Astronomy and Computing (A&C)
Change leaders and guidelines
Social coding sites and archival services
Astronomy and Computing (A&C)
The EWASS/NAM Software in Astronomy Symposium gets underway at 9:00 AM today in Room 11A of the Liverpool ACC. This six-session Symposium includes presentations on:
The last session of the Symposium is a Software Publishing Special Interest Group meeting, and will take place on Thursday from 4:30 to 6:00 PM.
For more information on this session, including abstracts, check the interactive guide for Symposium S6a – S6f. See you there!
How much have things changed? The previous “big 4” journals that had citations to ASCL entries have been joined by AJ and the percentage of citations from MNRAS has dropped a bit, but overall, the wedges of these two piecharts, one from October, 2015 and the second from today, look remarkably similar.
At the time the 2015 piechart was created, ASCL entries had been cited 465 times; today, ADS shows 2093 citations to ASCL entries. Seventeen percent of ASCL entries had been cited in October 2015, and as of today, over 29% of ASCL entries have citations.
Of course there are other ways to cite software, and the ASCL supports all citable methods and ASCL entries include preferred citation information where possible.
Do we list how your software should be cited? If not, please let us know your preferred method and we will add it to the entry!
Sixteen codes were added in February 2018:
AntiparticleDM: Discriminating between Majorana and Dirac Dark Matter
ARTIP: Automated Radio Telescope Image Processing Pipeline
astroplan: Observation planning package for astronomers
BHMcalc: Binary Habitability Mechanism Calculator
Glimpse: Sparsity based weak lensing mass-mapping tool
HiGal_SED_Fitter: SED fitting tools for Herschel Hi-Gal data
mrpy: Renormalized generalized gamma distribution for HMF and galaxy ensemble properties comparisons
PyOSE: Orbital sampling effect (OSE) simulator
Sixteen codes were added in December 2017:
Bitshuffle: Filter for improving compression of typed binary data
CosApps: Simulate gravitational lensing through ray tracing and shear calculation
draco: Analysis and simulation of drift scan radio data
FBEye: Analyzing Kepler light curves and validating flares
MPI_XSTAR: MPI-based parallelization of XSTAR program
Nyx: Adaptive mesh, massively-parallel, cosmological simulation code
photodynam: Photodynamical code for fitting the light curves of multiple body systems
Py-SPHViewer: Cosmological simulations using Smoothed Particle Hydrodynamics
QATS: Quasiperiodic Automated Transit Search
RODRIGUES: RATT Online Deconvolved Radio Image Generation Using Esoteric Software
SFoF: Friends-of-friends galaxy cluster detection algorithm
SgrbWorldModel: Short-duration Gamma-Ray Burst World Model
And twelve codes were added in January 2018:
BANYAN_Sigma: Bayesian classifier for members of young stellar associations
BOND: Bayesian Oxygen and Nitrogen abundance Determinations
cambmag: Magnetic Fields in CAMB
DecouplingModes: Passive modes amplitudes
InitialConditions: Initial series solutions for perturbations in our Universe
iWander: Dynamics of interstellar wanderers
RadVel: General toolkit for modeling Radial Velocities
Stan: Statistical inference
The ASCL will receive funding for two years from NASA’s Astrophysics Data Analysis Program (ADAP) to improve the discoverability of NASA-funded astrophysics research software through the ASCL. The project will run under the direction of Dr. Peter Teuben, PI, and Alice Allen, Co-I, through the University of Maryland, College Park.
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.
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.
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.
Some of the main points from each presentation are summarized below; the titles of each are links to the slides used by the presenters.
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. Discussion was lively and may be covered in more depth in a future post, but some of the major points were:
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.
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
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