From ACT-ONE to Miranda, a Translation Experiment

It is now almost universally acknowledged that the data language ACT-ONE associated with the formal description technique LOTOS is inappropriate for the purpose of OSI formal description. In response to this the LOTOS restandardisation activity plans to replace ACT-ONE with a functional language. Thus, compatibility between ACT-ONE and the replacement data language becomes an issue. In response to this, we present an experimental investigation of backward compatibility between ACT-ONE and the new LOTOS data language. Specifically, we investigate translating ACT-ONE data types into the functional language Miranda. Miranda has been chosen as it is a widely used functional programming language and it is close in form to the anticipated new data language. This work serves as a ``verification of concept'' for translating ACT-ONE to the E-LOTOS data language. It identifies the bounds on embedding ACT-ONE in a functional data language. In particular, it indicates what can be translated and what cannot be translated. In addition, the paper reveals pertinent issues which can inform the E-LOTOS work. For example, which constructs are needed in E-LOTOS in order to support the class of data type specifications typically made in the LOTOS setting? We conclude with a number of specific recommendations for the E-LOTOS data language

Re-designing the substrate binding pocket of laccase for enhanced oxidation of sinapic acid

Iterative saturation mutagenesis was performed over six residues delimiting the substrate binding pocket of a high-redox potential chimeric laccase with the aim of enhancing its activity over sinapic acid, a lignin-related phenol of industrial interest. In total, more than 15000 clones were screened and two selected variants, together with the parent-type laccase, were purified and characterized. The new variants presented shifted pH activity profiles and enhanced turnover rates on sinapic acid and its methyl ester, whereas the oxidation of related phenols was not significantly enhanced. Neither the enzyme's redox potential nor the mechanism of the reaction were affected. Thus, quantum mechanics and molecular dynamics calculations were done to rationalize the effect of the selected mutations, revealing the critical role of the residues of the enzyme pocket to provide the precise binding of the substrate that enables an efficient electron transfer to the T1 copper. The results presented highlight the power of combining directed evolution and computational approaches to give novel solutions in enzyme engineering and to understand the mechanistic reasons behind them, offering new insights for further rational design towards specific targets

Model Transformations in MT

Model transformations are recognised as a vital aspect of Model Driven Development,but current approaches cover only a small part of the possible spectrum. In this paper I present the MT model transformation which shows how a QVT-like language can be extended with novel pattern matching constructs, how tracing information can be automatically constructed and visualized, and how the transformed model is pruned of extraneous elements. As MT is implemented as a DSL within the Converge language, this paper also demonstrates how a general purpose language can be embedded in a model transformation language, and how DSL development can aid experimentation and exploration of new parts of the model transformation spectrum

Projector - a partially typed language for querying XML

We describe Projector, a language that can be used to perform a mixture of typed and untyped computation against data represented in XML. For some problems, notably when the data is unstructured or semistructured, the most desirable programming model is against the tree structure underlying the document. When this tree structure has been used to model regular data structures, then these regular structures themselves are a more desirable programming model. The language Projector, described here in outline, gives both models within a single partially typed algebra and is well suited for hybrid applications, for example when fragments of a known structure are embedded in a document whose overall structure is unknown. Projector is an extension of ECMA-262 (aka JavaScript), and therefore inherits an untyped DOM interface. To this has been added some static typing and a dynamic projection primitive, which can be used to assert the presence of a regular structure modelled within the XML. If this structure does exist, the data is extracted and presented as a typed value within the programming language

IVOA Recommendation: Universal Worker Service Pattern Version 1.0

The Universal Worker Service (UWS) pattern defines how to manage asynchronous execution of jobs on a service. Any application of the pattern defines a family of related services with a common service contract. Possible uses of the pattern are also described

Supporting process reuse in PROMENADE

Process reuse (the ability to construct new processes by assembling already built ones) and process harvesting (the ability to build generic processes that may be further reused, from existing ones) are two crucial issues in process technology. Both activities involve defining a set of mechanisms, like abstraction, adaptation, composition, etc. which are appropriate to achieve their goals. In this report, we define a general framework to process reuse and harvesting that proposes a complete set of mechanisms to deal with both activities. This general framework is particularized to the context of a process modelling language to model software processes, called PROMENADE. A definition of the identified reuse and harvesting mecha-nisms is proposed in the context of PROMENADE. Finally, two process reuse case studies which composes various reuse mechanisms are presented.Postprint (published version