Taverna Workflows: Syntax and Semantics

This paper presents the formal syntax and the operational semantics of Taverna, a workflow management system with a large user base among the e-Science community. Such formal foundation, which has so far been lacking, opens the way to the translation between Taverna workflows and other process models. In particular, the ability to automatically compile a simple domain-specific process description into Taverna facilitates its adoption by e-scientists who are not expert workflow developers. We demonstrate this potential through a practical use case

Towards a Mathematical Operational Semantics

We present a categorical theory of ‘well-behaved’ operational semantics which aims at complementing the established theory of domains and denotational semantics to form a coherent whole. It is shown that, if the operational rules of a programming language can be modelled as a natural transformation of a suitable general form, depending on functorial notions of syntax and behaviour, then one gets the following for free: an operational model satisfying the rules and a canonical, internally fully abstract denotational model which satisfies the operational rules. The theory is based on distributive laws and bialgebras; it specialises to the known classes of well-behaved rules for structural operational semantics, such as GSOS

Abstract Syntax and Variable Binding (Extended Abstract)

We develop a theory of abstract syntax with variable binding. To every binding signature we associate a category of models consisting of variable sets endowed with compatible algebra and substitution structures. The syntax generated by the signature is the initial model. This gives a notion of initial algebra semantics encompassing the traditional one; besides compositionality, it automatically veri- fies the semantic substitution lemma

Development of a PCR assay for the detection of animal tissues in ruminant feeds.

The European Community ban on use of meat and bone meal in ruminant feed, as a consequence of the spread of bovine spongiform encephalopathy in Europe, has prompted a number of investigations about the possibility of detecting animal tissues in feedstuff. In this paper, a study on vertebrate primers, designed in the 16S rRNA gene of mitochondrial DNA, is described. These primers were able to amplify fragments that contained between 234 and 265 bp. The fragments were specific for bovine, porcine, goat, sheep, horse, rabbit, chicken, trout, and European pilchard and were confirmed by sequence analysis amplicons. The primers were used in a PCR assay applied to five samples of meat and blood meals of different species and subjected to severe rendering treatments (134.4 to 141.9 degrees C and 3.03 to 4.03 bar for 24 min). The presence of vertebrate tissues was detected in all samples. The assay proved to be rapid and sensitive (detection limit 0.0625%). It can be used as a routine method to detect animal-derived ingredients in animal feedstuff

Binary and ternary mixed metal complexes of terminally free peptides containing two different histidyl binding sites

Copper(II), nickel(II) and zinc(II) complexes of the terminally free peptides AHAAAHG and AAHAAAHG have been studied by combined applications of potentiometric and various spectroscopic techniques, including UV-visible, CD and EPR for copper(II) and UV-visible, CD and NMR for nickel(II). It was found that the octapeptide AAHAAAHG can easily bind two equivalents of copper(II) or nickel(II) ions and the amino terminus was identified as the primary ligating site of the molecule. On the other hand, this peptide has a relatively low zinc(II) binding affinity. Mono- and di-nuclear copper(II) and nickel(II) complexes were also formed with the heptapeptide AHAAAHG but this peptide can effectively bind one equivalent of zinc(II) ions, too, with the involvement of the deprotonated amide nitrogen in zinc(II) binding. The enhanced stability of the [MH-1L] species of AHAAAHG was explained by the tridentate (NH2,N-,Nim) coordination of the amino terminus supported by the macrochelation of the internal histidyl residue. Mixed metal copper(II)-nickel(II) complexes were also formed with both peptides and copper(II) ions were coordinated to the amino terminal, while nickel(II) ions to the internal histidyl sites. © 2013 Elsevier Inc

Non-Deterministic Kleene Coalgebras

In this paper, we present a systematic way of deriving (1) languages of (generalised) regular expressions, and (2) sound and complete axiomatizations thereof, for a wide variety of systems. This generalizes both the results of Kleene (on regular languages and deterministic finite automata) and Milner (on regular behaviours and finite labelled transition systems), and includes many other systems such as Mealy and Moore machines

Innocent strategies as presheaves and interactive equivalences for CCS

Seeking a general framework for reasoning about and comparing programming languages, we derive a new view of Milner's CCS. We construct a category E of plays, and a subcategory V of views. We argue that presheaves on V adequately represent innocent strategies, in the sense of game semantics. We then equip innocent strategies with a simple notion of interaction. This results in an interpretation of CCS. Based on this, we propose a notion of interactive equivalence for innocent strategies, which is close in spirit to Beffara's interpretation of testing equivalences in concurrency theory. In this framework we prove that the analogues of fair and must testing equivalences coincide, while they differ in the standard setting.Comment: In Proceedings ICE 2011, arXiv:1108.014

Interaction and observation, categorically

This paper proposes to use dialgebras to specify the semantics of interactive systems in a natural way. Dialgebras are a conservative extension of coalgebras. In this categorical model, from the point of view that we provide, the notions of observation and interaction are separate features. This is useful, for example, in the specification of process equivalences, which are obtained as kernels of the homomorphisms of dialgebras. As an example we present the asynchronous semantics of the CCS.Comment: In Proceedings ICE 2011, arXiv:1108.014

The First Provenance Challenge

The first Provenance Challenge was set up in order to provide a forum for the community to help understand the capabilities of different provenance systems and the expressiveness of their provenance representations. To this end, a Functional Magnetic Resonance Imaging workflow was defined, which participants had to either simulate or run in order to produce some provenance representation, from which a set of identified queries had to be implemented and executed. Sixteen teams responded to the challenge, and submitted their inputs. In this paper, we present the challenge workflow and queries, and summarise the participants contributions

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries