Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance

Gil, Yolanda; David, Cédric H.; Demir, İbrahim; Essawy, Bakinam T.; Fulweiler, Robinson W.; Goodall, Jonathan L.; Karlstrom, L.; Lee, Huikyo; Mills, Heath J.; Oh, Jihyun; Pierce, Suzanne A.; Pope, Allen; Tzeng, Mimi W.; Villamizar, S. R.; Yu, Xuan

doi:10.1002/2015ea000136

Cited by 155 publications

(170 citation statements)

References 128 publications

(132 reference statements)

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“…Barnes 2010;Lees 2012;Easterbrook 2014;David et al 2016;Gil et al, 2016). Nevertheless, an enormous amount of free software exist for geoscientific research or for geotechnical engineering offices.…”

Section: Specific Geoscientific Softwarementioning

confidence: 99%

“…If the source codes of abandoned applications would not made public, many files would be not easily accessible in future. A fact which is getting important with the increasing demand for open data, data archiving and reproducibility (see e.g., Lees 2012;Davis et al, 2016;Gil et al, 2016). Vendor lock-in is one of the main reasons for keeping the common proprietary software.…”

Section: Openness To Alternative Softwarementioning

confidence: 99%

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Using Free/Libre and Open Source Software in the Geological Sciences

D¹,

Schenk²

2017

AJES

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In the Geological Sciences, as in any other academic field, computers and software aided work are essential tools. Although Free and Open Source software is largely used in academic institutions for several purposes it is not yet state-of-the-art for the everyday usage. The usage of free and open source software is, besides the freedom of its ease of use, distribution, and modification, also recommended due to the increasing financial burden. There are many suited and effective alternative free software applications to the most common used proprietary commercial ones. Many common work steps can even be done entirely with the free operating system Linux. A selection of free software applications is compiled which are useful for geoscientific data evaluation and presentation. The provided information aims to lower the threshold of reservations against a potential migration and gives an overview about currently available alternative software useful in the Geological Sciences.In den geologischen Wissenschaften, wie auch in allen anderen Disziplinen, sind Computer, sowie softwareunterstützte Tätig-keiten, längst unverzichtbare Werkzeuge. Obgleich Freie und Open Source Software in vielen speziellen Einsatzgebieten verbreitet ist, wird diese noch nicht umfassend für den täglichen Gebrauch benutzt. Die Verwendung von Freier und Open Source Software ist, neben der Freiheit sie uneingeschränkt nutzen, verteilen und modifizieren zu können, auch wegen zunehmender budgetärer Einschränkungen zu empfehlen. Mit diesem Artikel möchten wir die geologische Gemeinschaft auf die vielen geeigneten Programme hinweisen, die als Alternativen zu den üblicherweise häufig benutzten proprietären, kommerziellen Programmen existieren. Viele alltägliche computergestützte Aufgaben können auch zur Gänze mit dem freien Betriebsystem Linux durchgeführt werden, ohne Einbußen in Funktionalität oder Professionalität befürchten zu müssen. Eine ausgewählte Liste geowissenchaftlich interessanter freier Anwendungen wird durch Referenzen ergänzt. Dieser Artikel soll über die Möglichkeiten freier alternativer Software informieren, die Zurückhaltung vor einer eventuellen Migration mindern, sowie einen Überblick über die aktuell verfügbare freie geowissenschaftliche Software geben.

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Section: Specific Geoscientific Softwarementioning

confidence: 99%

Section: Openness To Alternative Softwarementioning

confidence: 99%

Using Free/Libre and Open Source Software in the Geological Sciences

D¹,

Schenk²

2017

AJES

View full text Add to dashboard Cite

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“…Inspired by and partnering with early career researchers, I developed the Scientific Paper of the Future (SPF) Initiative to teach scientists how to write papers that describe and cite explicitly not just data but also software and methods (workflows and provenance) [11]. The Initiative includes a special issue of a journal where submissions discuss the scientist's motivation for structuring and reporting their research products more thoroughly.…”

Section: Initiative-driven Thais: Access To the Scientific Recordmentioning

confidence: 99%

Thoughtful artificial intelligence: Forging a new partnership for data science and scientific discovery

Gil

2017

Self Cite

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Abstract. Artificial intelligence will play an increasingly more prominent role in scientific research ecosystems, and will become indispensable as more interdisciplinary science questions are tackled. While in recent years computers have propelled science by crunching through data and leading to a data science revolution, qualitatively different scientific advances will result from advanced intelligent technologies for crunching through knowledge and ideas. We propose seven principles for developing thoughtful artificial intelligence, which will turn intelligent systems into partners for scientists. We present a personal perspective on a research agenda for thoughtful artificial intelligence, and discuss its potential for data science and scientific discovery.

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“…From a pragmatic perspective, this is an inefficient use of a scientist's or engineer's time. Perhaps more importantly, it inhibits the ability to reproduce or reuse studies that have a significant computational modeling component Essawy et al, 2016;Gil et al, 2016). One way to begin to address these challenges is through better approaches for sharing and reusing models built by others.…”

Section: Chapter 1: Introductionmentioning

confidence: 99%

“…From a pragmatic perspective, it is an inefficient use of scientists' time. Perhaps more importantly, it inhibits scientists' ability to reproduce studies that have a significant computational modeling component Essawy et al, 2016;Gil et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Cyberinfrastructure to Support Flood Modeling from Catchment to Regional Scales

Morsy

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Flooding events are projected to increase in frequency and intensity in coming years due to climate change. New tools and approaches are needed to assist decision makers in better understanding and addressing societal impacts due to flooding and how to mitigate these impacts.This research addressed three challenges related to flooding impacts: (i) better understanding how distributed stormwater infrastructure can mitigate flooding in urban catchments, (ii) designing and building spatially-detailed, real-time flood warning systems for emergency management purposes, and (iii) designing and building cyberinfrastructure to support reuse and transparency in both flood modeling and hydrologic modeling more broadly. The goal of this research was to address these challenges by conducting three studies. The second study explored building an automated cloud-based system for forecasting flooded roadway and bridge locations at a regional-scale. Because the study area has very low topographic relief, a two-dimensional (2D), computationally-expensive hydrodynamic model is required. This study demonstrated the ability of using instances in a public cloud with powerful graphical processing units (GPUs) to run a large (average of 4 million nodes) 2D hydrodynamic model in a time frame relevant to real-time emergency management applications. The steps required to build this system were (i) creating an automated workflow for obtaining and processing ii forecast rainfall data, (ii) running the 2D model in the cloud, (iii) using geospatial analysis tools to identify flooded bridges, and (iv) presenting the results online for decision makers. The system automates forecast data access and pre-processing, execution of a high-resolution 2D hydrodynamic model, and map-based visualization of model outputs using Amazon Web Services (AWS).The third study advanced approaches for sharing hydrologic models, such as the models created in this dissertation, through community supported cyberinfrastructure. Sharing models is important for scientific reproducibility, reuse, and fidelity. In this study, the first task was to design a metadata framework for hydrologic models that is flexible and applicable across the wide variety of models used by hydrologists. Then the study demonstrated the utility of this framework for sharing, publishing, and reusing models through an implementation within the HydroShare cyberinfrastructure system.In the first study, the results suggest that rain gardens with 30 cm berm heights and a total area equal to 20% of the impervious surfaces within the watershed should provide sufficient storage to mitigate flooding for rain events up to and including a 10 year return period storm event.The results also suggest approximately 15%, 27%, and 38% of the runoff generated from impervious surfaces should be diverted to the rain gardens to mitigate flooding from 2, 5, and 10 year return period storm events, respectively. Given prior work on the adoption of LID approaches for other watersheds, rain gardens could effectivel...

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Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance

Cited by 155 publications

References 128 publications

Using Free/Libre and Open Source Software in the Geological Sciences

Using Free/Libre and Open Source Software in the Geological Sciences

Thoughtful artificial intelligence: Forging a new partnership for data science and scientific discovery

Cyberinfrastructure to Support Flood Modeling from Catchment to Regional Scales

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