XML-based approaches for the integration of heterogeneous bio-molecular data

Background: The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. Results: In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. Conclusion: XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources. </p

Category Theory and Model-Driven Engineering: From Formal Semantics to Design Patterns and Beyond

There is a hidden intrigue in the title. CT is one of the most abstract mathematical disciplines, sometimes nicknamed "abstract nonsense". MDE is a recent trend in software development, industrially supported by standards, tools, and the status of a new "silver bullet". Surprisingly, categorical patterns turn out to be directly applicable to mathematical modeling of structures appearing in everyday MDE practice. Model merging, transformation, synchronization, and other important model management scenarios can be seen as executions of categorical specifications. Moreover, the paper aims to elucidate a claim that relationships between CT and MDE are more complex and richer than is normally assumed for "applied mathematics". CT provides a toolbox of design patterns and structural principles of real practical value for MDE. We will present examples of how an elementary categorical arrangement of a model management scenario reveals deficiencies in the architecture of modern tools automating the scenario.Comment: In Proceedings ACCAT 2012, arXiv:1208.430

Secure data sharing and processing in heterogeneous clouds

The extensive cloud adoption among the European Public Sector Players empowered them to own and operate a range of cloud infrastructures. These deployments vary both in the size and capabilities, as well as in the range of employed technologies and processes. The public sector, however, lacks the necessary technology to enable effective, interoperable and secure integration of a multitude of its computing clouds and services. In this work we focus on the federation of private clouds and the approaches that enable secure data sharing and processing among the collaborating infrastructures and services of public entities. We investigate the aspects of access control, data and security policy languages, as well as cryptographic approaches that enable fine-grained security and data processing in semi-trusted environments. We identify the main challenges and frame the future work that serve as an enabler of interoperability among heterogeneous infrastructures and services. Our goal is to enable both security and legal conformance as well as to facilitate transparency, privacy and effectivity of private cloud federations for the public sector needs. © 2015 The Authors