@article {RN186, title = {An Object Model for Seafloor Observatory Sensor Control in the East China Sea}, journal = {Journal of Marine Science and Engineering}, volume = {8}, number = {9}, year = {2020}, pages = {716}, type = {Journal Article}, abstract = {Seafloor observatories enable long-term, real-time, and continuous observation that marks a new way for oceanographic measurements. In terms of seafloor observatory research, sensor control is a key issue for the stable and effective operations of functional observatories. In this paper, an object model is proposed to standardize seafloor observatory sensor control and data acquisition. The object model is conceptionally designed as a set of sensor resource objects, based on the attributes and operations of which a client{\textendash}server sensor control architecture is enabled for bidirectional information flow of control commands and observation data. The object model-based architecture is implemented with a prototype control system for plug-and-play enablement. The prototype system was put into a series of tests before applied to the East China Sea Experimental Seafloor Observatory, performing consistently with all the project requirements. Given the successful experiment, the object model design and prototype implementation are feasible to resolve seafloor observatory sensor control and beneficial for ocean observatory sciences.}, keywords = {in situ measurements, object model, seafloor observatories, sensor control}, doi = {10.3390/jmse8090716}, url = {https://app.dimensions.ai/details/publication/pub.1130914583}, author = {Yu, Yang and Xu, Huiping and Xu, Changwei} } @article {RN166, title = {The Virtual Data Collaboratory: A Regional Cyberinfrastructure for Collaborative Data-Driven Research}, journal = {Computing}, volume = {22}, number = {3}, year = {2020}, pages = {79-92}, type = {Journal Article}, abstract = {The Virtual Data Collaboratory is a federated data cyberinfrastructure designed to drive data-intensive, interdisciplinary, and collaborative research that will impact researchers, educators, and entrepreneurs across a broad range of disciplines and domains as well as institutional and geographic boundaries.}, keywords = {big data, Cloud computing, Collaboration, Computer architecture, Education, Software engineering, Virtual reality}, doi = {10.1109/mcse.2019.2908850}, url = {https://app.dimensions.ai/details/publication/pub.1113521625}, author = {Parashar, Manish and Simonet, Anthony and Rodero, Ivan and Ghahramani, Forough and Agnew, Grace and Jantz, Ron and Honavar, Vasant} } @article {RN78, title = {Data Cyber-Infrastructure for End-to-end Science: Experiences from the NSF Ocean Observatories Initiative}, journal = {Computing in Science \& Engineering}, year = {2019}, pages = {1-1}, type = {Journal Article}, abstract = {Large-scale scientific facilities provide a broad community of researchers and educators with open access to instrumentation and data products generated from geographically distributed instruments and sensors. This paper discusses key architectural design, deployment, and operational aspects of a production cyberinfrastructure for the acquisition, processing, and delivery of data from large scientific facilities using experiences from the National Science Foundation{\textquoteright}s Ocean Observatories Initiative. This paper also outlines new models for data delivery and opportunities for insights in a wide range of scientific and engineering domains as the volumes and variety of data from facilities grow.}, keywords = {Cloud computing, Data acquisition, Design methodology, Distributed databases, Information processing, Laboratories, Observatories, Oceanography, US Government}, issn = {1521-9615}, doi = {10.1109/MCSE.2019.2892769}, author = {Rodero, I. and Parashar, M.} } @article {RN83, title = {Open science, reproducibility, and transparency in ecology}, journal = {Ecological Applications}, volume = {29}, number = {1}, year = {2019}, pages = {e01822}, type = {Journal Article}, abstract = {Reproducibility is a key tenet of the scientific process that dictates the reliability and generality of results and methods. The complexities of ecological observations and data present novel challenges in satisfying needs for reproducibility and also transparency. Ecological systems are dynamic and heterogeneous, interacting with numerous factors that sculpt natural history and that investigators cannot completely control. Observations may be highly dependent on spatial and temporal context, making them very difficult to reproduce, but computational reproducibility can still be achieved. Computational reproducibility often refers to the ability to produce equivalent analytical outcomes from the same data set using the same code and software as the original study. When coded workflows are shared, authors and editors provide transparency for readers and allow other researchers to build directly and efficiently on primary work. These qualities may be especially important in ecological applications that have important or controversial implications for science, management, and policy. Expectations for computational reproducibility and transparency are shifting rapidly in the sciences. In this work, we highlight many of the unique challenges for ecology along with practical guidelines for reproducibility and transparency, as ecologists continue to participate in the stewardship of critical environmental information and ensure that research methods demonstrate integrity. Ecologists have long faced a novel challenge not routinely encountered in less field-oriented sciences: repeated testing is fundamental to the scientific method (Popper 1934) yet it is impossible to perfectly repeat observational studies of the natural world (Vanderbilt and Blankman 2017). This issue is timely as scientists across disciplines increasingly recognize the challenges of reproducing published results, and the threats that irreproducible results pose to the scientific process (Munafo et al. 2017). Reproducibility and transparency issues are particularly important for scientists engaged in actionable science and ecological applications; this work often feeds back rapidly and directly on biota, ecosystems, and people who have stakes in conservation or management outcomes, in turn affecting perceptions about the integrity of our field. For ecologists engaged in observational and field-based studies, data are often highly dependent on the spatial and temporal context of the specific system (Huang 2014, Schnitzer and Carson 2016, LaDeau et al. 2017, Peters and Okin 2017). The weather does not recycle itself. Gradual changes over time, regime shifts, and legacies of past events can greatly influence how natural systems work, as well as our perceptions about how they work (Magnuson 1990). With this complexity, ecology has relied on deep understanding of natural history as a source of ideas about pattern and process (Anderson 2017), often through long periods of intensive observation that could be argued as irreproducible. Even if we could bring back our predecessors, many of their study systems now bear little resemblance to earlier states. Such irregularities in the natural world can torment experimental ecologists. Repeated or replicated sequences in time are elusive and, likewise, neighboring populations, communities, or ecosystems observed within the same day or year can still differ in important ways that affect the outcomes of studies. Thus, while broad guidelines for reproducible research in the sciences are available (Sandve et al. 2013), ecologists face novel challenges that complicate adoption of such general practices. These challenges are linked to the heterogeneity of the systems we study, as well as the approaches and information we use. Strategies that increase the reproducibility of ecological studies are being pursued (Milcu et al. 2018) and it is important that ecologists address these issues if we are to continue serving a critical role in understanding the complex dynamics of the biosphere in the Anthropocene. }, issn = {1051-0761}, doi = {10.1002/eap.1822}, url = {https://doi.org/10.1002/eap.1822}, author = {Powers, Stephen M. and Hampton, Stephanie E.} } @article {RN123, title = {A Sensor Web Prototype for Cabled Seafloor Observatories in the East China Sea}, journal = {Journal of Marine Science and Engineering}, volume = {7}, number = {11}, year = {2019}, pages = {414}, type = {Journal Article}, abstract = {Seafloor observatories enable continuous power supply and real-time bidirectional data transmission, which marks a new way for marine environment monitoring. As in situ observation produces massive data in a constant way, the research involved with data acquisition, data transmission, data analysis, and user-oriented data application is vital to the close-loop operations of seafloor observatories. In this paper, we design and implement a sensor web prototype (ESOSW) to resolve seafloor observatory information processing in a plug-and-play way. A sensor web architecture is first introduced, which is information-oriented and structured into four layers enabling bidirectional information flow of observation data and control commands. Based on the layered architecture, the GOE Control Method and the Hot Swapping Interpretation Method are proposed as the plug-and-play mechanism for sensor control and data processing of seafloor observatory networks. ESOSW was thus implemented with the remote-control system, the data management system, and the real-time monitoring system, supporting managed sensor control and on-demand measurement. ESOSW was tested for plug-and-play enablement through a series of trials and was put into service for the East China Sea Seafloor Observation System. The experiment shows that the sensor web prototype design and implementation are feasible and could be a general reference to related seafloor observatory networks.}, keywords = {control systems, data processing, plug-and-play, seafloor observatories, sensor web}, issn = {2077-1312}, doi = {10.3390/jmse7110414}, url = {https://www.mdpi.com/2077-1312/7/11/414}, author = {Yu, Yang and Xu, Huiping and Xu, Changwei} } @article {RN94, title = {Submarine: A subscription-based data streaming framework for integrating large facilities and advanced cyberinfrastructure}, journal = {Concurrency and Computation Practice and Experience}, year = {2019}, pages = {e5256}, type = {Journal Article}, abstract = {Large scientific facilities provide researchers with instrumentation, data, and data products that can accelerate scientific discovery. However, increasing data volumes coupled with limited local computational power prevents researchers from taking full advantage of what these facilities can offer. Many researchers looked into using commercial and academic cyberinfrastructure (CI) to process these data. Nevertheless, there remains a disconnect between large facilities and CI that requires researchers to be actively part of the data processing cycle. The increasing complexity of CI and data scale necessitates new data delivery models, those that can autonomously integrate large-scale scientific facilities and CI to deliver real-time data and insights. In this paper, we present our initial efforts using the Ocean Observatories Initiative project as a use case. In particular, we present a subscription-based data streaming service for data delivery that leverages the Apache Kafka data streaming platform. We also show how our solution can automatically integrate large-scale facilities with CI services for automated data processing.}, doi = {10.1002/cpe.5256}, url = {https://app.dimensions.ai/details/publication/pub.1113381084}, author = {Zamani, Ali Reza and AbdelBaky, Moustafa and Balouek-Thomert, Daniel and Villalobos, J. J. and Rodero, Ivan and Parashar, Manish} } @article {RN144, title = {Towards a computing continuum: Enabling edge-to-cloud integration for data-driven workflows}, journal = {The International Journal of High Performance Computing Applications}, volume = {33}, number = {6}, year = {2019}, pages = {1159-1174}, type = {Journal Article}, abstract = {Dramatic changes in the technology landscape marked by increasing scales and pervasiveness of compute and data have resulted in the proliferation of edge applications aimed at effectively processing data in a timely manner. As the levels and fidelity of instrumentation increases and the types and volumes of available data grow, new classes of applications are being explored that seamlessly combine real-time data with complex models and data analytics to monitor and manage systems of interest. However, these applications require a fluid integration of resources at the edge, the core, and along the data path to support dynamic and data-driven application workflows, that is, they need to leverage a computing continuum. In this article, we present our vision for enabling such a computing continuum and specifically focus on enabling edge-to-cloud integration to support data-driven workflows. The research is driven by an online data-driven tsunami warning use case that is supported by the deployment of large-scale national environment observation systems. This article presents our overall approach as well as current status and next steps.}, keywords = {Continuum computing, data-driven workflows, edge-to-cloud integration, programming systems, streaming data-analytics}, doi = {10.1177/1094342019877383}, url = {https://app.dimensions.ai/details/publication/pub.1121117342}, author = {Balouek-Thomert, Daniel and Renart, Eduard Gibert and Zamani, Ali Reza and Simonet, Anthony and Parashar, Manish} } @article {RN93, title = {Autonomous Data Collection Using a Self-Organizing Map}, volume = {29}, number = {5}, year = {2018}, pages = {1703-1715}, type = {Journal Article}, abstract = {The self-organizing map (SOM) is an unsupervised learning technique providing a transformation of a high-dimensional input space into a lower dimensional output space. In this paper, we utilize the SOM for the traveling salesman problem (TSP) to develop a solution to autonomous data collection. Autonomous data collection requires gathering data from predeployed sensors by moving within a limited communication radius. We propose a new growing SOM that adapts the number of neurons during learning, which also allows our approach to apply in cases where some sensors can be ignored due to a lower priority. Based on a comparison with available combinatorial heuristic algorithms for relevant variants of the TSP, the proposed approach demonstrates improved results, while also being less computationally demanding. Moreover, the proposed learning procedure can be extended to cases where particular sensors have varying communication radii, and it can also be extended to multivehicle planning.}, keywords = {Data collection, Neurons, Planning, Robot sensing systems, Urban areas}, doi = {10.1109/tnnls.2017.2678482}, url = {https://app.dimensions.ai/details/publication/pub.1084207070}, author = {Faigl, Jan and Hollinger, Geoffrey A.} } @article {RN220, title = {SIDEBAR Accessing OOI Data}, journal = {Oceanography}, volume = {31}, number = {1}, year = {2018}, pages = {36-37}, type = {Journal Article}, issn = {1042-8275}, doi = {10.5670/oceanog.2018.106}, author = {Vardaro, M. F. and McDonnell, J.} } @article {RN221, title = {SIDEBAR SeaView: Bringing Together an Ocean of Data}, journal = {Oceanography}, volume = {31}, number = {1}, year = {2018}, pages = {71-71}, type = {Journal Article}, abstract = {The Ocean Observatories Initiative (OOI) supports a comprehensive information management system for data collected by OOI assets, providing access to a wealth of new information for scientists. But what of those wishing to access data from the region of an OOI research array that is not from OOI assets, perhaps to look at longer term trends from before the launch of OOI, or to build a larger regional context? Despite the excellent work of ocean data repositories, finding, accessing, understanding, and reformatting data for use in a desired visualization or analysis tool remains challenging, especially when data are held in multiple repositories.}, issn = {1042-8275}, doi = {10.5670/oceanog.2018.111}, author = {Stocks, K. and Diggs, S. and Olson, C. and Pham, A. and Arko, R. and Shepherd, A. and Kinkade, D.} } @article {RN49, title = {Monitoring networks through multiparty session types}, journal = {Theoretical Computer Science}, volume = {669}, year = {2017}, pages = {33-58}, type = {Journal Article}, abstract = {In large-scale distributed infrastructures, applications are realised through communications among distributed components. The need for methods for assuring safe interactions in such environments is recognized, however the existing frameworks, relying on centralised verification or restricted specification methods, have limited applicability. This paper proposes a new theory of monitored π-calculus with dynamic usage of multiparty session types (MPST), offering a rigorous foundation for safety assurance of distributed components which asynchronously communicate through multiparty sessions. Our theory establishes a framework for semantically precise decentralised run-time enforcement and provides reasoning principles over monitored distributed applications, which complement existing static analysis techniques. We introduce asynchrony through the means of explicit routers and global queues, and propose novel equivalences between networks, that capture the notion of interface equivalence, i.e. equating networks offering the same services to a user. We illustrate our static-dynamic analysis system with an ATM protocol as a running example and justify our theory with results: satisfaction equivalence, local/global safety and transparency, and session fidelity.}, keywords = {Global Type, Local Type, Partial Network, Satisfaction Relation, Session Type}, issn = {0304-3975}, doi = {10.1016/j.tcs.2017.02.009}, url = {://WOS:000397690600003}, author = {Bocchi, L. and Chen, T. C. and Demangeon, R. and Honda, K. and Yoshida, N.} } @article {RN53, title = {Characterizing Complex Marine Systems and Technology Using Visualized Vocabularies}, journal = {Marine Technology Society Journal}, volume = {49}, number = {4}, year = {2015}, pages = {53-63}, type = {Journal Article}, abstract = {The next decade will usher in significant changes in ocean observational infrastructure and how students engage with marine sciences content. Faced with the challenge of helping undergraduate students make sense of very complicated marine systems, a computer sciences-based organizational structure (i.e., ontology) has been employed to characterize the Ocean Observatories Initiative (OOI). Five interlinked vocabularies that include terms, descriptions, and images define the overall system from high-level science themes to specialized data products. Given the importance of visual representations in learning, particularly for novices, an associated interactive tool called the {\textquotedblleft}Vocabulary Navigator{\textquotedblright} has been developed. Created in tandem, the design of the vocabularies and their visualizer is based on principles related to the needs of the target audience such as placing information in a broader context and promoting self-directed discovery. Overall, this effort has resulted in not only innovative online resources for learning about the OOI but also, perhaps more importantly, valuable {\textquotedblleft}lessons learned{\textquotedblright} and transferable software that could be used by other marine technology endeavors. }, keywords = {marine technology, ocean observing, ontology, vocabulary}, issn = {0025-3324}, doi = {10.4031/Mtsj.49.4.2}, url = {://WOS:000361344000010}, author = {deCharon, A. and Smith, L. M. and Companion, C.} } @article {RN54, title = {Practical interruptible conversations: distributed dynamic verification with multiparty session types and Python}, journal = {Formal Methods in System Design}, volume = {46}, number = {3}, year = {2015}, pages = {197-225}, type = {Journal Article}, abstract = {The rigorous and comprehensive verification of communication-based software is an important engineering challenge in distributed systems. Drawn from our industrial collaborations (Ocean Observatories Initative, http://www.oceanobservatories.org/, JBoss Savara Project, http://www.jboss.org/savara) on Scribble, a choreography description language based on multiparty session types, and its theoretical foundations (Honda et al., in POPL, pp 273{\textendash}284, 2008), this article proposes a dynamic verification framework for structured interruptible conversation programming. We first present our extension of Scribble to support the specification of asynchronously interruptible conversations. We then implement a concise API for conversation programming with interrupts in Python that enables session types properties to be dynamically verified for distributed processes. Finally, we expose the underlying theory of our interrupt mechanism, studying its syntax and semantics, its integration in MPST theory and proving the correctness of our design. Our framework ensures the global safety of a system in the presence of asynchronous interrupts through independent runtime monitoring of each endpoint, checking the conformance of the local execution trace to the specified protocol. The usability of our framework for describing and verifying choreographic communications has been tested by integration into the large scientific cyberinfrastructure developed by the Ocean Observatories Initiative. Asynchronous interrupts have proven expressive enough to represent and verify their main classes of communication patterns, including asynchronous streaming and various timeout-based protocols, without introducing any implicit synchronisations. Benchmarks show conversation programming and monitoring can be realised with little overhead.}, keywords = {Distributed systems, Python, Runtime monitoring, Session types}, issn = {0925-9856}, doi = {10.1007/s10703-014-0218-8}, url = {://WOS:000360940700001}, author = {Demangeon, R. and Honda, K. and Hu, R. and Neykova, R. and Yoshida, N.} } @article {RN55, title = {Globally Governed Session Semantics}, journal = {Logical Methods in Computer Science}, volume = {10}, number = {4}, year = {2014}, type = {Journal Article}, abstract = {This paper proposes a bisimulation theory based on multiparty session types where a choreography specification governs the behaviour of session typed processes and their observer. The bisimulation is defined with the observer cooperating with the observed process in order to form complete global session scenarios and usable for proving correctness of optimisations for globally coordinating threads and processes. The induced bisimulation is strictly more fine-grained than the standard session bisimulation. The difference between the governed and standard bisimulations only appears when more than two interleaved multiparty sessions exist. This distinct feature enables to reason real scenarios in the large-scale distributed system where multiple choreographic sessions need to be interleaved. The compositionality of the governed bisimilarity is proved through the soundness and completeness with respect to the governed reduction-based congruence. Finally, its usage is demonstrated by a thread transformation governed under multiple sessions in a real usecase in the large-scale cyberinfrustracture.}, issn = {1860-5974}, doi = {10.2168/Lmcs-10(4:20)2014}, url = {://WOS:000350399900021}, author = {Kouzapas, D. and Yoshida, N.} } @article {RN58, title = {Parameterised Multiparty Session Types}, journal = {Logical Methods in Computer Science}, volume = {8}, number = {4}, year = {2012}, type = {Journal Article}, abstract = {For many application-level distributed protocols and parallel algorithms, the set of participants, the number of messages or the interaction structure are only known at run-time. This paper proposes a dependent type theory for multiparty sessions which can statically guarantee type-safe, deadlock-free multiparty interactions among processes whose specifications are parameterised by indices. We use the primitive recursion operator from G{\"o}del{\textquoteright}s System T to express a wide range of communication patterns while keeping type checking decidable. To type individual distributed processes, a parameterised global type is projected onto a generic generator which represents a class of all possible end-point types. We prove the termination of the type-checking algorithm in the full system with both multiparty session types and recursive types. We illustrate our type theory through non-trivial programming and verification examples taken from parallel algorithms and Web services usecases. }, keywords = {Computer Science, D.1.3, F.1.1, F.1.2, F.3.3, Logic in Computer Science}, issn = {1860-5974}, doi = {10.2168/Lmcs-8(4:6)2012}, url = {://WOS:000315381600008}, author = {Denielou, P. M. and Yoshida, N. and Bejleri, A. and Hu, R.} } @article {RN236, title = {Everything, everywhere}, journal = {Nature}, volume = {440}, number = {7083}, year = {2006}, pages = {402-405}, type = {Journal Article}, abstract = {Tiny computers that constantly monitor ecosystems, buildings and even human bodies could turn science on its head. Declan Butler investigates.}, issn = {0028-0836}, doi = {10.1038/440402a}, author = {Butler, D.} } @article {RN237, title = {Oceanography: All wired up}, journal = {Nature}, volume = {427}, number = {6969}, year = {2004}, pages = {10-12}, type = {Journal Article}, abstract = {The ocean floor is being covered with remote-controlled observatories, letting oceanographers keep tabs on the sea without getting wet. Jon Copley investigates.}, issn = {0028-0836}, doi = {10.1038/427010a}, author = {Copley, J.} }