Software and the Scientist: Coding and Citation Practices in Geodynamics

Abstract

In geodynamics as in other scientific areas, computation has become a core component of research, complementing field observation, laboratory analysis, experiment, and theory. Computational tools for data analysis, mapping, visualization, modeling, and simulation are essential for all aspects of the scientific workflow. Specialized scientific software is often developed by geodynamicists for their own use, and this effort represents a distinctive intellectual contribution. Drawing on a geodynamics community that focuses on developing and disseminating scientific software, we assess the current practices of software development and attribution, as well as attitudes about the need and best practices for software citation. We analyzed publications by participants in the Computational Infrastructure for Geodynamics and conducted mixed method surveys of the solid earth geophysics community. From this we learned that coding skills are typically learned informally. Participants considered good code as trusted, reusable, readable, and not overly complex and considered a good coder as one that participates in the community in an open and reasonable manor contributing to both long-and short-term community projects. Participants strongly supported citing software reflected by the high rate a software package was named in the literature and the high rate of citations in the references. However, lacking are clear instructions from developers on how to cite and education of users on what to cite. In addition, citations did not always lead to discoverability of the resource. A unique identifier to the software package itself, community education, and citation tools would contribute to better attribution practices.

A Visual Survey of Global Slab Geometries With ShowEarthModel and Implications for a Three‐Dimensional Subduction Paradigm

“…As data assimilation and working with numerical modeling output from large‐scale parallel simulations become an integral part of modern scientific research, new tools are required to analyze and conceptualize the information (Anderson et al, ; Billen et al, ; Damon et al, ; Erlebacher et al, ; Jadamec et al, ; Kellogg et al, ; Kreylos et al, ; Suarez et al, ; Wessel et al, ; Zhou & Liu, ). With the new digital framework for research, scientific contributions are taking the form of multiple formats from contributed software (Hwang et al, ; Zhong et al, ) and workflows (Jadamec, ), to large‐scale data sets and integrated parsers (Anderson et al, ; Haxby et al, ; Hutko et al, ; Trabant et al, ), to fully visual formats to communicate the digital and 3‐D information, as in this paper.…”

“…As data assimilation and working with numerical modeling output from large-scale parallel simulations become an integral part of modern scientific research, new tools are required to analyze and conceptualize the information (Anderson et al, 2009;Billen et al, 2008;Damon et al, 2008;Erlebacher et al, 2001;Kellogg et al, 2008;Kreylos et al, 2006;Suarez et al, 2008;Wessel et al, 2013;Zhou & Liu, 2017). With the new digital framework for research, scientific contributions are taking the form of multiple formats from contributed software (Hwang et al, 2017;Zhong et al, 2015) and workflows (Jadamec, 2016a), to large-scale data sets and integrated parsers (Anderson et al, 2009;Haxby et al, 2010;Hutko et al, 2017;Trabant et al, 2012), to fully visual formats to communicate the digital and 3-D information, as in this paper. This need has also trickled down into the undergraduate and graduate curriculum, as students are now faced with manipulating large geologic and geophysical data sets, such as LIDAR and 3-D seismic, as well as output from parallel numerical simulations (Jadamec, 2016a;Kellogg et al, 2008).…”

Attributing and Referencing (Research) Software: Best Practices and Outlook From Inria

“…This led to the badging system that ACM promotes for articles presenting or using research software [4] and to the cloud-based software hosting solution used and put forward by IEEE and Taylor & Francis for their journals (Code Ocean). The need to take research software into account, making it available, referenceable, and citable, became apparent in many research communities [5], [20], [12], [11], and the limitation of the informal practices currently in use quickly surfaced [13], [7], [14]. An important effort to bring together these many different experiences, and to build a coherent point of view has been made by the FORCE11 Software Citation Working Group in 2016, which led to state a concise set of software citation principles [19].…”

Curation as “Interoperability With the Future”: Preserving Scholarly Research Software in Academic Libraries

“…(Bearman, 1987). The range of purposes for software creation and use include: to validate research results (Hwang, Fish, Soito, Smith, & Kellogg, 2017), to investigate and fix source code bugs (Abdalkareem, Shihab, & Rilling, 2017), and to increase efficiency (Banker & Kauffman, 1991). In ideal cases, conversations can be conducted with resource creators to gather crucial information about the intended purpose and functionality of the software.…”