Sprat: Hierarchies of Domain-Specific Languages for Marine Ecosystem Simulation Engineering

Scientific software is becoming more complex and its development nowadays is often an interdisciplinary process in which usually scientists - most of them without training in software engineering - implement the software themselves. To help them achieve a good code quality, we propose to employ a process called Sprat based on the concept of hierarchies of domain-specific languages (DSLs). In such a hierarchy, every DSL constitutes an implementation platform for the DSL directly above it. Each role in the development process (i.e., a scientist from a specific discipline) implements a layer of the software in a DSL belonging to the hierarchy. Therefore, the scientists only deal with abstractions they are familiar with from their respective domain and a clear separation of components is attained. To evaluate the Sprat approach, we present its application to the development of the Sprat simulation - a marine ecosystem model for long-term fish stock prediction

Hierarchical Combination of Internal and External Domain-Specific Languages for Scientific Computing

To adapt established methods of software engineering for scientific computing, we propose a software development approach for interdisciplinary teams of scientists called Sprat. The approach is organized around a hierarchical architecture that combines internal and external domain-specific languages (DSLs). For its evaluation, Sprat is employed in the implementation of a marine ecosystem model. We highlight what is to be observed while integrating the DSLs into the hierarchy in order to enable a successful cooperation of scientists in interdisciplinary teams as well as to achieve a maintainable code base

Model-Driven Software Engineering for Computational Science Applied to a Marine Ecosystem Model

The ever-increasing complexity of in silico experiments in computational science is reflected in the growing complexity of the simulation software enabling these experiments. However, computational scientists rarely employ state-of-the-art software engineering methods, which negatively affects their productivity as well as the reliability of their scientific results. To tackle this challenge, this book introduces the Sprat Approach, which hierarchically integrates multiple domain-specific languages to facilitate the cooperation of scientists from different disciplines and to support them in creating well-engineered software without extensive software engineering training. To evaluate the Sprat Approach, it is applied to the implementation of the Sprat Marine Ecosystem Model in an exploratory case study. The Sprat Marine Ecosystem Model is a novel end-to-end ecosystem model based on population balance equations. In order to evaluate the Sprat Model, it is parametrized for the eastern Scotian Shelf ecosystem with its intertwined direct and indirect fish stock interactions, which previously could not be modeled satisfactorily. The simulation results described in this book provide new insights into the main drivers of regime shifts in marine ecosystems

OceanTEA: Exploring Ocean-Derived Climate Data Using Microservices

Ocean observation systems gather an increasing amount of climate-relevant time series data. To interactively explore and analyze such high-dimensionaldatasets, we developed the software OceanTEA. Our open-source tool leverages modern web technology to support interactive data visualization, spatial analysis of current patterns, and temporal pattern discovery via machine learning methods. The microservice architecture of OceanTEA ensures a maintainable implementation that seamlessly scales from desktop computers to cloud computing infrastructure

Evaluating Hierarchical Domain-Specific Languages for Computational Science: Applying the Sprat Approach to a Marine Ecosystem Model

In this chapter, we present a Model-Driven Software Engineering (MDSE) approach called Sprat, which adapts traditional software engineering practices in order to employ them in computational science. The approach is based on the hierarchical integration of so-called Domain-Specific Languages (DSLs) to facilitate the collaboration of scientists from different disciplines in the development of complex simulation software. We describe how multiple DSLs can be integrated to achieve a clear separation of concerns among the disciplines and how to apply Sprat during the different phases of the software life cycle. To evaluate our approach, we discuss results from a case study in which Sprat has been utilized for the implementation of a coupled marine ecosystem model for spatially-explicit fish stock prediction. We report on the DSLs developed for this case study, how scientists benefit from them, and on lessons learned. In particular, we analyze the results from expert interviews conducted with both scientists and professional DSL developers

OceanTEA: Exploring Ocean-Derived Climate Data Using Microservices (Poster)

Ocean observation systems gather an increasing amount of climate-relevant time series data. To interactively explore and analyze such high-dimensionaldatasets, we developed the software OceanTEA. Our open-source tool leverages modern web technology to support interactive data visualization, spatial analysis of current patterns, and temporal pattern discovery via machine learning methods. The microservice architecture of OceanTEA ensures a maintainable implementation that seamlessly scales from desktop computers to cloud computing infrastructure

OceanTEA: A Platform for Sharing Oceanographic Data and Analyses

Ocean observation systems, such as Argo floats or the modular ocean laboratory MoLab, produce an increasing amount of time series data. Both, statistical data mining techniques and manual exploration via visualization are necessary for oceanographers to extract scientific knowledge from such vast datasets. Therefore, scientists require a platform to explore and analyze data visually, supporting their collaboration and research. To deliver results and foster the impact of publications, such platform should facilitate automatic and interactive access to research results for scientists, their peers and the public. Our software platform OceanTEA (Oceanographic TimeSeries Exploration and Analysis) supports oceanographers in their research and publication efforts. The platform leverages modern web technology to support the interactive exploration and analysis of high-dimensional datasets. OceanTEA relies on a microservice architecture which can be deployed on desktops and on cloud computing infrastructure

Revision of European Wormaldia species (Trichoptera, Philopotamidae): Chimeric taxa of integrative organisation

We have recognised significant incongruences among the most commonly used taxonomic characters in the European species of Wormaldia genus of the Philopotamidae caddisfly family. During taxonomical analysis and ranking procedures we have recorded incongruent, discorcordant characters also in the taxa in Rhyacophilidae, Hydropsychidae and Limnephilidae caddisfly families. Based on theoretical background we concluded that taxa of examined caddisflies and probably all living creatures are chimeric entities composed of components of different origin. Genomes and phenomes are tree-like on the surface but more reticulated in the deep. We understand chimerism with universal consequences, expanding well beyond the evolutionary tree-thinking of reductionism and determinism. Taxa are chimeric or at least chimerical in a stochastic universe under the permanent fluxes of the external and internal impacts created by intercourses between entropy and energy gradients. We have surveyed how to create and correct synonymies in the splitter/lumper perspectives along the principles of compositional and specification hierarchies understood as quantitative variability of non-adaptive neutral and qualitative stability of adaptive, non-neutral traits. We outlined how the apophantic (declaratory) hybris creates synonymies and underestimates biodiversity. After redrawing the diverging genitalic structures, particularly the speciation traits we have reinstated species status of eight taxa: W. trifida Andersen, 1983 stat.restit, stat. nov., W. albanica Oláh, 2010 stat. restit., W. bulgarica Novak, 1971 stat. nov., W. daga Oláh, 2014 stat. restit., W. graeca Oláh, 2014 stat. restit., W. busa Oláh, 2014 stat. restit., W. homora Oláh, 2014 stat. restit. W. nielseni Moretti, 1981 stat. nov. Character selection and lineage sorting procedures established the following species groups, species complexes and species clades in the European species of Wormaldia: W. occipitalis species group: W. occipitalis species complex; W. charalambi species group; W. copiosa species group; W. triangulifera species group: W. bulgarica species complex, W. khourmai species complex, W. subnigra species complex: W. asterusia species clade, W. subnigra species clade, W. vercorsica species clade; W. triangulifera species complex, W. variegate species complex. Unplaced species: W. ambigua, W. algirica, W. sarda. In this revision we have described fourteen new species: W. longiseta, W. carpathica, W. kurta, W. parba, W. foslana, W. kumanskii, W. libohova, W. silva, W. gorba, W. kera, W. rona, W. sima, W. granada, W. telva.publishedVersio

Dichlorvos exposure impedes extraction and amplification of DNA from insects in museum collections

<p>Abstract</p> <p>Background</p> <p>The insecticides dichlorvos, paradichlorobenzene and naphthalene have been commonly used to eradicate pest insects from natural history collections. However, it is not known how these chemicals affect the DNA of the specimens in the collections. We thus tested the effect of dichlorvos, paradichlorobenzene and naphthalene on DNA of insects (<it>Musca domestica</it>) by extracting and amplifying DNA from specimens exposed to insecticides in two different concentrations over increasing time intervals.</p> <p>Results</p> <p>The results clearly show that dichlorvos impedes both extraction and amplification of mitochondrial and nuclear DNA after relatively short time, whereas paradichlorobenzene and naphthalene do not.</p> <p>Conclusion</p> <p>Collections treated with paradichlorobenzene and naphthalene, are better preserved concerning DNA, than those treated with dichlorvos. Non toxic pest control methods should, however, be preferred due to physical damage of specimens and putative health risks by chemicals.</p

On the Trichoptera of Korea with Eastern Palaearctic relatives

The caddisfly materials collected by Hungarian zoologists during 25 collecting trips between the years of 1970 and 2016 in the Korean Peninsula was identified and compared when required with Eastern Palaearctic relatives. The appen-dicular genital terminology was adopted and applied to several representatives of Polyphorae taxa. We identified 95 caddisfly species, including 5 new records for the Korean Peninsula: Tinodes higashiyamanus Tsuda, 1942, Apatania yenchingensis Ulmer, 1932, Neophylax relictus (Martynov, 1935), Limnephilus quadratus Martynov, 1914, and Hydatophylax soldatovi (Martynov, 1914). We have described the following 12 species new to science: Plectrocnemia ussurica Oláh & Johanson sp. nov. (Russia); Psychomyia tompa Oláh & Johanson sp. nov. (Russia); Psychomyia vandor Oláh & Johanson sp. nov. (Russia); Agapetus vastag Oláh & Johanson sp. nov. (Russia); Agapetus vekon Oláh & Johanson sp. nov. (Russia); Neophylax goguriensis Oláh & Park sp. nov. (North Korea); Neophylax sillensis Park & Oláh sp. nov. (South Korea); Dicosmoecus coreanus Oláh & Park sp. nov. (South Korea); Dicosmoecus juliarum Oláh sp. nov. (Russia); Dicosmoecus mongolicus Oláh sp. nov. (Mongolia); Asynarchus mongolicus Oláh sp. nov. (Mongolia); Psilotreta kerka Oláh sp. nov. (North Korea)