Author Archives: Alice Allen

ASCL tags and finding software in ADS

The ASCL makes it easy to cite the software astro research depends on. Every astronomy journal and many others such as Science and Nature accept ASCL references; ADS shows citations to ASCL entries from nearly 90 journals. Citations to ASCL entries are tracked by ADS, Web of Science, and other indices.

bar chart showing citations to ASCL entries per year as of December 5, 2018, with the 2018 bar labeled with 1,161 citations
Citations to ASCL entries from ADS as of 12/05/2018

ADS makes it easy to search for software in its holdings through the use of the “software” doctype.
Image of the ADS Bumblebee query box with the search term doctype:software in it

ASCL has started tagging NASA software among its entries, allowing you to search ASCL and ADS for this software.
ADS bumblebee query field showing search terms doctype:software keyword:nasa
Screenshot showing entries in ASCL with the NASA keyword

You can find the tags on an entry below the “Discuss” button.Partial screenshot of Kadenza code entry with a red arrow indication the location of the keywords

Citation information and other statistics, such as the number of site links we most recently checked, when we checked them, and how many are healthy, appear on our dashboard, which is updated on Tuesdays and Fridays.
Partial screenshot of dashboard showing 3382 site links (96.77%) are working as of 2018-12-04 03:57:42. Statistics: There are 1833 codes in the ASCL, and 24 submitted. There are 2847 citations to ASCL entries in ADS. 1833 (100.00%) ASCL codes are in ADS. 584 (31.86%) have ADS citations. Bar charts of code additions by year and citations by year
If you have any questions about citing ASCL entries, we’re happy to help! Email editor@ascl.net or tweet to @asclnet.

November 2018 additions to the ASCL

Twenty codes were added to the ASCL in November 2018:

binaryBHexp: On-the-fly visualizations of precessing binary black holes
DiskSim: Modeling Accretion Disk Dynamics with SPH
DRAGONS: Gemini Observatory data reduction platform
Flame: Near-infrared and optical spectroscopy data reduction pipeline
gdr2_completeness: GaiaDR2 data retrieval and manipulation

MillCgs: Searching for Compact Groups in the Millennium Simulation
muLAn: gravitational MICROlensing Analysis Software
PENTACLE: Large-scale particle simulations code for planet formation
PulsarHunter: Searching for and confirming pulsars
pygad: Analysing Gadget Simulations with Python

Pylians: Python libraries for the analysis of numerical simulations
QuickSip: Project survey image properties onto the sky into Healpix maps
radon: Streak detection using the Fast Radon Transform
RLOS: Time-resolved imaging of model astrophysical jets
SEP: Source Extraction and Photometry

Shark: Flexible semi-analytic galaxy formation model
SIM5: Library for ray-tracing and radiation transport in general relativity
synphot: Synthetic photometry using Astropy
VoigtFit: Absorption line fitting for Voigt profiles
Vplanet: Virtual planet simulator

ASCL research poster at ADASS XXVIII


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 and data, 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 accessible in September and October, 2017. We repeated this test a year later to determine what percentage of these links were still accessible. This poster will present what we learned about software availability and URL accessibility in astronomy.

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

Download poster

Resources mentioned in ADASS 2018 presentation on receiving credit for research software

Presentation slides (PDF)

Journals

Journal of Open Source Software (JORS)

Astronomy and Computing (A&C)

Computational Astrophysics and Cosmology (ComAC)

SoftwareX

Journal of Open Source Software (JOSS)

Research Notes of the AAS

Change leaders and guidelines

Force11/Force11 Software Citation Principles

CodeMeta

Working toward Sustainable Software for Science: Practice and Experiences (WSSSPE)

FAIR principles

Social coding sites and archival services

Bitbucket

GitHub

Figshare

Zenodo

Other resources

Asclepias

arXiv/arXiv Next Generation

DataCite

October 2018 additions to the ASCL

Twenty-one codes were added to the ASCL in October 2018:

APPLawD: Accurate Potentials in Power Law Disks
ARTES: 3D Monte Carlo scattering radiative transfer in planetary atmospheres
Barcode: Bayesian reconstruction of cosmic density fields
catsHTM: Catalog cross-matching tool
cuFFS: CUDA-accelerated Fast Faraday Synthesis

DDS: Debris Disk Radiative Transfer Simulator
Echelle++: Generic spectrum simulator
Eclairs: Efficient Codes for the LArge scales of the unIveRSe
Firefly: Interactive exploration of particle-based data
galfast: Milky Way mock catalog generator

GiRaFFE: General relativistic force-free electrodynamics code
JETGET: Hydrodynamic jet simulation visualization and analysis
MIEX: Mie scattering code for large grains
ODTBX: Orbit Determination Toolbox
pycraf: Spectrum-management compatibility

PyUltraLight: Pseudo-spectral Python code to compute ultralight dark matter dynamics
SOPHISM: Software Instrument Simulator
STARRY: Analytic computation of occultation light curves
STiC: Stockholm inversion code
VaeX: Visualization and eXploration of Out-of-Core DataFrames

XCLASS: eXtended CASA Line Analysis Software Suite

Increasing the visibility of NASA software

Until this week, a search in ADS for doctype:”software” keyword:”NASA” returned zero results. NASA has funded the ASCL to make its astronomy research software discoverable in ADS. This required changes to the ASCL structure and the ADS data feed, and edits to some current records; it also entails mining various NASA software sites for codes that meet the ASCL’s criteria and creating appropriately tagged entries for them. In the first phase of the project, started in July, our wonderful developer Judy Schmidt (@SpaceGeck) worked her magic on our infrastructure, keywords have been added to some existing records, and ADS has ingested the first entries we’ve tagged with the NASA keyword. We can now see first results from this two-year project:

ADS search results for NASA software with 43 records
Additional changes will be coming to the ASCL in the coming months as we continue this funded work. We love this project; at its core, it’s a simple concept, and leverages existing resources (ADS, various NASA code sites, and ASCL) to make research software more discoverable and provides information about NASA software that was not readily available before. It furthers the excellent work NASA has been doing to release software, demonstrates yet another value of ADS (which has many superpowers!), and makes the ASCL more useful, too.

September 2018 additions to the ASCL

Sixteen codes were added to the ASCL in September 2018:

dynesty: Dynamic Nested Sampling package
Isca: Idealized global circulation modeling
LEMON: Differential photometry pipeline
MrMoose: Multi-Resolution Multi-Object/Origin Spectral Energy distribution fitting procedure

NEBULA: Radiative transfer code of ionized nebulae at radio wavelengths
nestcheck: Nested sampling calculations analysis
PASTA: Python Astronomical Stacking Tool Array
PCCDPACK: Polarimetry with CCD

perfectns: “Perfect” dynamic and standard nested sampling for spherically symmetric likelihoods and priors
PyQSOFit: Python code to fit the spectrum of quasars
qp: Quantile parametrization for probability distribution functions
RequiSim: Variance weighted overlap calculator

spops: Spinning black-hole binary population synthesis
stepped_luneburg: Stacked-based ray tracing code to model a stepped Luneburg lens
surfinBH: Surrogate final black hole properties for mergers of binary black holes
VBBINARYLENSING: Microlensing light-curve computation

Seminar at Centre de Recherche Astrophysique de Lyon

I gave a seminar at the Centre de Recherche Astrophysique de Lyon on Friday, September 14, at the invitation of Mohammad Akhlaghi, a post-doc there. Mohammad is very interested and has done a lot of work on reproducibility, ensuring that his work is reproducible and developing a reproducibility framework that can be adopted by others. The seminar took place on CRAL’s lovely historic campus at the Observatoire de Lyon in Saint-Genis-Laval. The title, abstract, and link to the slides are below.


Title: Make your code famous! (or at least discoverable).

Abstract: Source codes are increasingly important for the advancement of science in general and astrophysics in particular. Journal articles detail the general logic behind new results and ideas, but often the source codes that enable these results remain hidden from public view. In this presentation, I will discuss our recent study on the availability of source codes used for published research and how this affects the transparency and reproducibility of astro research. I will cover what the Astrophysics Source Code Library (ASCL, ascl.net) is, how to submit software to the resource, and the benefits of doing so. I will share what happens after software is submitted, how ASCL entries are indexed by ADS, the links between literature and software entries, and how an ASCL ID can be used for citing your code. I will cover good and bad ways to cite software, avenues for publishing software, and how journals are changing to include and recognize the contribution software makes to our discipline.

Slides (PDF)

August 2018 additions to the ASCL

Eleven codes were added to the ASCL in August 2018:

2DSF: Vectorized Structure Function Algorithm
Barycorrpy: Barycentric velocity calculation and leap second management
CPF: Corral Pipeline Framework
Fips: An OpenGL based FITS viewer
hfof: Friends-of-Friends via spatial hashing

hi_class: Horndeski in the Cosmic Linear Anisotropy Solving System
ImPlaneIA: Image Plane Approach to Interferometric Analysis
py-sdm: Support Distribution Machines
PyMieDap: Python Mie Doubling Adding Program
Robbie: Radio transients and variables detection workflow

rsigma: Resonant disturbance

ASCL poster as IAU 2018 General Assembly

ASCL poster for IAU 2018 meeting

Abstract: Astrophysics research relies on software and all robust science requires transparency and reproducibility, yet the computational methods used in our discipline are often not shared or are difficult to find. In recent preliminary research, 40% of the software used in the 2015 papers we examined did not offer source code and restricting the reproducibility of this research. The Astrophysics Source Code Library (ASCL. ascl.net) registers astrophysics research source codes that have been used in refereed research, benefiting the field in numerous ways, including increasing the discoverability of software and making the published research record more robust. With over 1,700 codes, the ASCL is the largest indexed resource for astronomy research codes in existence. This free online registry was established in 1999 and is indexed by ADS and Web of Science. ASCL registration allows your software to be cited on its own merits and provides a citation method that is trackable and accepted by all astronomy journals and journals such as Science and Nature. This presentation covers the benefits of registering astronomy research software with the ASCL, upcoming changes that will enable greater software discovery initially for NASA software and potentially for software funded by other organizations, changes to the ASCL and ADS that benefit researchers, and our research into software use in astronomy.

Alice Allen, Astrophysics Source Code Library/University of Maryland
Robert J. Nemiroff, Michigan Technological University
Peter J. Teuben, University of Maryland

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