A modelling language for the effective design of Java annotations

This paper describes a new modelling language for the ef- fective design of Java annotations. Since their inclusion in the 5th edition of Java, annotations have grown from a use- ful tool for the addition of meta-data to play a central role in many popular software projects. Usually they are con- ceived as sets with dependency and integrity constraints within them; however, the native support provided by Java for expressing this design is very limited. To overcome its deficiencies and make explicit the rich conceptual model which lies behind a set of annotations, we propose a domain-specific modelling language. The proposal has been implemented as an Eclipse plug- in, including an editor and an integrated code generator that synthesises annotation processors. The language has been tested using a real set of annotations from the Java Per- sistence API (JPA). It has proven to cover a greater scope with respect to other related work in diferent shared areas of application

A modelling language for the effective design of Java annotations

This is the author's version of the work. It is posted here for your personal use. Not for redistribution. The definitive Version of Record was published in SAC '15 Proceedings of the 30th Annual ACM Symposium on Applied Computing, http://dx.doi.org/10.1145/2695664.2695717.This paper describes a new modelling language for the ef- fective design of Java annotations. Since their inclusion in the 5th edition of Java, annotations have grown from a use- ful tool for the addition of meta-data to play a central role in many popular software projects. Usually they are con- ceived as sets with dependency and integrity constraints within them; however, the native support provided by Java for expressing this design is very limited. To overcome its de ciencies and make explicit the rich conceptual model which lies behind a set of annotations, we propose a domain-speci c modelling language. The proposal has been implemented as an Eclipse plug- in, including an editor and an integrated code generator that synthesises annotation processors. The language has been tested using a real set of annotations from the Java Per- sistence API (JPA). It has proven to cover a greater scope with respect to other related work in di erent shared areas of application.This work was supported by the Spanish Ministry of Economy and Competitivity with project Go-Lite (TIN2011-24139) and the Community of Madrid with project SICOMORO (S2013/ICE-3006)

Ann: a domain-specific language for the effective design and validation of Java annotations

This paper describes a new modelling language for the effective design and validation of Java annotations. Since their inclusion in the 5th edition of Java, annotations have grown from a useful tool for the addition of meta-data to play a central role in many popular software projects. Usually they are not conceived in isolation, but in groups, with dependency and integrity constraints between them. However, the native support provided by Java for expressing this design is very limited. To over come its deficiencies and make explicit the rich conceptual model which lies behind a set of annotations,we propose a domain-specific modelling language.The proposal has been implemented as an Eclipse plug-in, including an editor and an integrated code generator that synthesises annotation processors. The environmental so integrates a model finder,able to detectun satisfiable constraints between different annotations, and to provide examples of correct annotation usages for validation. The language has been tested using a real set of annotations from the Java Persistence API(JPA).Within this subset we have found enough rich semantics expressible with Ann and omitted nowadays by the Java language, which shows the benefits of Ann in are levant field of application

Ann: A domain-specific language for the effective design and validation of Java annotations

This is the author’s version of a work that was accepted for publication in Computer Languages, Systems & Structures. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Computer Languages, Systems & Structures, VOL 45, (2016) DOI 10.1016/j.cl.2016.02.002This paper describes a new modelling language for the effective design and validation of Java annotations. Since their inclusion in the 5th edition of Java, annotations have grown from a useful tool for the addition of meta-data to play a central role in many popular software projects. Usually they are not conceived in isolation, but in groups, with dependency and integrity constraints between them. However, the native support provided by Java for expressing this design is very limited. To overcome its deficiencies and make explicit the rich conceptual model which lies behind a set of annotations, we propose a domain-specific modelling language. The proposal has been implemented as an Eclipse plug-in, including an editor and an integrated code generator that synthesises annotation processors. The environment also integrates a model finder, able to detect unsatisfiable constraints between different annotations, and to provide examples of correct annotation usages for validation. The language has been tested using a real set of annotations from the Java Persistence API (JPA). Within this subset we have found enough rich semantics expressible with Ann and omitted nowadays by the Java language, which shows the benefits of Ann in a relevant field of application.We would like to thank the reviewers for their detailed comments, which helped us in improving a previous version of this paper. This work has been partially supported by the Spanish Ministry of Economy and Competitivity with project FLEXOR (TIN2014-52129-R) and the Community of Madrid with project SICOMORO-CM (S2013/ICE-3006)

Semantically Resolving Type Mismatches in Scientific Workflows

Scientists are increasingly utilizing Grids to manage large data sets and execute scientific experiments on distributed resources. Scientific workflows are used as means for modeling and enacting scientific experiments. Windows Workflow Foundation (WF) is a major component of Microsoft’s .NET technology which offers lightweight support for long-running workflows. It provides a comfortable graphical and programmatic environment for the development of extended BPEL-style workflows. WF’s visual features ease the syntactic composition of Web services into scientific workflows but do nothing to assure that information passed between services has consistent semantic types or representations or that deviant flows, errors and compensations are handled meaningfully. In this paper we introduce SAWSDL-compliant annotations for WF and use them with a semantic reasoner to guarantee semantic type correctness in scientific workflows. Examples from bioinformatics are presented

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

Background: Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification. Description: BioModels Database http://www.ebi.ac.uk/biomodels/ is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database. Conclusions: BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge https://sourceforge.net/projects/biomodels/ under the GNU General Public License

Proceedings of International Workshop "Global Computing: Programming Environments, Languages, Security and Analysis of Systems"

According to the IST/ FET proactive initiative on GLOBAL COMPUTING, the goal is to obtain techniques (models, frameworks, methods, algorithms) for constructing systems that are flexible, dependable, secure, robust and efficient. The dominant concerns are not those of representing and manipulating data efficiently but rather those of handling the co-ordination and interaction, security, reliability, robustness, failure modes, and control of risk of the entities in the system and the overall design, description and performance of the system itself. Completely different paradigms of computer science may have to be developed to tackle these issues effectively. The research should concentrate on systems having the following characteristics: • The systems are composed of autonomous computational entities where activity is not centrally controlled, either because global control is impossible or impractical, or because the entities are created or controlled by different owners. • The computational entities are mobile, due to the movement of the physical platforms or by movement of the entity from one platform to another. • The configuration varies over time. For instance, the system is open to the introduction of new computational entities and likewise their deletion. The behaviour of the entities may vary over time. • The systems operate with incomplete information about the environment. For instance, information becomes rapidly out of date and mobility requires information about the environment to be discovered. The ultimate goal of the research action is to provide a solid scientific foundation for the design of such systems, and to lay the groundwork for achieving effective principles for building and analysing such systems. This workshop covers the aspects related to languages and programming environments as well as analysis of systems and resources involving 9 projects (AGILE , DART, DEGAS , MIKADO, MRG, MYTHS, PEPITO, PROFUNDIS, SECURE) out of the 13 founded under the initiative. After an year from the start of the projects, the goal of the workshop is to fix the state of the art on the topics covered by the two clusters related to programming environments and analysis of systems as well as to devise strategies and new ideas to profitably continue the research effort towards the overall objective of the initiative. We acknowledge the Dipartimento di Informatica and Tlc of the University of Trento, the Comune di Rovereto, the project DEGAS for partially funding the event and the Events and Meetings Office of the University of Trento for the valuable collaboration