development. In this thesis, we aim at combining the advantages of each by introducing methods from component-based development into MDSD. In MDSD, all artefacts that describe a software system are regarded as models of the system and are treated as the central development artefacts. To obtain a system implementation from such models, they are transformed and integrated until implementation code can be generated from them. Models in MDSD can have very different forms: they can be documents, diagrams, or textual specifications defined in different modelling languages. Integrating these models of different formats and abstraction in a consistent way is a central challenge in MDSD. We propose to tackle this challenge by explicitly separating the tasks of defining model components and composing model components, which is also known as distinguishing programming-in-the-small and programming-in-the-large. That is, we promote a separation of models into models for modelling-in-the-small (models that are components) and models for modelling-in-the-large (models that describe compositions of model components). To perform such component-based modelling, we introduce two architectural styles for developing systems with component-based MDSD (CB-MDSD). For CB-MDSD, we require a universal composition technique that can handle models defined in arbitrary modelling languages. A technique that can handle arbitrary textual languages is universal invasive software composition for code fragment composition. We extend this technique to universal invasive software composition for graph fragments (U-ISC/Graph) which can handle arbitrary models, including graphical and textual ones, as components. Such components are called graph fragments, because we treat each model as a typed graph and support reuse of partial models. To put the composition technique into practice, we developed the tool Reuseware that implements U-ISC/Graph. The tool is based on the Eclipse Modelling Framework and can therefore be integrated into existing MDSD development environments based on the framework. To evaluate the applicability of CB-MDSD, we realised for each of our two architectural styles a model-driven architecture with Reuseware. The first style, which we name ModelSoC, is based on the component-based development paradigm of multi-dimensional separation of concerns. The architecture we realised with that style shows how a system that involves multiple modelling languages can be developed with CB-MDSD. The second style, which we name ModelHiC, is based on hierarchical composition. With this style, we developed abstraction and reuse support for a large modelling language for telecommunication networks that implements the Common Information Model industry standard

Modular Web Queries — From Rules to Stores

Even with all the progress in Semantic technology, accessing Web data remains a challenging issue with new Web query languages and approaches appearing regularly. Yet most of these languages, including W3C approaches such as XQuery and SPARQL, do little to cope with the explosion of the data size and schemata diversity and richness on the Web. In this paper we propose a straightforward step toward the improvement of this situation that is simple to realize and yet effective: Advanced module systems that make partitioning of (a) the evaluation and (b) the conceptual design of complex Web queries possible. They provide the query programmer with a powerful, but easy to use high-level abstraction for packaging, encapsulating, and reusing conceptually related parts (in our case, rules) of a Web query. The proposed module system combines ease of use thanks to a simple core concept, the partitioning of rules and their consequences in flexible “stores”, with ease of deployment thanks to a reduction semantics. We focus on extending the rule-based Semantic Web query language Xcerpt with such a module system though the same approach can be applied to other (rule-based) languages as well

Component-Based Model-Driven Software Development

Model-driven software development (MDSD) and component-based software development are both paradigms for reducing complexity and for increasing abstraction and reuse in software development. In this thesis, we aim at combining the advantages of each by introducing methods from component-based development into MDSD. In MDSD, all artefacts that describe a software system are regarded as models of the system and are treated as the central development artefacts. To obtain a system implementation from such models, they are transformed and integrated until implementation code can be generated from them. Models in MDSD can have very different forms: they can be documents, diagrams, or textual specifications defined in different modelling languages. Integrating these models of different formats and abstraction in a consistent way is a central challenge in MDSD. We propose to tackle this challenge by explicitly separating the tasks of defining model components and composing model components, which is also known as distinguishing programming-in-the-small and programming-in-the-large. That is, we promote a separation of models into models for modelling-in-the-small (models that are components) and models for modelling-in-the-large (models that describe compositions of model components). To perform such component-based modelling, we introduce two architectural styles for developing systems with component-based MDSD (CB-MDSD). For CB-MDSD, we require a universal composition technique that can handle models defined in arbitrary modelling languages. A technique that can handle arbitrary textual languages is universal invasive software composition for code fragment composition. We extend this technique to universal invasive software composition for graph fragments (U-ISC/Graph) which can handle arbitrary models, including graphical and textual ones, as components. Such components are called graph fragments, because we treat each model as a typed graph and support reuse of partial models. To put the composition technique into practice, we developed the tool Reuseware that implements U-ISC/Graph. The tool is based on the Eclipse Modelling Framework and can therefore be integrated into existing MDSD development environments based on the framework. To evaluate the applicability of CB-MDSD, we realised for each of our two architectural styles a model-driven architecture with Reuseware. The first style, which we name ModelSoC, is based on the component-based development paradigm of multi-dimensional separation of concerns. The architecture we realised with that style shows how a system that involves multiple modelling languages can be developed with CB-MDSD. The second style, which we name ModelHiC, is based on hierarchical composition. With this style, we developed abstraction and reuse support for a large modelling language for telecommunication networks that implements the Common Information Model industry standard

Component-Based Model-Driven Software Development

Model-driven software development (MDSD) and component-based software development are both paradigms for reducing complexity and for increasing abstraction and reuse in software development. In this thesis, we aim at combining the advantages of each by introducing methods from component-based development into MDSD. In MDSD, all artefacts that describe a software system are regarded as models of the system and are treated as the central development artefacts. To obtain a system implementation from such models, they are transformed and integrated until implementation code can be generated from them. Models in MDSD can have very different forms: they can be documents, diagrams, or textual specifications defined in different modelling languages. Integrating these models of different formats and abstraction in a consistent way is a central challenge in MDSD. We propose to tackle this challenge by explicitly separating the tasks of defining model components and composing model components, which is also known as distinguishing programming-in-the-small and programming-in-the-large. That is, we promote a separation of models into models for modelling-in-the-small (models that are components) and models for modelling-in-the-large (models that describe compositions of model components). To perform such component-based modelling, we introduce two architectural styles for developing systems with component-based MDSD (CB-MDSD). For CB-MDSD, we require a universal composition technique that can handle models defined in arbitrary modelling languages. A technique that can handle arbitrary textual languages is universal invasive software composition for code fragment composition. We extend this technique to universal invasive software composition for graph fragments (U-ISC/Graph) which can handle arbitrary models, including graphical and textual ones, as components. Such components are called graph fragments, because we treat each model as a typed graph and support reuse of partial models. To put the composition technique into practice, we developed the tool Reuseware that implements U-ISC/Graph. The tool is based on the Eclipse Modelling Framework and can therefore be integrated into existing MDSD development environments based on the framework. To evaluate the applicability of CB-MDSD, we realised for each of our two architectural styles a model-driven architecture with Reuseware. The first style, which we name ModelSoC, is based on the component-based development paradigm of multi-dimensional separation of concerns. The architecture we realised with that style shows how a system that involves multiple modelling languages can be developed with CB-MDSD. The second style, which we name ModelHiC, is based on hierarchical composition. With this style, we developed abstraction and reuse support for a large modelling language for telecommunication networks that implements the Common Information Model industry standard

From DARPins to LoopDARPins: novel LoopDARPin design allows the selection of low picomolar binders in a single round of ribosome display

Antibodies are the most versatile binding proteins in nature with six loops creating a flexible continuous interaction surface. However, in some molecular formats, antibodies are aggregation prone. Designed ankyrin repeat proteins (DARPins) were successfully created as alternative design solutions. Nevertheless, their concave shape, rigidity and incompletely randomized binding surface may limit the epitopes that can be targeted by this extremely stable scaffold. Combining conformational diversity and a continuous convex paratope found in many antibodies with the beneficial biophysical properties of DARPins, we created LoopDARPins, a next generation of DARPins with extended epitope binding properties. We employed X-ray structure determination of a LoopDARPin for design validation. Biophysical characterizations show that the introduction of an elongated loop through consensus design does not decrease the stability of the scaffold,consistent with molecular dynamics simulations. Ribosome-display selections against extracellular signal-regulated kinase 2 (ERK2) and four members of the BCL-2 family (BCL-2, BCL-XL, BCL-W and MCL-1) of anti-apoptotic regulators yielded LoopDARPins with affinities in the mid-picomolar to low nanomol arrange against all targets. The BCL-2 family binders block the interaction with their natural interaction partner and will be valuable reagents to test the apoptotic response in functional assays. With the LoopDARPin scaffold, binders for BCL-2 with an affinity of 30 pM were isolated with only a single round of ribosome display,an enrichment that has not been described for any scaffold. Identical stringent one-round selections with conventional DARPins without loop yielded no binders. The LoopDARPin scaffold may become a highly valuable tool for biotechnological high-throughput applications

Co-crystallization with conformation-specific designed ankyrin repeat proteins explains the conformational flexibility of BCL-W

BCL-W is a member of the BCL-2 family of anti-apoptotic proteins. A key event in the regulation of apoptosis is the heterodimerization between anti-apoptotic and pro-apoptotic family members, which involves a conserved surface-exposed groove on the anti-apoptotic proteins. Crystal structures of the ligand binding-competent conformation exist for all anti-apoptotic family members, with the exception of BCL-W, due to the flexibility of the BCL-W groove region. Existing structures had suggested major deviations of the BCL-W groove region from the otherwise structurally highly related remaining anti-apoptotic family members. To capture its ligand binding-competent conformation by counteracting the conformational flexibility of the BCL-W groove, we had selected high-affinity groove-binding designed ankyrin repeat proteins (DARPins) using ribosome display. We now determined two high-resolution crystal structures of human BCL-W in complex with different DARPins at resolutions 1.5 and 1.85Å, in which the structure of BCL-W is virtually identical, and BCL-W adopts a conformation extremely similar to the ligand-free conformation of its closest relative BCL-XL in both structures. However, distinct differences to all previous BCL-W structures are evident, notably in the ligand-binding region. We provide the first structural explanation for the conformational flexibility of the BCL-W groove region in comparison to other BCL-2 family members. Due to the importance of the anti-apoptotic BCL-2 family as drug targets, the presented crystal structure of ligand binding-competent BCL-W may serve as a valuable basis for structure-based drug design in the future and provides a missing piece for the structural characterization of this protein family

Learning portfolios of automatically tuned planners

Portfolio planners and parameter tuning are two ideas that have recently attracted significant attention in the domain-independent planning community. We combine these two ideas and present a portfolio planner that runs automatically configured planners. We let the automatic parameter tuning framework ParamILS find fast configurations of the Fast Downward planning system for a number of planning domains. Afterwards we learn a portfolio of those planner configurations. Evaluation of our portfolio planner on the IPC 2011 domains shows that it has a significantly higher IPC score than the winner of the sequential satisficing track