ASCL News
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One of the unconference sessions (proposed during the event) held at December's .Astronomy was on software citation, this subject having come up in an earlier session on improving credit for software.
Discussion and comments in the session inspired me to look at astronomy's current practices for citing software. Though not an exhaustive list, I looked in more than a dozen journals for citations for codes used in research, and below are some of the examples I gathered.
The most common way to cite software is to reference a paper describing the code. This is how, for example, the authors of yt would like that software cited, as shown from a recent MNRAS paper:
Sometimes a link to the website for a code is listed as a reference to it, as was done in a Classical and Quantum Gravity paper:
Conference proceedings are cited in some cases, as the citation below for WCSTools in an The Astrophysical Journal paper demonstrates:
ASCL entries can be cited, too, as shown in this citation for pynbody in a paper published in Physical Review D:
Someone -- I don't remember who -- reported that Google Scholar does not index mentions of codes, GitHub repos, etc. as citations, because they are not papers. An opinion tweeted out about this summed up the sentiment in the room pretty well! I plan to take this up with Google after the AAS meeting. Fortunately, ADS does index properly formatted software references; the only reference listed in this post that I didn't see captured by ADS was the URL for CAMB, which is not surprising (nor expected).A subsequent post will include additional information and a list of resources about software citation, to be posted before the first Special Interest Group on software publishing meeting scheduled at AAS225 that will be held on Tuesday, January 6, from 3:45 PM – 4:45 PM in 615 in the Convention Center. The main topic of this meeting will be software citation, and all interested parties are welcome to attend.
The journals below were part of my hunting grounds for software citations. Ever had a citation to software you used in research refused by a publication? If so, I'm interested in knowing the details; please share here or send them to editor@ascl.net. Thanks!
American Institute of Physics Proceedings
Astronomy & Astrophysics
Astronomy and Computing
The Astronomical Journal
The Astrophysical Journal
The Astrophysical Journal Supplement
Classical and Quantum Gravity
Icarus
Monthly Notices of the Royal Astronomical Society
Nature
Physical Review D
Proceedings of the SPIE
Publications of the Astronomical Society of Australia
Publications of the Astronomical Society of Japan
Publications of the Astronomical Society of the PacificAdditional screenshots of software citations:
Formatting counts! Below, two citations for Turbospectrum, the first formatted in a way ADS can pick up and count the citation, the second one not.
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The ASCL is at .Astronomy ("dot astronomy"), which officially starts tomorrow morning. Three days of unconference, discussion, sessions, hacking, ideas, collaborating, fun, cool buttons, and, rumor has it, Belgian chocolate, in the magnificent city of Chicago. Follow along on Twitter, hashtag #dotastro!
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Twenty-seven codes were added in November:
Anmap: Image and data analysis
BKGE: Fermi-LAT Background Estimator
CGS3DR: UKIRT CGS3 data reduction software
ECCSAMPLES: Bayesian Priors for Orbital Eccentricity
Flicker: Mean stellar densities from flickergalpy: Galactic dynamics package
GPI Pipeline: Gemini Planet Imager Data Pipeline
HOPE: Just-in-time Python compiler for astrophysical computations
iDealCam: Interactive Data Reduction and Analysis for CanariCam
JCMT COADD: UKT14 continuum and photometry data reductionNAFE: Noise Adaptive Fuzzy Equalization
NDF: Extensible N-dimensional Data Format Library
NEAT: Nebular Empirical Analysis Tool
OPERA: Open-source Pipeline for Espadons Reduction and Analysis
POSTMORTEM: Visibility data reduction and map making packagepyGadgetReader: GADGET snapshot reader for python
PyMGC3: Finding stellar streams in the Galactic Halo using a family of Great Circle Cell counts methods
pysovo: A library for implementing alerts triggered by VOEvents
Raga: Monte Carlo simulations of gravitational dynamics of non-spherical stellar systems
RC3 mosaicking pipeline: Creating mosaics for the RC3 CataloguesegueSelect: SDSS/SEGUE selection function modelling
sic: Sparse Inpainting Code
SPOTROD: Semi-analytic model for transits of spotted stars
SPT Lensing Likelihood: South Pole Telescope CMB lensing likelihood code
Starlink Figaro: Starlink version of the Figaro data reduction software packageutil_2comp: Planck-based two-component dust model utilities
voevent-parse: Parse, manipulate, and generate VOEvent XML packets -
Five codes were added to the ASCL in October:
DIAMONDS: high-DImensional And multi-MOdal NesteD Sampling
GIZMO: Multi-method magneto-hydrodynamics+gravity code
MEPSA: Multiple Excess Peak Search Algorithm
RICH: Numerical simulation of compressible hydrodynamics on a moving Voronoi mesh
UVOTPY: Swift UVOT grism data reduction -
Thirteen codes were added to the ASCL in September:
CHLOE: A tool for automatic detection of peculiar galaxies
CosmoSIS: Cosmological parameter estimation
IM3SHAPE: Maximum likelihood galaxy shear measurement code for cosmic gravitational lensing
IFSFIT: Spectral Fitting for Integral Field Spectrographs
IFSRED: Data Reduction for Integral Field SpectrographsiSpec: Stellar atmospheric parameters and chemical abundances
LANL*: Radiation belt drift shell modeling
mixT: single-temperature fit for a multi-component thermal plasma
Nahoon: Time-dependent gas-phase chemical model
ORBS: A reduction software for SITELLE and SpiOMM datarmfit: Forward-folding spectral analysis software
Slim: Numerical data compression for scientific data sets
Tsyganenko Geomagnetic Field Models -
Twenty-three codes were added to the ASCL in August:
APS: Active Parameter Searching
bamr: Bayesian analysis of mass and radius observations
CosmoPhotoz: Photometric redshift estimation using generalized linear models
GALAPAGOS-C: Galaxy Analysis over Large Areas
GALIC: Galaxy initial conditions constructionHEAsoft: Unified Release of FTOOLS and XANADU
IIPImage: Large-image visualization
Imfit: A Fast, Flexible Program for Astronomical Image Fitting
LIA: LWS Interactive Analysis
LightcurveMC: An extensible lightcurve simulation programNumCosmo: Numerical Cosmology
O2scl: Object-oriented scientific computing library
PhotoRApToR: PHOTOmetric Research APplication TO Redshifts
PIA: ISOPHOT Interactive Analysis
pieflag: CASA task to efficiently flag bad dataPOET: Planetary Orbital Evolution due to Tides
RDGEN: Routines for data handling, display, and adjusting
Skycorr: Sky emission subtraction for observations without plain sky information
SPAM: Source Peeling and Atmospheric Modeling
VisiOmatic: Celestial image viewerVPFIT: Voigt profile fitting program
vpguess: Fitting multiple Voigt profiles to spectroscopic data
WSClean: Widefield interferometric imager -
Twenty codes were added to the ASCL in July:
AstroML: Machine learning and data mining in astronomy
ASTRORAY: General relativistic polarized radiative transfer code
BayesFlare: Bayesian method for detecting stellar flares
Brut: Automatic bubble classifier
CLE: Coronal line synthesise-MERLIN data reduction pipeline
Exopop: Exoplanet population inference
EZ_Ages: Stellar population age calculator
Halogen: Multimass spherical structure models for N-body simulations
kungifu: Calibration and reduction of fiber-fed IFU astronomical spectroscopyMATLAB package for astronomy and astrophysics
MCMAC: Monte Carlo Merger Analysis Code
Period04: Statistical analysis of large astronomical time series
PINGSoft2: Integral Field Spectroscopy Software
SAMI: Sydney-AAO Multi-object Integral field spectrograph pipelineSPECDRE: Spectroscopy Data Reduction
The Starfish Diagram: Statistical visualization tool
TWODSPEC: Long-slit and optical fiber array spectra extensions for FIGARO
VIDE: The Void IDentification and Examination toolkit
VStar: Variable star data visualization and analysis tool -
Twenty codes were added to the ASCL in June:
ASTROM: Basic astrometry program
ASURV: Astronomical SURVival Statistics
Autoastrom: Autoastrometry for Mosaics
CGS4DR: Automated reduction of data from CGS4
COCO: Conversion of Celestial CoordinatesCoREAS: CORSIKA-based Radio Emission from Air Showers simulator
FROG: Time-series analysis
GAUSSCLUMPS: Gaussian-shaped clumping from a spectral map
IRAS90: IRAS Data Processing
IRCAMDR: IRCAM3 Data Reduction SoftwareIUEDR: IUE Data Reduction package
JCMTDR: Applications for reducing JCMT continuum data in GSD format
MATCH: A program for matching star lists
PAMELA: Optimal extraction code for long-slit CCD spectroscopy
PERIOD: Time-series analysis packagePOLMAP: Interactive data analysis package for linear spectropolarimetry
RV: Radial Components of Observer's Velocity
STARMAN: Stellar photometry and image/table handling
TSP: Time-Series/Polarimetry Package
VADER: Viscous Accretion Disk Evolution Resource -
Eighteen codes were added to the ASCL in May:
ATV: Image display tool
CURSA: Catalog and Table Manipulation Applications
DATACUBE: A datacube manipulation package
Defringeflat: Fringe pattern removal
DIPSO: Spectrum analysis codeECHOMOP: Echelle data reduction package
ESP: Extended Surface Photometry
FLUXES: Position and flux density of planets
FORWARD: Forward modeling of coronal observables
HIIPHOT: Automated Photometry of H II RegionsLBLRTM: Line-By-Line Radiative Transfer Model
PHOTOM: Photometry of digitized images
PISA: Position Intensity and Shape Analysis
POLPACK: Imaging polarimetry reduction package
PROPER: Optical propagation routinesTelFit: Fitting the telluric absorption spectrum
The Hammer: An IDL Spectral Typing Suite
TRIPP: Time Resolved Imaging Photometry Package -
Twenty-six codes were added to the ASCL in March:
ASTERIX: X-ray Data Processing System
BAOlab: Image processing program
CCDPACK: CCD Data Reduction Package
CHIMERA: Core-collapse supernovae simulation code
computePk: Power spectrum computationdisc2vel: Tangential and radial velocity components derivation
GAIA: Graphical Astronomy and Image Analysis Tool
GPU-D: Generating cosmological microlensing magnification maps
GRay: Massive parallel ODE integrator
Inverse Beta: Inverse cumulative density function (CDF) of a Beta distributionISAP: ISO Spectral Analysis Package
JAM: Jeans Anisotropic MGE modeling method
KAPPA: Kernel Applications Package
KINEMETRY: Analysis of 2D maps of kinematic moments of LOSVD
Lightcone: Light-cone generating scriptMGE_FIT_SECTORS: Multi-Gaussian Expansion fits to galaxy images
MLZ: Machine Learning for photo-Z
pyExtinction: Atmospheric extinction
RMHB: Hierarchical Reverberation Mapping
SLALIB: A Positional Astronomy LibrarySOFA: Standards of Fundamental Astronomy
SURF: Submm User Reduction Facility
T(dust) as a function of sSFR
Unified EOS for neutron stars
Viewpoints: Fast interactive linked plotting of large multivariate data setsYNOGKM: Time-like geodesics in the Kerr-Newmann Spacetime calculations
And seventeen codes were added to the ASCL in April:
AMBIG: Automated Ambiguity-Resolution Code
AST: World Coordinate Systems in Astronomy
CAP_LOESS_1D & CAP_LOESS_2D: Recover mean trends from noisy data
carma_pack: MCMC sampler for Bayesian inference
Comet: Multifunction VOEvent brokerLTS_LINEFIT & LTS_PLANEFIT: LTS fit of lines or planes
macula: Model of rotational modulations of a spotted star
RegPT: Regularized cosmological power spectrum
SAS: Science Analysis System for XMM-Newton observatory
SER: Subpixel Event Repositioning AlgorithmsSpecPro: Astronomical spectra viewer and analyzer
Spextool: Spectral EXtraction tool
TORUS: Radiation transport and hydrodynamics code
TTVFast: Transit timing inversion
VictoriaReginaModels: Stellar evolutionary tracksWFC3UV_GC: WFC3 UVIS geometric-distortion correction
ZDCF: Z-Transformed Discrete Correlation Function
