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The protein classification workflow described in this report enables users to get information about a novel protein sequence automatically. The information is derived by different bioinformatic analysis tools which calculate or predict features of a protein sequence. Also, databases are used to compare the novel sequence with known proteins.
Lessons Learned
(2014)
This chapter summarizes the experience and the lessons we learned concerning the application of the jABC as a framework for design and execution of scientific workflows. It reports experiences from the domain modeling (especially service integration) and workflow design phases and evaluates the resulting models statistically with respect to the SIB library and hierarchy levels.
The Course's SIB Libraries
(2014)
This chapter gives a detailed description of the service framework underlying all the example projects that form the foundation of this book. It describes the different SIB libraries that we made available for the course “Process modeling in the natural sciences” to provide the functionality that was required for the envisaged applications. The students used these SIB libraries to realize their projects.
A major part of the scientific experiments that are carried out today requires thorough computational support. While database and algorithm providers face the problem of bundling resources to create and sustain powerful computation nodes, the users have to deal with combining sets of (remote) services into specific data analysis and transformation processes. Today’s attention to “big data” amplifies the issues of size, heterogeneity, and process-level diversity/integration. In the last decade, especially workflow-based approaches to deal with these processes have enjoyed great popularity. This book concerns a particularly agile and model-driven approach to manage scientific workflows that is based on the XMDD paradigm. In this chapter we explain the scope and purpose of the book, briefly describe the concepts and technologies of the XMDD paradigm, explain the principal differences to related approaches, and outline the structure of the book.
We summarize here the main characteristics and features of the jABC framework, used in the case studies as a graphical tool for modeling scientific processes and workflows. As a comprehensive environment for service-oriented modeling and design according to the XMDD (eXtreme Model-Driven Design) paradigm, the jABC offers much more than the pure modeling capability. Associated technologies and plugins provide in fact means for a rich variety of supporting functionality, such as remote service integration, taxonomical service classification, model execution, model verification, model synthesis, and model compilation. We describe here in short both the essential jABC features and the service integration philosophy followed in the environment. In our work over the last years we have seen that this kind of service definition and provisioning platform has the potential to become a core technology in interdisciplinary service orchestration and technology transfer: Domain experts, like scientists not specially trained in computer science, directly define complex service orchestrations as process models and use efficient and complex domain-specific tools in a simple and intuitive way.
It has been long agreed by formal and functional researchers (primarily based on English data) that contrastive topic marking, namely marking a constituent as a contrastive topic via the B-accent/the rising intonation contour) requires the co-occurrence of focus marking via the A-accent/the falling intonation contour (see Sturgeon 2006, and references therein). However, this consensus has recently been disputed by new findings indicating the occurrence of utterances with only B-accent, dubbed as lone contrastive topic (Büring 2003, Constant 2014). In this paper, I argue, based on the data in Vietnamese, that the presence of lone contrastive topic is just apparent, and that the focus that co-occurs with the seemingly lone contrastive topic is a verum focus.
Singular quantified terms
(2016)
In this paper, I discuss the behavior of singular partitives, focusing on Hebrew. I show that group noun-headed singular quantified terms behave essentially different from other singular quantified terms. Specifically, the domain of quantification in the former is a discrete set (the members of the group), while in the latter the domain of quantification is a set of mass entities. I propose a preliminary analysis of singular quantified terms in Hebrew, respecting the properties peculiar to this language as well as the observations about group vs. non-group singular quantified terms. This analysis is based on a novel class of quantifiers I name ’Measure Quantifiers’, which instantiate relations between algebraic sums. Using shifts between algebraic sums, we can represent the different readings of singular and plural individual or group terms.
This paper investigates an unnoticed difference in Mandarin between the Q-adjectives and the gradable adjectives of quality and shows that this observation follows straightforwardly from a theory that differentiates gradable predication of quantity and that of quality (e.g., Rett 2008; Lin 2014; Solt 2015; a.o.).
Recent work in semantics has shown that languages can vary in whether or not they include degrees (that is, elements of type < d >) in their semantic ontology. Several authors have argued that their languages of study lack degrees, including Bochnak (2013) for Washo (isolate, USA), Pearson (2009) for Fijian (Austronesian, Fiji), and Beck, et al. (2009) for Motu (Austronesian, Papua New Guinea). In this paper, I follow the tests proposed in Beck, et al. (2009) to assess the status of degrees in Warlpiri (Pama-Nyungan, Australia).
I use Warlpiri data collected following the Beck, et al. survey to argue that Warlpiri gradable predicates do not combine with a degree argument. (Like many other Australian languages, adjectival concepts like big and small are expressed using nouns in Warlpiri (Dixon 1982, Bittner & Hale 1995, among others). I refer to these lexical items as “gradable predicates” in this paper.) This paper represents a first pass at assessing the status of degrees in an Australian language, which have otherwise been unexamined from the point of view of degree semantics.
Theses
(2016)