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Graincast™: monitoring crop production across the Australian grainbelt

CROP & PASTURE SCIENCE 2023年第6期74卷 509-523页

作者： Lawes, R. Hochman, Z. Jakku, E. Butler, R. Chai, J. Chen, Y. Waldner, F. Mata, G. Donohue, R. CSIRO Agr & Food 147 Underwood Ave Floreat WA 6014 Australia CSIRO Agr & Food 306 Carmody Rd St Lucia Qld 4067 Australia CSIRO Land & Water 306 Carmody Rd St Lucia Qld 4067 Australia CSIRO Data61 315 Brunswick St Fortitude Valley Qld 4006 Australia CSIRO Data61 26 Dick Perry Ave Kensington WA 6151 Australia CSIRO Data61 34 Village St Docklands Vic 3008 Australia European Commiss Joint Res Ctr Food Secur I-21027 Ispra Varese Italy CSIRO Land & Water GPO Box 1700 Canberra ACT 2061 Australia

The Australian dryland grain-cropping landscape occupies 60 Mha. The broader agricultural sector (farmers and agronomic advisors, grain handlers, commodity forecasters, input suppliers, insurance providers) required information at many spatial and temporal scales. Temporal scales included hindcasts, nowcasts and forecasts, at spatial scales ranging from sub-field to the continent. International crop-monitoring systems could not service the need of local industry for digital information on crop production estimates. Therefore, we combined a broad suite of satellite-based crop-mapping, crop-modelling and data-delivery techniques to create an integrated analytics system (Graincast (TM)) that covers the Australian cropping landscape. In parallel with technical developments, a set of user requirements was identified through a human-centred design process, resulting in an end-product that delivered a viable crop-monitoring service to industry. This integrated analytics solution can now produce crop information at scale and on demand and can deliver the output via an application programming interface. The technology was designed to underpin digital agriculture developments for Australia. End-users are now using crop-monitoring data for operational purposes, and we argue that a vertically integrated data supply chain is required to develop crop-monitoring technology further.

关键词： application programming interface big data analytics crop modelling integrated land management land use mapping participatory research remote sensing user centred design

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Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective

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BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014年第1期1844卷 63-76页

作者： Perez-Riverol, Yasset Wang, Rui Hermjakob, Henning Mueller, Markus Vesada, Vladimir Vizcaino, Juan Antonio European Bioinformat Inst EMBL Outstn Cambridge CB10 1SD England Ctr Genet Engn & Biotechnol Dept Prote Havana Cuba CMU Swiss Inst Bioinformat Proteome Informat Grp CH-1211 Geneva Switzerland

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. (C) 2013 Elsevier B.V. All rights reserved.

关键词： Proteomics Databases Bioinformatics Software libraries application programming interface Open source software

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Evaluating client application status for V-World Open API service

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SPATIAL INFORMATION RESEARCH 2016年第4期24卷 367-376页

作者： Jang, Han-sol Kim, Dong-kyu Kim, Jung-min Jang, In-sung ICTWAY IT Res Lab Seoul South Korea SNA Global Mkt Dept Seoul South Korea ETRI Spatial Informat Technol Res Team Daejeon South Korea

Since the V-World, the spatial information open platform service, has introduced to public in 2012, V-World users have been continuously increased. Specifically, V-World provides Open API to public institution and various enterprises. Responding to the future demands and expanding the V-World's services systematically, it is necessary to understand specific status of the public users' applied fields and top contents in order to predict the future demands and to enhance the service efficiency. In this paper, we verified V-World's applied fields and top contents based on web server logs which collected from 16 different web servers in May 2015, we evaluated the status of V-World's usage and suggested further considerations for the future service and expansion of the Open API.

关键词： Client application status application programming interface Spatial information open platform V-World

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Fast extraction of high-quality framework-specific models from application code

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AUTOMATED SOFTWARE ENGINEERING 2009年第1期16卷 101-144页

作者： Antkiewicz, Michal Bartolomei, Thiago Tonelli Czarnecki, Krzysztof Univ Waterloo Generat Software Dev Lab Waterloo ON N2L 3G1 Canada

Framework-specific models represent the design of application code from the framework viewpoint by showing how framework-provided concepts are instantiated in the code. Retrieving such models quickly and precisely is necessary for practical model-supported software engineering, in which developers use design models for development tasks such as code understanding, verifying framework usage rules, and round-trip engineering. Also, comparing models extracted at different times of the software lifecycle supports software evolution tasks. We describe an experimental study of the static analyses necessary to automatically retrieve framework-specific models from application code. We reverse engineer a number of applications based on three open-source frameworks and evaluate the quality of the retrieved models. The models are expressed using framework-specific modeling languages (FSMLs), each designed for an open-source framework. For reverse engineering, we use prototype implementations of the three FSMLs. Our results show that for the considered frameworks and a large body of application code rather simple code analyses are sufficient for automatically retrieving framework-specific models with high precision and recall. Based on the initial results, we refine the static analyses and repeat the study on a larger set of applications to provide more evidence and confirm the results. The refined static analyses provide precision and recall of close to 100% for the analyzed applications.

关键词： Reverse engineering Framework-specific models Framework-specific modeling languages Static analysis Object-oriented frameworks application programming interface API

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Designing sea ice web APIs for ice information services

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EARTH SCIENCE INFORMATICS 2015年第3期8卷 483-497页

作者： Liu, Xintao Li, Songnian Huang, Wei Gong, Jun Ryerson Univ Dept Civil Engn Toronto ON M5B 2K3 Canada Jiangxi Normal Univ Sch Software Nanchang 330022 Peoples R China

Due to climate change and global warming, sea ice studies have recently gained more and more attention from various fields. Despite previous work on sea ice data collection, digitalization and dissemination over the web, efficient sharing of ice data and information remains unsolved. Further, little has been done on analyzing specific sea ice data user requirements and developing flexible web-based processing and analytical services based on existing studies, which are useful for both sea ice and non-sea-ice data users. In this paper, we aim to develop a series of Google Maps-like sea ice web application programming interfaces (API) for JavaScript, which provide a flexible and easy-to-use way to enable online sea ice data sharing, visualization and spatio-temporal analyses. We identify sea ice data user requirements at different levels through investigating a group of interested Canadian northerners, and then we design and implement an online sea ice web APIs prototype. We also provide a web tool for registering and sharing other ice web services and an online web coding and debugging sandbox to facilitate and attract more sea ice users and developers. We believe this work will be a good example and potentially benefit the development of web APIs for sea ice data and information services as well as other relevant studies.

关键词： Sea ice Web application programming interface Sharing Service Climate

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An intelligent listening framework for capturing encounter notes from a doctor-patient dialog

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BMC MEDICAL INFORMATICS AND DECISION MAKING 2009年第1期9卷 1-10页

作者： Klann, Jeffrey G. Szolovits, Peter Regenstrief Inst Hlth Care Indianapolis IN 46202 USA Indiana Univ Indianapolis IN 46202 USA MIT Comp Sci & Artificial Intelligence Lab Clin Decis Making Grp Cambridge MA 02139 USA

Background: Capturing accurate and machine-interpretable primary data from clinical encounters is a challenging task, yet critical to the integrity of the practice of medicine. We explore the intriguing possibility that technology can help accurately capture structured data from the clinical encounter using a combination of automated speech recognition (ASR) systems and tools for extraction of clinical meaning from narrative medical text. Our goal is to produce a displayed evolving encounter note, visible and editable (using speech) during the encounter. Results: This is very ambitious, and so far we have taken only the most preliminary steps. We report a simple proof-of-concept system and the design of the more comprehensive one we are building, discussing both the engineering design and challenges encountered. Without a formal evaluation, we were encouraged by our initial results. The proof-of-concept, despite a few false positives, correctly recognized the proper category of single- and multi-word phrases in uncorrected ASR output. The more comprehensive system captures and transcribes speech and stores alternative phrase interpretations in an XML-based format used by a text-engineering framework. It does not yet use the framework to perform the language processing present in the proof-of-concept. Conclusion: The work here encouraged us that the goal is reachable, so we conclude with proposed next steps. Some challenging steps include acquiring a corpus of doctor-patient conversations, exploring a workable microphone setup, performing user interface research, and developing a multi-speaker version of our tools.

关键词： application programming interface Automate Speech Recognition Clinical Encounter Computerize Physician Order Entry Automate Speech Recognition System

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PathwayVoyager: pathway mapping using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database

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BMC GENOMICS 2005年第1期6卷 1-7页

作者： Altermann, E Klaenhammer, TR N Carolina State Univ Dept Food Sci Raleigh NC 27695 USA

Background: Equally important and challenging as genome annotation, is the subsequent classification of predicted genes into their respective pathways. The Kyoto Encyclopedia of Genes and Genomes ( KEGG) represents a database consisting of known genes and their respective biochemical functionalities. Although accessible online, analyses of multiple genes are time consuming and are not suitable for analyzing data sets that are proprietary. Results: Presented here is a new software solution that utilizes the KEGG online database for pathway mapping of partial and whole prokaryotic genomes. PathwayVoyager retrieves user defined subsets of the KEGG database and stores the data as local, blast- formatted databases. Previously selected datasets can be re- used, reducing run- time significantly. Whole or partial genomes can be automatically analyzed using NCBI's BlastP algorithm and ORFs with similarities below the user- defined threshold will be marked on pathway maps. Multiple gene hits are sorted by similarity. Since no sequence information is transmitted over the Internet, PathwayVoyager is an ideal solution for pathway mapping and reconstruction of confidential DNA sequence data. Conclusion: PathwayVoyager represents an alternative approach to many already existing, more complex pathway reconstructions software solutions. This software does not require any dedicated hardware or software and is flexible and straightforward to use. It is ideally suited for environments where analyses on variable datasets are desired.

关键词： application programming interface Pathway Mapping Triosephosphate Isomerase Pathway Reconstruction Dedicated Hardware

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OpenFDA: an innovative platform providing access to a wealth of FDA's publicly available data

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JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 2016年第3期23卷 596-600页

作者： Kass-Hout, Taha A. Xu, Zhiheng Mohebbi, Matthew Nelsen, Hans Baker, Adam Levine, Jonathan Johanson, Elaine Bright, Roselie A. US FDA Silver Spring MD USA Iodine Inc 34 Clyde St San Francisco CA 94107 USA

Objective The objective of openFDA is to facilitate access and use of big important Food and Drug Administration public datasets by developers, researchers, and the public through harmonization of data across disparate FDA datasets provided via application programming interfaces (APIs). Materials and Methods Using cutting-edge technologies deployed on FDA's new public cloud computing infrastructure, openFDA provides open data for easier, faster (over 300 requests per second per process), and better access to FDA datasets;open source code and documentation shared on GitHub for open community contributions of examples, apps and ideas;and infrastructure that can be adopted for other public health big data challenges. Results Since its launch on June 2, 2014, openFDA has developed four APIs for drug and device adverse events, recall information for all FDA-regulated products, and drug labeling. There have been more than 20 million API calls (more than half from outside the United States), 6000 registered users, 20,000 connected Internet Protocol addresses, and dozens of new software (mobile or web) apps developed. A case study demonstrates a use of openFDA data to understand an apparent association of a drug with an adverse event. Conclusion With easier and faster access to these datasets, consumers worldwide can learn more about FDA-regulated products.

关键词： openFDA drug safety adverse event API application programming interface open data open source

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A high performance message-passing system for network of workstations

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JOURNAL OF SUPERCOMPUTING 1997年第2期11卷 159-179页

作者： Park, SY Hariri, S Department of Electrical Engineering and Computer Science Syracuse University Syracuse

With the proliferation of Network of Workstations (NOW) environment, there has been a great demand for a high performance message-passing system to implement High Performance Distributed Computing (HPDC) applications over NOW environment. NYNET (ATM wide area network testbed in New York state) Communication System (NCS) is a multithreaded message-passing system developed at Syracuse University that provides low-latency and high-throughput communication services over the Asynchronous Transfer Mode (ATM) based HPDC environment. NCS provides High Performance application Communication interface (HPI) to support applications that demand high-throughput and low-latency communication services. This paper outlines the general architecture of NCS and presents the implementation approach of NCS HPI over an ATM network. This interface has been developed by modifying Fore Systems' ATM application programming interface (API) and its device driver. NCS HPI uses read/write trap routines to bypass traditional operating system calls and kernel-level communication interface (e.g., UNIX System V Streams). It reduces latency, data transfer time, and avoid using traditional communication protocols (e.g., TCP/IP). This substantially improves the communication performance.

关键词： application programming interface message-passing tool ATM Network of Workstations multithreading High Performance Distributed Computing

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Conceptualizing a Genomics Software Institute (GSI)

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STANDARDS IN GENOMIC SCIENCES 2012年第1期6卷 136-144页

作者： Gilbert, Jack A. Catlett, Charlie Desai, Narayan Knight, Rob White, Owen Robbins, Robert Sankaran, Rajesh Sansone, Susanna-Assunta Field, Dawn Meyer, Folker Argonne Natl Lab Argonne IL 60439 USA Univ Chicago Dept Ecol & Evolut Chicago IL 60637 USA Univ Chicago Computat Inst Chicago IL 60637 USA Univ Colorado Dept Chem & Biochem Boulder CO 80309 USA Univ Colorado Howard Hughes Med Inst Boulder CO 80309 USA Univ Maryland Sch Med Inst Genome Sci Baltimore MD 21201 USA Univ Calif San Diego La Jolla CA 92093 USA Univ Oxford Oxford E Res Ctr Oxford England NERC Ctr Ecol & Hydrol Wallingford Oxon England

Microbial ecology has been enhanced greatly by the ongoing 'omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time;indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation;data and results validation, curation, and search;application programming interfaces for modeling and analysis tools;and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI).

关键词： Microbial Community application programming interface Microbial Ecosystem Genomic Standard Consortium Life Science Community

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