AMOD: a morpholino oligonucleotide selection tool

AMOD is a web-based program that aids in the functional evaluation of nucleotide sequences through sequence characterization and antisense morpholino oligonucleotide (target site) selection. Submitted sequences are analyzed by translation initiation site prediction algorithms and sequence-to-sequence comparisons; results are used to characterize sequence features required for morpholino design. Within a defined subsequence, base composition and homodimerization values are computed for all putative morpholino oligonucleotides. Using these properties, morpholino candidates are selected and compared with genomic and transcriptome databases with the goal to identify target-specific enriched morpholinos. AMOD has been used at the University of Minnesota to design ∼200 morpholinos for a functional genomics screen in zebrafish. The AMOD web server and a tutorial are freely available to both academic and commercial users at

Quality-aware model-driven service engineering

Service engineering and service-oriented architecture as an integration and platform technology is a recent approach to software systems integration. Quality aspects ranging from interoperability to maintainability to performance are of central importance for the integration of heterogeneous, distributed service-based systems. Architecture models can substantially influence quality attributes of the implemented software systems. Besides the benefits of explicit architectures on maintainability and reuse, architectural constraints such as styles, reference architectures and architectural patterns can influence observable software properties such as performance. Empirical performance evaluation is a process of measuring and evaluating the performance of implemented software. We present an approach for addressing the quality of services and service-based systems at the model-level in the context of model-driven service engineering. The focus on architecture-level models is a consequence of the black-box character of services

Model-driven performance evaluation for service engineering

Service engineering and service-oriented architecture as an integration and platform technology is a recent approach to software systems integration. Software quality aspects such as performance are of central importance for the integration of heterogeneous, distributed service-based systems. Empirical performance evaluation is a process of measuring and calculating performance metrics of the implemented software. We present an approach for the empirical, model-based performance evaluation of services and service compositions in the context of model-driven service engineering. Temporal databases theory is utilised for the empirical performance evaluation of model-driven developed service systems

Context modeling and constraints binding in web service business processes

Context awareness is a principle used in pervasive services applications to enhance their exibility and adaptability to changing conditions and dynamic environments. Ontologies provide a suitable framework for context modeling and reasoning. We develop a context model for executable business processes { captured as an ontology for the web services domain. A web service description is attached to a service context profile, which is bound to the context ontology. Context instances can be generated dynamically at services runtime and are bound to context constraint services. Constraint services facilitate both setting up constraint properties and constraint checkers, which determine the dynamic validity of context instances. Data collectors focus on capturing context instances. Runtime integration of both constraint services and data collectors permit the business process to achieve dynamic business goals

Context constraint integration and validation in dynamic web service compositions

System architectures that cross organisational boundaries are usually implemented based on Web service technologies due to their inherent interoperability benets. With increasing exibility requirements, such as on-demand service provision, a dynamic approach to service architecture focussing on composition at runtime is needed. The possibility of technical faults, but also violations of functional and semantic constraints require a comprehensive notion of context that captures composition-relevant aspects. Context-aware techniques are consequently required to support constraint validation for dynamic service composition. We present techniques to respond to problems occurring during the execution of dynamically composed Web services implemented in WS-BPEL. A notion of context { covering physical and contractual faults and violations { is used to safeguard composed service executions dynamically. Our aim is to present an architectural framework from an application-oriented perspective, addressing practical considerations of a technical framework

Modelling electronic service systems using UML

This paper presents a profile for modelling systems of electronic services using UML. Electronic services encapsulate business services, an organisational unit focused on delivering benefit to a consumer, to enhance communication, coordination and information management. Our profile is based on a formal, workflow-oriented description of electronic services that is abstracted from particular implementation technologies. Resulting models provide the basis for a formal analysis to verify behavioural properties of services. The models can also relate services to management components, including workflow managers and Electronic Service Management Systems (ESMSs), a novel concept drawn from experience of HP Service Composer and DySCo (Dynamic Service Composer), providing the starting point for integration and implementation tasks. Their UML basis and platform-independent nature is consistent with a Model-Driven Architecture (MDA) development strategy, appropriate to the challenge of developing electronic service systems using heterogeneous technology, and incorporating legacy systems

A RESTful API for exchanging Materials Data in the AFLOWLIB.org consortium

The continued advancement of science depends on shared and reproducible data. In the field of computational materials science and rational materials design this entails the construction of large open databases of materials properties. To this end, an Application Program Interface (API) following REST principles is introduced for the AFLOWLIB.org materials data repositories consortium. AUIDs (Aflowlib Unique IDentifier) and AURLs (Aflowlib Uniform Resource locator) are assigned to the database resources according to a well-defined protocol described herein, which enables the client to access, through appropriate queries, the desired data for post-processing. This introduces a new level of openness into the AFLOWLIB repository, allowing the community to construct high-level work-flows and tools exploiting its rich data set of calculated structural, thermodynamic, and electronic properties. Furthermore, federating these tools would open the door to collaborative investigation of the data by an unprecedented extended community of users to accelerate the advancement of computational materials design and development.Comment: 22 pages, 7 figure