Category Archives: AAS

Research poster at AAS 233

URLs have often been used as proxy citations for software and data. We extracted URLs from one journal’s 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 September and October 2017. We repeated this test a year later to determine what percentage of these links were still accessible. We will present what we learned about URL accessibility in astronomy.

P. Wesley Ryan, Astrophysics Source Code Library

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ASCL poster at AAS #233

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 code.nasa.gov and software.nasa.gov 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’s astronomy software has not been fruitful; NASA has funded the Astrophysics Source Code Library (ASCL ascl.net) to improve the discoverability of these codes. The ASCL, now celebrating its 20th anniversary, is a free online registry of software used in astronomy research and is indexed by ADS, Web of Science, and other resources. Adding NASA and HITS astronomy research codes to the ASCL with appropriate tags enables finding this software easily not only in the ASCL but also in ADS and other services that index the ASCL. This poster presentation covers the changes the ASCL has made to enable discovery of NASA software in ADS and the results of this work.

Alice Allen, Astrophysics Source Code Library/University of Maryland, College Park
Peter Teuben, University of Maryland, College Park
Judy Schmidt, Astrophysics Source Code Library
Robert Nemiroff, Michigan Technological University

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Software activities at AAS 233 in Seattle, Jan 2019

It’s that time of year again when software folks — users and authors alike — dream of all the software activities at the winter AAS meeting. So here is the ASCL’s (abbreviated*) annual round-up to jumpstart your dreams and warm your code-loving heart! If you have items you want added, please let me know in the comments below or send an email to editor@ascl.net. Thank you!

All rooms are in the Washington State Convention Center unless otherwise specified.


SATURDAY, 5 JANUARY 2019
Workshops
Introduction to Software Carpentry (Day 1), 9:00 AM – 5:00 PM; 211
The AAS Chandra/CIAO Workshop, 9:00 AM – 6:00 PM; 204
Using Python to Search NASA’s Astrophysics Archives, 10:00 AM – 11:30 AM; 213


SUNDAY, 6 JANUARY 2019
Workshops
SOFIA Workshop for FORCAST and HAWC+ Data Analysis, 8:30 AM – 5:15 PM; 201
Adding LISA to your Astronomy Tool Box, 9:00 AM – 5:00 PM; 213
Introduction to Software Carpentry (Day 2), 9:00 AM – 5:00 PM; 211
Using Python and Astropy for Astronomical Data Analysis, 9:00 AM – 5:00 PM; 4C-4
The AAS Chandra/CIAO Workshop, 9:00 AM – 6:00 PM; 204
Advanced Searching in the New ADS: On the Web and Using the API, 3:00 PM – 4:30 PM; 304


MONDAY, 7 JANUARY 2019
Splinter meetings
Data Science, 8:00 AM – 6:00 PM, 4C-1
Updates on Implementing Software Citation in Astronomy, 12:30 PM – 2:00 PM; 203
An Open Discussion on Astronomy Software, 2:00 PM – 3:30 PM; 4C-4

Open event
AAS WorldWide Telescope presents: Advances in Astronomical Visualization, 10:00 AM – 11:30 AM; 214

Oral presentations
Session 126. Machine Learning in Astronomical Data Analysis, 2:00 PM – 3:30 PM; 607 (5 presentations)

Also:
112.01. Constraining BH formation with 2M05215658+4359220, 10:00 AM – 10:10 AM, 612
109.03. Real-time data reduction pipeline and image analysis software for FIREBall-2: first flight with a δ-doped UV-EMCCDs operating in counting mode, 10:30 AM – 10:40 AM, 608
175.06. Python, Unix, Observing, and LaTeX: Introducing First Year Undergraduates to Astronomical Research, 10:50 AM – 11:00 AM, 620
109.08. TESS Data Analysis using the community-developed Lightkurve Python Package, 11:20 AM – 11:30 AM, 608
123.02D. A Uniform Analysis of Exoplanet Atmosphere Spectra Observed by HST WFC3 Is Consistent with Watery Worlds, 2:10 PM – 2:30 PM, 6C
129.06. Reconstructing the Orphan Stream Progenitor with MilkyWay@home Volunteer Computing, 3:00 PM – 3:10 PM, 611

Selected posters
144.25. Identifying and Comparing Centrally Star-Forming Galaxies Using MaNGA
144.29. Deriving star formation histories from photometric spectral energy distributions with diffusion k-means
144.30. Using Convolutional Neural Networks to predict Galaxy Metallicity from Three-Color Images
144.35. Automatic Detection and Analysis of Debris from Galactic Accretion Events
145.05. Galaxy Gradients Across Simulations
145.07. Reduction and Analysis of GMOS Spectroscopy for Herschel Sources in CANDELS
145.25. Comparison of the HI Signal Extraction Algorithms of SoFiA and ALFALFA
140.02. Tracking the TESS Pipeline
140.12. Undergraduates Can Find Planets Too
140.16. Identifying Transiting Exoplanets in with Deep Learning in K2 Data
140.20. The Impact of Small Statistics on Identifying Background False Positives in Kepler Data
140.23. AutoRegressive Planet Search for Ground-Based Transit Surveys
140.29. Getting to Know Your Star: A comparison of analytic techniques for deriving stellar parameters and abundances
149.18. NANOGrav: Data Accessibility, Analysis and Automation using Python
150.01. Revised Simulations of the Planetary Nebulae Luminosity Function
150.15. Identifying Binary Central Stars of Planetary Nebulae with PSF Fitting
158.02. HaloSat: X-Ray Calibration and Spectral Analysis for a NASA CubeSat
162.04. The Starchive

Selected iPosters
167.02. Modeling circumstellar dust around low-mass-loss rate carbon-rich AGB stars
167.04. The response of optical Fe II emission in AGNs to changes in the ionizing continuum, I: photoionization modelling
164.02. A Maximum Likelihood Approach to Extracting Photon-Starved Spectra of Directly Imaged Exoplanets
166.02. Smoothed Particle Inference Analysis of SNR DEM L71
171.03. The State of Software Tools for the Space Telescope Imaging Spectrograph

Other activities of possible interest
Monday, January 7: Data Science Splinter Meeting, 8:00 AM – 6:00 PM, 4C-1


TUESDAY, 8 JANUARY 2019
Workshop
LSST Science Pipelines Stack Tutorial for AAS, 9:00 AM – 5:00 PM; 310

Splinter meeting
Cafe SCiMMA: Conceptualizing an NSF Center for Scalable Cyberinfrastructure for Multimessenger Astrophysics, 3:15 PM – 5:15 PM; Redwood (Sheraton Seattle Hotel)

Oral presentations
Session 225. Computation, Data Science, and Image Analysis, 2:00 PM – 3:30 PM, 6E (6 presentations)

Also:
218.05. A Uniform Analysis of Kepler/K2 Exoplanet Transit Parameters, 10:40 AM – 10:50 AM, 603
206.05D. High Resolution spatial analysis of z ~2 lensed galaxy using pixelated source-reconstruction algorithm, 10:50 AM – 11:10 AM, 605/610
203.05. Atmosphere Retrieval of Planetary Mass Companions with the APOLLO Code: A Case Study of HD 106906b and Prospects for JWST, 11:00 AM – 11:10 AM, 6B
207.10. astroquery: An Astronomical Web-Querying Package in Python, 11:03 AM – 11:10 AM, 606
239.04D. Kinematics of Circumgalactic Gas and Cold Gas Accretion at Redshift z=0.2, 2:40 PM – 3:00 PM, 609
227.07. Mu and You: Public Microlensing Analysis Tools and Survey Data, 3:12 PM – 3:24 PM, 606

Poster presentations
Session 245. Computation, Data Science, and Image Analysis posters (31 posters!)

Selected posters
243.08. Utilizing Independent Component Analysis to Explore the Diversity of Quasars
245.01. Making organizational research software more discoverable
245.27. The MAESTROeX low Mach number stellar hydrodynamics code
245.29. The Castro Adaptive Mesh Refinement Hydrodynamics Code: Applications, Algorithm Development, and Performance Portability
247.30. Chemical Analysis of Tabby’s Star (KIC 8462852)
247.35. VPLanet: The VIrtual Planet Simulator
249.11. Know Your Neighbors: New Catalogs and Analysis of Star Clusters in the LMC, SMC, & M33
250.02. X-Ray Source Analysis In The Globular Clusters NGC 6341 and NGC 6541
253.06. Structure Function Analysis of Turbulent Properties in the Small and Large Magellanic Clouds
259.05. Forward-Modeling Analysis of Late-T Dwarf Atmospheres
259.15. Finding age relations for low mass stars using magnetic activity and kinematics
259.24. A Uniform Retrieval Analysis on a Sample of 16 T-dwarfs
258.25. SuperNovae Analysis aPplication (SNAP): Identifing and Understanding the Physics of Supernovae

Selected iPosters
268.02. Towards 3D Parameter Space Studies of CCSNe With Grey, Two-Moment Neutrino Transport
261.12. Using Machine Learning to Predict the Masses of Galaxy Clusters
261.15. Mapping Galaxy Cluster Orientations from Cosmo-OWLS Simulations
261.16. A Hydrodynamical Simulation of the Off-Axis Cluster Merger Abell 115


WEDNESDAY, 9 JANUARY 2019
Open meeting
AAS WorldWide Telescope with Python and Astropy, 10:00 AM – 11:30 AM; 214

Oral presentations
316.04D. Feedback and Chemical Enrichment in Low Mass Dwarf Galaxies: Insights from Simulations Tracking Individual Stars, 10:30 AM – 10:50 AM, 617
304.03. Recent upgrades to the pyLIMA software for microlensing modeling and analysis of two binary events, 10:10 AM – 10:20 AM, 6E
311.05. Quantifying the effects of spatial resolution and noise on galaxy metallicity gradients, 11:00 AM – 11:10 AM, 612
313.05D. Probabilistic data analysis methods for large photometric surveys, 10:50 AM – 11:10 AM, 614
336.04D. Simultaneous modelling of X-rays emission and optical polarization of intermediate polars using the CYCLOPS code: the case of V405 Aurigae, 2:40 PM – 3:00 PM, 614
342.06. On Open Cluster Disruption, 3:00 PM – 3:10 PM, 620
341.01. Reproducing Stellar Rotation Periods in the Kepler Field via Magnetic Braking and Tidal Torques

Selected posters
346.04. Designing a Python Module for the Calculation of Molecular Parameters and Production Rates in Comets
347.01. Hyperlink preservation in astrophysics papers
348.19. The COBAIN code. Basic principles and geometrical considerations
348.27. Considerations and Design Principles for the 2.1 Release of the PHOEBE Eclipsing Binary Modeling Code
356.06. Analysis of a large number of spiral galaxies shows asymmetry between clockwise and counterclockwise galaxies

Session 381. Computation, Data Science, and Image Analysis session (8 iPosters)

Selected iPosters
381.03. ASTROstream: Automated claSsification of Transient astRonomical phenOmena in the streaming mode
381.05. Understanding and using the Fermitools
381.07. Polarization Calibration Post-Pipeline in CASA: Pilot Implementation
381.08. Transitioning from ADS Classic to the new ADS search platform


THURSDAY, 10 JANUARY 2019
Hack Together Day
8:30 AM – 7:00 PM; 4C-2

Oral presentations
413.06. The Radio Astronomy Software Group: Foundational Tools for 21 cm Cosmology and Beyond, 11:10 AM – 11:20 AM, 614
408.07D. Hundreds of New Planet Candidates from K2, 11:00 AM – 11:20 AM, 608
411.05D. AzTEC Survey of the Central Molecular Zone: Modeling Dust SEDs and N-PDF with Hierarchical Bayesian Analysis, 10:40 AM – 11:00 AM, 612
405.05. How can new data analysis methods get more out of Kepler/K2 data?, 10:40 AM – 10:50 AM, 605/610
425.01. The Dedalus project: open source science in astrophysics with examples in convection and stellar dynamos, 2:00 PM – 2:22 PM, 606
430.02D. Analysis of the spatially-resolved V-3.6μm colors and dust extinction within 257 nearby NGC and IC galaxies, 2:20 PM – 2:40 PM, 612

Selected posters
443.11. WFC3 PSF Database and Analysis Tools
457.02. The Stak Notebooks: Transitioning From IRAF to Python
442.01. ExoPhotons: Exoplanet Monte Carlo Radiative Transfer
442.02. Quantifying inhomogeneities in the HI distributions of simulated galaxies
445.01. Lightkurve v1.0: Kepler, K2, and TESS time series analysis in Python
445.05. Using Kepler DR25 Products to Compute Exoplanet Ocurrence Rates
465.07. Distribution of stellar rotation periods using light curve analysis of second phase Kepler data


* abbreviated as in I haven’t listed all the posters that could be listed here, as the list was getting very very long…

An Open Discussion on Astronomy Software Splinter Meeting at AAS 233

MONDAY, 7 JANUARY 2019
Splinter Meeting: An Open Discussion on Astronomy Software
2:00 pm – 3:30 pm
Room 4C-4, Washington State Convention Center

The Astrophysics Source Code Library (ASCL) has organized a Splinter Meeting at January’s AAS  meeting. The session, An Open Discussion on Astronomy Software, is offered in recognition of the ASCL’s 20th anniversary.

Though progress has been made on various fronts, there is still work to be done to improve how astronomers (and other scientists) design, write, share, publish, maintain, archive, and receive credit, recognition, and steady positions for software. This open discussion on software will cover issues, topics, and questions attendees would like addressed, with a panel of software authors to reflect on the topics along with attendees. The session could potentially cover topics such as the sustainability of core astronomical software, whether astronomy should have a Decadal Plan for software and whether publishing need to change, and if so, how? Please submit the issues and questions you would like to see addressed this Google document (https://tinyurl.com/AAS233SWDiscussion). The panel members are:

Megan Ansdell, University of California Berkeley
Rory Barnes, University of Washington
C.E. Brasseur, Space Telescope Science Institute (@cebrasseur)
Tess Jaffe, University of Maryland/NASA Goddard Space Flight Center
Mario Juric, University of Washington (@mjuric)
Amanda Kepley, National Radio Astronomy Observatory (@aakepley)
Rocio Kiman, City University of New York (@rociokiman)

The meeting will be moderated by Alice Allen (ASCL/UMD) and will end with celebratory food (yes, there will be cake!!) for the ASCL’s 20th anniversary.

ASCL at the AAS231 Hack Together Day

The ASCL was well-represented at the AAS 231 Hack Together Day on Friday, January 12, with Advisory Committee Chairman Peter Teuben working on two hacks, one of which hopes to provide better guidance regarding software to reviewers, dashboard developer PW Ryan also working on two hacks, both related to the ASCL and research we’re conducting, and yours truly; I mostly worked on ASCL tasks that have been backlogged, such as adding preferred citation information to ASCL entries. The ASCL currently has preferred citation information listed for 25% of our entries; we will be adding this information to more records in 2018 where we can find it, though I note that many code sites do not list a preferred citation on their download sites.

For one of his hacks, Ryan grabbed all the Github links in ASCL entries, and then using a Ruby Gem that looks for licenses in Github repos, reported on the licensing information available. These results are preliminary, so please don’t take them as gospel, but it appears that a whopping 34% of these codes do not have licensing information in the repo. The most popular license is MIT, which does not surprise me, as Daniel Foreman-Mackey reported in the Special Session we held at AAS 225 that MIT was the popular license across all Github repos that have licensing info.

Report on the Astronomy Software Publishing Special Session at AAS231

On Thursday, January 11, the Astrophysics Source Code Library (ASCL) and Astronomical Data Group at the Flatiron Institute organized a Special Session at the 231st AAS meeting in National Harbor, MD on Astronomy Software Publishing: Community Roles and Services, the sixth in a series of software-focused sessions that the ASCL, sometimes with others, has organized at AAS meetings.

"Really glad to see software article publication and citation getting attention at the #AAS231 meeting. Great articles like Daniel Foreman-Mackey's "emcee: The MCMC Hammer in PASP is a perfect example of a highly-referenced software article."Peter Teuben from the University of Maryland and chair of the ASCL’s Advisory Committee) opened the session with a few words about the use of software in research articles. He outlined the layout of the session. A talk by Matteo Cantiello set the scene on how we have reached the point where we are now. Four presentations by representatives from different journals presented their policies on software publication followed Cantiello’s talk, and they were followed by presentations by representatives of others with roles in publishing software: the software author, the data editor, the ADS and the ASCL. The floor was then opened for discussion and Q&A. Teuben moderated the discussion, and at the end of it, turned the podium over to Robert Nemiroff from Michigan Technological University, and a founder of the ASCL, for a summary and closing remarks.

Presentations
Some of the main points from each presentation are summarized below; the titles of each are links to the slides used by the presenters.

  • The Evolution of Software Publication in Astronomy, Matteo Cantiello (Flatiron Institute)
    Cantiello states that the complexity of astrophysics requires computationally intensive models, making astronomy a digital science, and that astronomers have a rich computational environment available, allowing them to easily version, share, and deploy astronomy software. Reproducibility paradoxDespite this, software is often not shared, resulting in a reproducibility paradox: astronomers use computation to provide precise, accurate results, but research has become less transparent with the increase in the use of computational methods. Adding external links to papers to link to software is not a reliable solution to software sharing because of link rot. Formats have changed very little in the last 400 years; despite progress both technologically and socially, the format of papers is still largely the same. He stated that astronomy now has an opportunity to rethink scientific papers as research repositories, with executable objects containing narrative, figures, data, and code.
  • Software papers and citation in the AAS Journals, Chris Lintott (AAS Journals)
    The AAS journals policy on software until recently was set in 1964, which stated that the “need for communication between astronomers interested in computation is already supplied by associations of users of automated computing machines.” The AAS journals changed their policies at the beginning of 2016, and recognized that if novel code is important to published research then it is likely appropriate to describe it in such a paper. Papers can be short, descriptive, and need not include research resultsAAS journals are interested in disclosing software in a form that is currently recognized: the research article, so now allow short papers on code that can be short, descriptive, and do not need to include scientific results. AAS formally recommends open source licensing but does not require it. AAS journals ask people to cite the software paper, as this is the currency the field cares about and also ask people to cite the code. In addition, they request people use the \software{} tag to create a software section in a paper; this is similar to the \facilities{} tag already in use. AAS Publishing continues to think about how to improve, and are introducing the concept of ‘living’ papers, which can be updated with new sections and expanded author lists, so software authors don’t need to publish a new paper to give credit to software authors who have contributed to a new version of the software. Lintott encouraged those interested in living papers to contact him.
  • Software policies and guidelines at Nature, Leslie J. Sage (Nature)
    First, Sage explained the context in which Nature‘s policy is created: Nature is driven by biologists, who live in a very different world from astronomers. Unlike astronomers, biologists live in Windows world. Right now, two journals, Nature Methods and Nature Biotech, require code to be made available, and there are ongoing discussions about whether Nature should do this for other journals. There are formidable problems because of the issue of very specialized code, for example, code that is optimized to compile on a particular Beowulf cluster that may not compile anywhere else. There will be a call for public comment, and Sage hopes astronomers will provide input that is useful for astronomers within that context. Sage raised a number of points that warrant public discussion, such as a preference voiced by some to see detailed descriptions of the algorithms used rather than having the scripts published. Another point to consider for input is that though a lot of software has been made publicly available, all software is written with certain constraints and boundary conditions; some people not aware of these constraints and conditions may drive the software beyond those limits; this raises the question as to whether the results are physically meaningful.
  • SpringerNature data and software policies for astrophysics journals, Ramon Khanna (Springer)
    Springer is encouraging authors to take care of transparency and reproducibility of their results presented in articles, allowing them to append relevant information on source code or the full code in an appendix of the paper; authors can also append the full code, or use other methods to provide this information, such as alternative repositories (e.g., CDS, ASCL, Figshare), and making this information available. They would like the full data and code available. Khanna acknowledged some challenges, including that authors are often not willing to share their software and/or data, editors are often not willing or at least not determined enough to execute policy, and citation standards are unclear. One of the questions is how to execute this policy in the face of unwillingness from authors, editors, reviewers, etc.Questions arise as to how software can be peer reviewed; this would require standards for documentation,  presenting how the results were obtained, making data and software available, and for reviewing the source code itself. How can referees handle this effort? Khanna pointed out that in a field as advanced as astronomy is, and already having some standards and domain resources such as archives, it’s not so much the publisher that should drive new standards, but the community itself.
  • Journal of Open Source Software (JOSS): Design and first-year review, Arfon M. Smith (STScI/JOSS)
    Smith stated that he created JOSS accidentally, from frustration about the overhead of publishing papers about software, and acknowledged that software papers are a hack of the current system to provide a citable, creditable research object for software.  JOSS (http://joss.theoj.org/) seeks to improve the quality of software; its peer review process is almost entirely about the software that’s submitted, and includes making sure the documentation is sufficiently fleshed out, that the package includes automated tests, and that the software has an open source license so can be reused. Smith said it should take about an hour to write a one-page paper for JOSS for those with a well set up repository for their code. The reviews are public on Github and accepted submissions appear on the JOSS site, which has published 200 papers online.
  • Lessons Learned through the Development and Publication of AstroImageJ, Karen Collins (Center for Astrophysics)
    Collins discussed her experience with publishing her software AstroImageJ, a data reduction and image display interface with analysis capabilities specialized for time series differential photometry. She developed the code over several years to support her research. She initially had no intention of releasing the code to the public, but her collaborators saw her plots and graphs and asked to use the software, which was posted to the university’s website to give team members access to it. AstroImageJ lessons learnedShe found her fellow KELT-FUN team members were an excellent focus group; they provided great feedback on the software before it was published, enabling her to add useful features to the software. Results using AstroImageJ started appearing in journals; she registered the software with the ASCL to give it a citable reference, and as usage (and support tasks) grew, she and others working on the code decided to submit a paper to the Astronomical Journal (AJ) to provide good exposure to the potential userbase for the software. This resulted in about 4K downloads of the software in the first year, and the paper is listed 4th on AJ’s most read list. Among the lessons learned in publishing AstroImageJ are to specify how your code is licensed and how it should be cited, make the source code easily accessible, and provide easy way to install and update the software.
  • The roles of the AAS Journals’ Data Editors, August Muench (AAS Journals)
    Muench covered the data editors’ workflow for all submitted manuscripts. A quick review of 60%-90% of all submitted manuscripts is performed, with scripts run on the manuscripts to identify references to code by looking for such things as Github repositories to see whether  their citations need to be reviewed. The editors make notes on the software, data, and figures for review by a scientific editor or the author with recommendations for improving citations for these research artifacts. A subset of accepted articles, 15-20%, undergo a more rigorous post-acceptance data review; this includes a review of tabular data, figures, and interactive elements in addition to software. If necessary, the data editors request that authors acquire DOIs or get preferred citati"People recognize software via plots (and other fingerprints). Make sure you cite the code. I still recognize plots made with PAW."ons for the software used in the research. Muench mentioned that he uses ten keywords in his scripts to identify software, and ends up with a surprising number of articles that do not mention code at all. He stated that part of a data editor’s role to improve software and data citation is educating authors.
  • The role of the ADS in software discovery and citation, Alberto Accomazzi (NASA Astrophysics Data System)
    Accomazzi described what ADS does to promote software discovery and citation, but first he shared ADS’s traditional core responsibilities: to discover content, typically science papers, related to astronomy. Some years ago, the capability to track citations was introduced. As the expectations of community have evolved, so have ADS’s policies, moving from ingesting records about scientific papers to records about scholarly works, including data catalogs, observing proposals, and other artifacts such as software. They have also evolved from tracking citations to articles to citations to tracking citations to scholarly content. How ADS awards citationsADS has an interest in enabling linking so users can easily and uniquely identify the software that was used. Accomazzi covered how ADS ingestion works; for content to be considered for inclusion in ADS, it must be scholarly, related to astronomy, and published formally — not just on a website, but following an explicit editorial process. He also discussed how citations are tracked and what ADS needs to count a citation, going through several examples of what does and does not work for citation. The bottom line for software is to cite it by using a formal citation and a unique identifier; a URL to a website or a DOI in a footnote are not captured as citations. ASCL, JOSS, and Zenodo are ways software can get a persistent identifier to use in a formal citation, and these citations can be tracked by ADS. Accomazzi also discussed how software may have several records in ADS, and that in the future, these records will be crosslinked, as will different versions of a software package so that eventually, ADS can provide cumulative metrics for all different versions of that software product, and like all citation data, this information will become publicly available through an API.
  • The Astrophysics Source Code Library: Supporting software publication and citation, Alice Allen (ASCL/UMD)
    Allen gave a brief overview of what the ASCL is, and stated that though entries in this citable online registry usually point to a software package’s download it, the ASCL can and does serve as a repository for those authors who want to deposit an archive file for their code. The ASCL assigns a DOI to software that it stores. She covered the three main reasons the ASCL exists: to make research more transparent, to improve communication about research computations, and to disseminate software of utility to others. Allen acknowledged that though there is software that might be useful to astronomy, the ASCL focuses on that which has been used in refereed research or submitted for refereeing, this to support the research record. ASCL editors take an active approach in looking for software in research papers and registering them; authors are encouraged to submit their own software, too, and submission by author increased 23% in 2017 over 2016. The ASCL supports software publication and citation in a number of ways, including providing a citation avenue for software and listing preferred citation information in ASCL entries. The ASCL has been online since 1999; it supports the Force11 software citation principles and was a party to  developing them. It was also party to a Dagstuhl Manifesto, another cross-disciplinary effort  that focused on steps members of a research community can take on their own. Among these steps is citing software properly — in a trackable way — and when reviewing a paper, ensuring that it cites the software used in the research.

Discussion
After the presentations, Teuben commented that he thought journals could do a better job in instructing referees about software, to identify when code is involved in research and insist on citations to it. He hoped the discussion would touch on this, and then opened the floor to all. People interested in software sustainability might want to follow @si2urssi (urssi.us) which is working to plan a US research software systainability institute - a first workshop will likely be in AprilDiscussion was lively and may be covered in more depth in a future post, but some of the major points were:

  • There’s still fear about releasing software, still resistance to doing so
  • Science is all about reproducibility; it’s not science if it’s not reproducible
  • Who should push for greater openness is an open question, with some wanting journals to do this, and others feeling it’s up to the astronomy community — us! — to enforce the standards we want
  • Astronomers are often not trained in software engineering techniques; greater education in this area would be helpful

"If software developers were well funded, ie would be easier to get people to share their code."

Teuben brought the discussion to an end and turned the floor over to Robert Nemiroff (Michigan Technological University), who briefly summarized the presentations and discussion and closed the session.

My thanks to David W. Hogg and Peter Teuben for work on developing the session, to Peter for his excellent moderating, to Robert for closing the session, and for PW Ryan for serving as scribe. My thanks to Matteo, Chris, Leslie, Ramon, Arfon, Karen, Gus, and Alberto for their excellent presentations and participation, to the Astronomical Data Group at the Flatiron Institute for partnering with the ASCL, and to the Heidelberg Institute for Theoretical Studies, the University of Maryland College Park, and Michigan Technological University for supporting the ASCL.

Slides from Astronomy Software Publishing: Community Roles and Services

THURSDAY, 11 JANUARY 2018
Special Session: Astronomy Software Publishing: Community Roles and Services
10:00 am – 11:30 am
National Harbor 2

The Astrophysics Source Code Library (ASCL) and Astronomical Data Group at the Flatiron Institute organized a Special Session at the 231st AAS meeting in National Harbor, MD on Astronomy Software Publishing: Community Roles and Services. Click on a talk’s title to download its slides.


Matteo Cantiello (Flatiron Institute), The Evolution of Software Publication in Astronomy
Chris Lintott (AAS Journals), Software papers and citation in the AAS Journals
Leslie J. Sage (Nature), Software policies and guidelines at Nature
Ramon Khanna (Springer), SpringerNature data and software policies for astrophysics journals
Arfon M. Smith (STScI/JOSS), Journal of Open Source Software (JOSS): Design and first-year review
Karen Collins (Center for Astrophysics), Lessons Learned through the Development and Publication of AstroImageJ
August Muench (AAS Journals), The roles of the AAS Journals’ Data Editors
Alberto Accomazzi (NASA Astrophysics Data System), The role of the ADS in software discovery and citation
Alice Allen (ASCL/UMD), The Astrophysics Source Code Library: Supporting software publication and citation

ASCL research poster as AAS 231

Poster for Schroedinger's Code research paper showing results
Astronomers use software for their research, but how many of the codes they use are available as source code? We examined a sample of 166 papers from 2015 for clearly identified software use, then searched for source code for the software packages 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 was not available, whether some other form of the software, such as a binary, was. Over 40% of the source code for the software used in our sample was not available for download.

As URLs have often been used as proxy citations for software, we also extracted URLs from one journal’s 2015 research articles, removed those from certain long-term, reliable domains, and tested the remainder to determine what percentage of these URLs were still accessible in September and October, 2017.

P. Wesley Ryan, Astrophysics Source Code Library
Alice Allen, Astrophysics Source Code Library/University of Maryland
Peter Teuben, University of Maryland

Download poster
Download article pre-print

ASCL poster at AAS 231

ASCL poster showing various statistics for ASCL, including increase in citations and growth of resource
The Astrophysics Source Code Library (ASCL, ascl.net) was founded in 1999 by Robert Nemiroff and John Wallin. ASCL editors seek both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and add entries for the found codes to the library. Software authors can submit their codes to the ASCL as well. This ensures a comprehensive listing covering a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL is indexed by both NASA’s Astrophysics Data System (ADS) and Web of Science, making software used in research more discoverable. This presentation covers the growth in the ASCL’s number of entries, the number of citations to its entries, and in which journals those citations appear.

Alice Allen, Astrophysics Source Code Library/University of Maryland
G. Bruce Berriman, Caltech/IPAC-NExScI
Kimberly DuPrie, Space Telescope Science Institute/Astrophysics Source Code Library
Jessica Mink, Smithsonian Astrophysical Observatory
Robert Nemiroff, Michigan Technological University
P.W. Ryan, Astrophysics Source Code Library
Judy Schmidt, Astrophysics Source Code Library
Lior Shamir, Lawrence Technological University
Keith Shortridge, Knave and Varlet
Peter Teuben, University of Maryland
John Wallin, Middle Tennessee State University
Rein H. Warmels, European Southern Observatory

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ASCL at AAS 231

It’s AAS meeting time, and that means a busy busy week! There are some of the ASCL’s activities at this meeting; we hope to see you at our posters and in the Special Session!


Poster 150.10: The Astrophysics Source Code Library by the numbers
Tuesday, January 09, Prince Georges Exhibit Hall

Abstract: The Astrophysics Source Code Library (ASCL, ascl.net) was founded in 1999 by Robert Nemiroff and John Wallin. ASCL editors seek both new and old peer-reviewed papers that describe methods or experiments that involve the development or use of source code, and add entries for the found codes to the library. Software authors can submit their codes to the ASCL as well. This ensures a comprehensive listing covering a significant number of the astrophysics source codes used in peer-reviewed studies. The ASCL is indexed by both NASA’s Astrophysics Data System (ADS) and Web of Science, making software used in research more discoverable. This presentation covers the growth in the ASCL’s number of entries, the number of citations to its entries, and in which journals those citations appear. It also discusses what changes have been made to the ASCL recently, and what its plans are for the future.


Poster 150.28: Schroedinger’s code: Source code availability and transparency in astrophysics
Tuesday, January 09, Prince Georges Exhibit Hall

Abstract: Astronomers use software for their research, but how many of the codes they use are available as source code? We examined a sample of 166 papers from 2015 for clearly identified software use, then searched for source code for the software packages 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 was not available, whether some other form of the software, such as a binary, was. Over 40% of the source code for the software used in our sample was not available for download.

As URLs have often been used as proxy citations for software, we also extracted URLs from one journal’s 2015 research articles, removed those from certain long-term, reliable domains, and tested the remainder to determine what percentage of these URLs were still accessible in September and October, 2017.


Special Session: Astronomy Software Publishing: Community Roles and Services
Thursday, January 11, 10:00 AM – 11:30 AM; National Harbor 2
Organizers: Astrophysics Source Code Library (ASCL)/Astronomical Data Group at the Flatiron Institute

The importance of software to astronomy research is well-established, and excellent arguments to reveal these computational methods to support the research record have been advanced and much discussed in recent years. But what avenues are open to software authors to publish their codes, and what roles and services exist in the community to support their efforts? This session, organized by the Astrophysics Source Code Library (ASCL) and Astronomical Data Group at the Flatiron Institute, answers that question. It builds on previous AAS special sessions and brings together a panel of experts to present on the various avenues for publishing codes and the pros and cons of these avenues, the roles of authors, data editors, and publication indexers in software publication, the benefits of publication to authors and the discipline, and efforts of related community projects to improve aspects of software publication. After the presentations, the floor will be open for discussion and questions.

The topics and panelists are:

Introductory remarks, Peter Teuben (University of Maryland)
The evolution of software publication in astronomy, Matteo Cantiello (Flatiron Institute, Center for Computational Astrophysics/Princeton University)
Software papers and citation in the AAS journals, Chris Lintott (AAS Journals/University of Oxford)
Software policies and guidelines at Nature, Leslie J. Sage (Physical Sciences, Nature)
SpringerNature data and software policies for astrophysics journals, Ramon Khanna (Astronomy, Springer)
Journal of Open Source Software (JOSS): design and first-year review, Arfon M. Smith (Space Telescope Science Institute)
Lessons learned through the development and publication of AstroImageJ, Karen Collins (Harvard-Smithsonian Center for Astrophysics)
The roles of the AAS Journals’ Data Editors, August Muench (Journals Division, AAS)
The role of the ADS in software discovery and citation, Alberto Accomazzi (Smithsonian Astrophysical Observatory)
The Astrophysics Source Code Library: Supporting software publication and citation, Alice Allen (ASCL/University of Maryland)
Open discussion and Q&A, Moderated by Peter Teuben (University of Maryland)
Summary and closing remarks, Robert J. Nemiroff (Michigan Technological University)