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Best practices for a future open code policy: Experiences and vision of the astrophysics source code library

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arXiv 2018年

作者： Shamir, Lior Berriman, Bruce Teuben, Peter Nemiroff, Robert Allen, Alice Lawrence Technological University Caltech/IPAC-NExScI University of Maryland Michigan Technological University Astrophysics Source Code Library

The astrophysics source code library: What’s new, what’s coming

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arXiv 2017年

作者： Allen, Alice Bruce Berriman, G. DuPrie, Kimberly Mink, Jessica Nemiroff, Robert Ryan, P. Wesley Schmidt, Judy Shamir, Lior Shortridge, Keith Taylor, Mark Teuben, Peter Wallin, John Warmels, Rein H. Astrophysics Source Code Library College ParkMD United States Caltech/IPAC-NExScI PasadenaCA United States Space Telescope Science Institute BaltimoreMD United States Smithsonian Astrophysical Observatory CambridgeMA United States Michigan Technological University HoughtonMI United States Lawrence Technological University SouthfieldMI United States Knave and Varlet McMahons PointNSW Australia H. H. Wills Physics Laboratory University of Bristol United Kingdom Astronomy Department University of Maryland College ParkMD United States Middle Tennessee State University MurfreesboroTN United States European Southern Observatory GarchingDE Germany

The astrophysics source code library (ASCL, ***), established in 1999, is a citable online registry of source codes used in research that are available for download;the ASCL’s main purpose is to improve the transparency, reproducibility, and falsifiability of research. In 2017, improvements to the resource included real-time data backup for submissions and newly-published entries, improved cross-matching of research papers with software entries in ADS, and expansion of preferred citation information for the software in the ASCL. Copyright © 2017, The Authors. All rights reserved.

关键词： Computer programming languages

It's your software! Get it cited the way you want!

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arXiv 2022年

作者： Allen, Alice Astrophysics Source Code Library HoughtonMI United States University of Maryland College Park College ParkMD United States

Are others using software you’ve written in their research and citing it as you want it to be cited? Software can be cited in different ways, some good, and some not good at all for tracking and counting citations in indexers such as ADS and Clarivate’s Web of Science. Generally, these resources need to match citations to resources, such as journal articles or software records, they ingest. This presentation covered common reasons as to why a code might not be cited well (in a trackable/countable way), which citation methods are trackable, how to specify this information for your software, and where this information should be placed. It also covered standard software metadata files, how to create them, and how to use them. Creating a metadata file, such as a *** or ***, and adding it to the root of your code repo is easy to do with the ASCL’s metadata file creation overlay, and will help out anyone wanting to give you credit for your computational method, whether it’s a huge carefully-written and tested package, or a short quick-and-dirty-but-oh-so-useful code. © 2022, CC BY.

关键词： Metadata

Citation method, please? A case study in astrophysics

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arXiv 2021年

作者： Allen, Alice University of Maryland Astrophysics Source Code Library College ParkMD United States

Software citation has accelerated in astrophysics in the past decade, resulting in the field now having multiple trackable ways to cite computational methods. Yet most software authors do not specify how they would like their code to be cited, while others specify a citation method that is not easily tracked (or tracked at all) by most indexers. Two metadata file formats, *** and ***, developed in 2016 and 2017 respectively, are useful for specifying how software should be cited. In 2020, the astrophysics source code library (ASCL, ***) undertook a year-long effort to generate and send these software metadata files, specific to each computational method, to code authors for editing and inclusion on their code sites. We wanted to answer the question, "Would sending these files to software authors increase adoption of one, the other, or both of these metadata files?" The answer in this case was no. Furthermore, only 41% of the 135 code sites examined for use of these files had citation information in any form available. The lack of such information creates an obstacle for article authors to provide credit to software creators, thus hindering citation of and recognition for computational contributions to research and the scientists who develop and maintain software. © 2021, CC BY-NC-SA.

关键词： astrophysics

Scicodes: Astronomy research software and beyond

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arXiv 2021年

作者： Allen, Alice Astrophysics Source Code Library University of Maryland College ParkMD United States

The astrophysics source code library (ASCL ***), started in 1999, is a free open registry of software used in refereed astronomy research. Over the past few years, it has spearheaded an effort to form a consortium of scientific software registries and repositories. In 2019 and 2020, ASCL contacted editors and maintainers of discipline and institutional software registries and repositories in math, biology, neuroscience, geophysics, remote sensing, and other fields to develop a list of best practices for these research software resources. At the completion of that project, performed as a Task Force for a FORCE11 working group, members decided to form Scicodes as an ongoing consortium. This presentation covered the consortium’s work so far, what it is currently working on, what it hopes to achieve for making scientific research software more discoverable across disciplines, and how the consortium can benefit astronomers. Copyright © 2021, The Authors. All rights reserved.

关键词： astrophysics

Making organizational software easier to find in ASCL and ADS

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arXiv 2020年

作者： Allen, Alice Mavuram, Siddha Nemiroff, Robert J. Schmidt, Judy Teuben, Peter Astrophysics Source Code Library United States University of Maryland College ParkMD United States Michigan Technological University HoughtonMI United States

Software is the most used instrument in astronomy, and organizations such as NASA and the Heidelberg Institute for Theoretical Physics (HITS) fund, develop, and release research software. NASA, for example, has created sites such as *** to share its software with the world, but how easy is it to see what NASA has? Until recently, searching NASA’s astrophysics Data System (ADS) for NASA astronomy research software has not been fruitful. Through its ADAP program, NASA funded the astrophysics source code library to improve the discoverability of these codes. Adding institutional tags to ASCL entries makes it easy to find this software not only in the ASCL but also in ADS and other services that index the ASCL. This presentation covered the changes the ASCL made as a result of this funding and how you can use the results of this work to better find organizational software in ASCL and ADS. Copyright © 2020, The Authors. All rights reserved.

关键词： NASA

Availability of hyperlinked resources in astrophysics papers

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arXiv 2019年

作者： Ryan, P. Wesley Allen, Alice Teuben, Peter Astrophysics Source Code Library Astronomy Department University of Maryland College Park United States

astrophysics papers often rely on software which may or may not be available, and URLs are often used as proxy citations for software and data. We extracted all URLs from two journals’ 2015 research articles, removed those from certain long-term reliable domains, and tested the remainder to determine what percentage of these URLs were accessible in October 2018. Copyright © 2019, The Authors. All rights reserved.

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Quantifying feedback from narrow line region outflows in nearby active galaxies. III. Results for the Seyfert 2 galaxies Markarian 3, Markarian 78, and NGC 1068

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arXiv 2021年

作者： Revalski, Mitchell Meena, Beena Martinez, Francisco Polack, Garrett E. Crenshaw, D. Michael Kraemer, Steven B. Collins, Nicholas R. Fischer, Travis C. Schmitt, Henrique R. Schmidt, Judy Maksym, W. Peter Rafelski, Marc Space Telescope Science Institute 3700 San Martin Drive BaltimoreMD21218 United States Department of Physics and Astronomy Georgia State University 25 Park Place Suite 605 AtlantaGA30303 United States Center for Relativistic Astrophysics School of Physics Georgia Institute of Technology AtlantaGA30332 United States Institute for Astrophysics and Computational Sciences Department of Physics Catholic University of America WashingtonDC20064 United States Telophase Corporation NASA’s Goddard Space Flight Center Code 667 GreenbeltMD20771 United States AURA for ESA Space Telescope Science Institute 3700 San Martin Drive BaltimoreMD21218 United States Naval Research Laboratory WashingtonDC20375 United States Astrophysics Source Code Library Harvard-Smithsonian Center for Astrophysics 60 Garden Street CambridgeMA02138 United States Department of Physics and Astronomy Johns Hopkins University BaltimoreMD21218 United States

Outflows of ionized gas driven by active galactic nuclei (AGN) may significantly impact the evolution of their host galaxies. However, determining the energetics of these outflows is difficult with spatially unresolved observations that are subject to strong global selection effects. We present part of an ongoing study using Hubble Space Telescope (HST) and Apache Point Observatory (APO) spectroscopy and imaging to derive spatially-resolved mass outflow rates and energetics for narrow line region (NLR) outflows in nearby AGN that are based on multi-component photoionization models to account for spatial variations in the gas ionization, density, abundances, and dust content. This expanded analysis adds Mrk 3, Mrk 78, and NGC 1068, doubling the sample in Revalski (2019). We find that the outflows contain total ionized gas masses of M ≈ 105.5 - 107.5 M☉ and reach peak velocities of v ≈ 800 - 2000 km s-1. The outflows reach maximum mass outflow rates of M·out ≈ 3 - 12 M☉ yr-1 and encompass total kinetic energies of E ≈ 1054 - 1056 erg. The outflows extend to radial distances of r ≈ 0.1 - 3 kpc from the nucleus, with the gas masses, outflow energetics, and radial extents positively correlated with AGN luminosity. The outflow rates are consistent with in situ ionization and acceleration where gas is radiatively driven at multiple radii. These radial variations indicate that spatially-resolved observations are essential for localizing AGN feedback and determining the most accurate outflow parameters. Copyright © 2021, The Authors. All rights reserved.

关键词： Ionization of gases

Schroedinger's code: A preliminary study on research source code availability and link persistence in astrophysics

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arXiv 2018年

作者： Allen, Alice Teuben, Peter J. Ryan, P. Wesley Astrophysics Source Code Library *** University of Maryland Department of Astronomy 4254 Stadium Drive College ParkMD20742

We examined software usage in a sample set of astrophysics research articles published in 2015 and searched for source code for the software mentioned in these research papers. We categorized the software to indicate whether source code is available for download and whether there are restrictions to accessing it, and if source code is not available, whether some other form of the software, such as a binary, is. We also extracted hyperlinks from one journal's 2015 research articles, as links in articles can serve as an acknowledgment of software use and lead to data used in the research, and tested them to determine which of these URLs are still accessible. For our sample of 715 software instances in the 166 articles we examined, we were able to categorize 418 records as to availability of source code and found that 285 unique codes were used, 58% of which offer source code available online for download. Of the 2,558 hyperlinks extracted from 1,669 research articles, at best, 90% of them were available over our testing period. Copyright © 2018, The Authors. All rights reserved.

关键词： Computer programming languages