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Toward Open and Reproducible Environmental Modeling by Integrating Online Data Repositories, Computational Environments, and Model Application Programming Interfaces

Young-Don Choi, Jonathan L. Goodall, Jeffrey M. Sadler, Anthony M. Castronova, Andrew Bennett, Zhiyu Li, Bart Nijssen, Shaowen Wang, Martyn P. Clark, Daniel P. Ames, Jeffery S. Horsburgh, Hong Yi (+4 others)
2020 Environmental Modelling & Software  
Recent efforts toward this goal have focused on advancing online repositories for data and model sharing, online computational environments along with containerization technology and notebooks for capturing  ...  reproducible computational studies, and Application Programming Interfaces (APIs) for simulation models to foster intuitive programmatic control.  ...  Acknowledgment This work was supported by the National Science Foundation under collaborative grants OAC-1664061, OAC-1664018, OAC-1664119, ICER-1928369, and ICER-1928315.  ... 
doi:10.1016/j.envsoft.2020.104888 fatcat:qkatdewc2zbftffckss6gsvp2e

Computing environments for reproducibility: Capturing the "Whole Tale"

Adam Brinckman, Kyle Chard, Niall Gaffney, Mihael Hategan, Matthew B. Jones, Kacper Kowalik, Sivakumar Kulasekaran, Bertram Ludäscher, Bryce D. Mecum, Jarek Nabrzyski, Victoria Stodden, Ian J. Taylor (+2 others)
2018 Future generations computer systems  
Acknowledgments This research was supported by NSF, United States grant 1541450 (CC*DNI DIBBS: Merging Science and Cyberinfrastructure Pathways: The Whole Tale).  ...  Its primary interface is a web-based application that allows users to manage data; create, modify, and share frontends for analyzing data; and create, publish, and reproduce tales by linking together datasets  ...  For example, the Wolfram Data Repository [82] provides tight coupling with the Wolfram programming environment for analyzing and visualizing hosted data.  ... 
doi:10.1016/j.future.2017.12.029 fatcat:quttkpfzkfamrlapqj4c7ykk64

Computing Environments for Reproducibility: Capturing the "Whole Tale" [article]

Adam Brinckman, Kyle Chard, Niall Gaffney, Mihael Hategan, Matthew B. Jones, Kacper Kowalik, Sivakumar Kulasekaran, Bertram Ludäscher, Bryce D. Mecum, Jarek Nabrzyski, Victoria Stodden, Ian J. Taylor (+1 others)
2018 arXiv   pre-print
The act of sharing scientific knowledge is rapidly evolving away from traditional articles and presentations to the delivery of executable objects that integrate the data and computational details (e.g  ...  The Whole Tale project aims to address these barriers by connecting computational, data-intensive research efforts with the larger research process--transforming the knowledge discovery and dissemination  ...  Acknowledgments This research was supported by NSF grant 1541450: CC*DNI DIBBS: Merging Science and Cyberinfrastructure Pathways: The Whole Tale.  ... 
arXiv:1805.00400v1 fatcat:xluy3bo3xzav3eoyetu34a2egy

Towards fast prototyping of cloud-based environmental decision support systems for environmental scientists using R Shiny and Docker

Yu Li
2020 Environmental Modelling & Software  
Environmental decision support systems (EDSS) have drawn an increasing attention among scientists to tackle with the growing complexity of environmental problems and to support policy makers.  ...  A public repository is created to promote access to more examples from literature, which users can adapt for their own studies.  ...  We also thank the developers of open-source ShinyProxy and other Docker-based software used in this work.  ... 
doi:10.1016/j.envsoft.2020.104797 fatcat:e5pkv7waobfljgf7cteopqt35q

Using R in hydrology: a review of recent developments and future directions

Louise J. Slater, Guillaume Thirel, Shaun Harrigan, Olivier Delaigue, Alexander Hurley, Abdou Khouakhi, Ilaria Prosdocimi, Claudia Vitolo, Katie Smith
2019 Hydrology and Earth System Sciences  
illustrate how to use packages); the role of integrated development environments (IDEs); and the challenges of big data and parallel computing in hydrology.  ...  </strong> The open-source programming language R has gained a central place in the hydrological sciences over the last decade, driven by the availability of diverse hydro-meteorological data archives and  ...  This paper was edited by Erwin Zehe and reviewed by Michael Stoelzle and two anonymous referees.  ... 
doi:10.5194/hess-23-2939-2019 fatcat:xhpmac63w5dk7cbd4nengojpwq

The Latin American Giant Observatory: A Successful Collaboration in Latin America Based on Cosmic Rays and Computer Science Domains

H. Asorey, L.A. Nunez, M. Suarez-Duran, L.A. Torres-Nino, M. Rodriguez-Pascual, A.J. Rubio-Montero, R. Mayo-Garcia
2016 2016 16th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)  
Metadata, Permanent Identifiers and the facilities from the LAGO Data Repository are described in this work jointly with the simulation codes used.  ...  With regard to the huge amount of data emerging from this network of sensors and from the computational simulations performed in a diversity of computing architectures and e-infrastructures, an effort  ...  In other words: user identification; execution of distributed applications with a simple web interface; usage of Open Access Document Repositories and Data Repositories; and reproducibility of the experiments  ... 
doi:10.1109/ccgrid.2016.110 dblp:conf/ccgrid/AsoreyNSTPRG16 fatcat:7edzt52e6rgsfass7vldtknczm

Web technologies for environmental Big Data

Claudia Vitolo, Yehia Elkhatib, Dominik Reusser, Christopher J.A. Macleod, Wouter Buytaert
2015 Environmental Modelling & Software  
Recent evolutions in computing science and web technology provide the environmental community with continuously expanding resources for data collection and analysis that pose unprecedented challenges to  ...  for processing large and heterogeneous datasets and discuss their relevance within the context of environmental data processing, simulation and prediction.  ...  Acknowledgements This work was supported by the Natural Environment Research Council pilot projects on Environmental Virtual Observatory technologies NE/I002200/1 and NE/I004017/1.  ... 
doi:10.1016/j.envsoft.2014.10.007 fatcat:df3mpg7yunaehbfhzysbutze5y

The MESSAGE Integrated Assessment Model and the ix modeling platform (ixmp): An open framework for integrated and cross-cutting analysis of energy, climate, the environment, and sustainable development

Daniel Huppmann, Matthew Gidden, Oliver Fricko, Peter Kolp, Clara Orthofer, Michael Pimmer, Nikolay Kushin, Adriano Vinca, Alessio Mastrucci, Keywan Riahi, Volker Krey
2019 Environmental Modelling & Software  
The MESSAGE Integrated Assessment Model (IAM) developed by IIASA has been a central tool of energy-environment-economy systems analysis in the global scientific and policy arena.  ...  ++ system model integrated with the MACRO economic model; ii) a Java/database backend for version-controlled data management, iii) interfaces for the scientific programming languages Python & R for efficient  ...  A web application for the modeling platform The programming interfaces described in the previous section are complemented by a web application, which is a graphical user interface (GUI) accessible through  ... 
doi:10.1016/j.envsoft.2018.11.012 fatcat:ihmvmrpicfgm5nzk5mxwvoyu2i

An Open Source Strategy For Public Online Algorithms And Data Services: The French Water Information System Experience

Alexandre Liccardi, Laurent Coudercy, Samuel Dembski, Anthony Mauclerc
2017 Zenodo  
The first water open data repository was released in 2013. The transparency policy expands with the publication of many APIs and data services aimed at citizens and specialists.  ...  These three projects are open source, available online and embody the will of their leaders (the French Agency for Biodiversity and the INSIDE cluster) to let a wider public invest the field of environmental  ...  This paper writing wouldn't have been possible without the previous theoretical work and the long-term strategy built by the F-WIS contributors, especially René Lalement (AFB) and Pierre Lagarde (BRGM)  ... 
doi:10.5281/zenodo.1025783 fatcat:plzpjxnh6fh7lcompszkydeymm

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Alex R. Hardisty, Finn Bacall, Niall Beard, Maria-Paula Balcázar-Vargas, Bachir Balech, Zoltán Barcza, Sarah J. Bourlat, Renato De Giovanni, Yde de Jong, Francesca De Leo, Laura Dobor, Giacinto Donvito (+40 others)
2016 BMC Ecology  
, model, simulate and predict using such data.  ...  We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services  ...  Townsend Peterson and Jorge Soberón (both of Biodiversity Institute and Natural History Museum, University of Kansas), Robert Guralnick (Florida Museum of Natural History, University of Florida) and Mark  ... 
doi:10.1186/s12898-016-0103-y pmid:27765035 pmcid:PMC5073428 fatcat:kphzgb67bzh4tdnwchbkvf2nvq

Lifting the Information Barriers to Address Sustainability Challenges with Data from Physical Geography and Earth Observation

Anthony Lehmann, Rebecca Chaplin-Kramer, Martin Lacayo, Grégory Giuliani, David Thau, Kevin Koy, Grace Goldberg, Richard Sharp Jr.
2017 Sustainability  
Additionally, application programming interfaces allow outsiders to elaborate and iterate on programs to explore novel uses of data and models, as seen in the Berkeley Ecoinformatics Engine.  ...  Data from Earth observation (, combined with models from physical geography, demographics, and statistical data, can provide the necessary information to inform about the SDG targets  ...  Google Earth Engine provides open access to a centralized repository of many such large collections of Earth observation data (Figure 4a) , a programming interface to analyze those data, and a cluster  ... 
doi:10.3390/su9050858 fatcat:yobebuzb2nexvgggcqlxiw737q

EarthCube Resources for the NSF Geo Domain-Data Workshops 2018-2019.pdf

Ouida W. Meier, D. Sarah Stamps, Lynne Schreiber
2018 Zenodo  
, atmosphere, and space environment systems.  ...  of geosciences data and related resources.  ...  ACKNOWLEDGEMENTS Resources here include those provided by people and groups who have openly shared their work and resource collections, including: NCEAS, DataONE, ESIP, FAIR advocates, and many EarthCube  ... 
doi:10.5281/zenodo.3371777 fatcat:fqphetw6c5fqrk6pvbr4idsnc4

Seeing the forest through the trees: A review of integrated environmental modelling tools

Carlos Granell, Sven Schade, Nicole Ostländer
2013 Computers, Environment and Urban Systems  
A unique integrated modelling solution, which is capable of dealing with any environmental scenario, seems to be unaffordable because of the great variety of data formats, models, environmental phenomena  ...  of virtual research environments -could lead to sustainable information systems, which would advance model sharing, reuse and integration.  ...  Acknowledgements This work has been partially supported by the ENVIROFI FP7 project (Grant Agreement No. 284898).  ... 
doi:10.1016/j.compenvurbsys.2013.06.001 fatcat:wxxwovwqz5h2tfodupgbtqdqgm

CSDMS: a community platform for numerical modeling of Earth surface processes

Gregory E. Tucker, Eric W. H. Hutton, Mark D. Piper, Benjamin Campforts, Tian Gan, Katherine R. Barnhart, Albert J. Kettner, Irina Overeem, Scott D. Peckham, Lynn McCready, Jaia Syvitski
2022 Geoscientific Model Development  
Computational modeling occupies a unique niche in Earth and environmental sciences.  ...  These include a community repository for model sharing and metadata, interface and ontology standards for model interoperability, language-bridging tools, a modular programming library for model construction  ...  Initial development of Landlab was supported by the NSF SI2 program (1450409).  ... 
doi:10.5194/gmd-15-1413-2022 fatcat:3cy54w2pxbf4fahztaaxexs4hu

Notebook-as-a-VRE (NaaVRE): from private notebooks to a collaborative cloud virtual research environment [article]

Zhiming Zhao, Spiros Koulouzis, Riccardo Bianchi, Siamak Farshidi, Zeshun Shi, Ruyue Xin, Yuandou Wang, Na Li, Yifang Shi, Joris Timmermans, W. Daniel Kissling
2021 arXiv   pre-print
Jupyter can support several popular languages that are used by data scientists, such as Python, R, and Julia.  ...  A typical VRE is often implemented as an integrated environment, which includes a catalog of research assets, a workflow management system, a data management framework, and tools for enabling collaboration  ...  ., big environmental challenges or cancer diagnosis, requires large data volumes, advanced modeling techniques, and distributed computing facilitates [1, 2] .  ... 
arXiv:2111.12785v1 fatcat:r5yku5fiibb7xmbmlh77nxlrry
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