Category Archives: codes

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 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

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

Using the ASCL for education

The Astronomy Department at the University of Maryland (College Park) offers a one-credit astronomy scientific computing class, ASTR 288P: Introduction to Astronomical Programming, to provide undergraduates with a foundation in computing. This course is a prerequisite to an advanced-level three-credit course on Computational Astrophysics (ASTR 415).

In ASTR 288P, students learn to work with the UNIX terminal, get the basics of coding with Python and some C, and learn what makefiles are and how to install software, among other topics. The course also introduces students to the ASCL, as for the final class project, students (either alone or in pairs) pick a code from the ASCL, give a short presentation on how they installed and used it, and discuss how that code fits in the large scheme of computing in astrophysics. This allows the students to get a feel for the computational work the astro community is doing and is a good match to test the skills they should have learned in the class.

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

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

July 2018 additions to the ASCL

Thirty-three codes were added to the ASCL in July 2018:

AngPow: Fast computation of accurate tomographic power spectra
ARKCoS: Radial kernel convolution on the sphere
ASP: Ames Stereo Pipeline
BARYCORR: Python interface for barycentric RV correction
CAESAR: Compact And Extended Source Automated Recognition

CLASSgal: Relativistic cosmological large scale structure code
DAMOCLES: Monte Carlo line radiative transfer code
EVEREST: Tools for de-trending stellar photometry
GLS: Generalized Lomb-Scargle periodogram
HELIOS: Radiative transfer code for exoplanetary atmospheres

HII-CHI-mistry_UV: Oxygen abundance and ionizionation parameters for ultraviolet emission lines
HII-CHI-mistry: Oxygen abundance and ionizionation parameters for optical emission lines
kplr: Tools for working with Kepler data using Python
ktransit: Exoplanet transit modeling tool in python
LSC: Supervised classification of time-series variable stars

MAPPINGS V: Astrophysical plasma modeling code
MIDLL: Markwardt IDL Library
nfield: Stochastic tool for QFT on inflationary backgrounds
NRPy+: Code generator for Numerical Relativity
POLARIS: POLArized RadIation Simulator

POWER: Python Open-source Waveform ExtractoR
PUMA: Low-frequency radio catalog cross-matching
PyAutoLens: Strong lens modeling
pyqz: Emission line code
SENR: Simple, Efficient Numerical Relativity

SPEGID: Single-Pulse Event Group IDentification
SSMM: Slotted Symbolic Markov Modeling for classifying variable star signatures
TBI: Three-Body Integration
THOR: Global Circulation Model for planetary atmospheres
Warpfield: Winds And Radiation Pressure: Feedback Induced Expansion, colLapse and Dissolution

wdmerger: Simulate white dwarf mergers with CASTRO
xGDS: Exploration Ground Data Systems
ZBARYCORR: Barycentric redshift calculator

June 2018 additions to the ASCL

Thirty-two codes were added to the ASCL in June 2018:

ASPIC: Accurate Slow-roll Predictions for Inflationary Cosmology
BHDD: Primordial black hole binaries code
BRATS: Broadband Radio Astronomy ToolS
BWED: Brane-world extra dimensions
DirectDM-mma: Dark matter direct detection

DirectDM-py: Dark matter direct detection
EXO-NAILER: EXOplanet traNsits and rAdIal veLocity fittER
exoinformatics: Compute the entropy of a planetary system’s size-ordering
fcmaker: Creating ESO-compliant finding charts for Observing Blocks on p2

foxi: Forecast Observations and their eXpected Information
GLASS: Parallel, free-form gravitational lens modeling tool and framework
gsf: galactic structure finder
Indri: Pulsar population synthesis toolset
Keras: The Python Deep Learning library

LASR: Linear Algorithm for Significance Reduction
OMEGA: One-zone Model for the Evolution of GAlaxies
P2DFFT: Parallelized technique for measuring galactic spiral arm pitch angles
pile-up: Monte Carlo simulations of star-disk torques on hot Jupiters
pwv_kpno: Modeling atmospheric absorption

PyAMOR: AMmOnia data Reduction
PyMUSE: VLT/MUSE data analyzer
pyZELDA: Python code for Zernike wavefront sensors
QE: Quantum opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization
RadFil: Radial density profile builder for interstellar filaments

RMextract: Ionospheric Faraday Rotation calculator
SpaghettiLens: Web-based gravitational lens modeling tool
Spheral++: Coupled hydrodynamical and gravitational numerical simulations
SpS: Single-pulse Searcher
SYGMA: Modeling stellar yields for galactic modeling

WDEC: White Dwarf Evolution Code
WiseView: Visualizing motion and variability of faint WISE sources

Linking literature and software

Most ASCL code entries have one or more links to articles that either describe or use the software in that entry. ADS ingests this information to associate the code with relevant literature. For example, the entry for 2LPTIC: 2nd-order Lagrangian Perturbation Theory Initial Conditions includes a link for an MNRAS paper in the “Appears in: field:

Going to the ADS entry for this software shows that the code is associated with a paper under Associated Articles:This, however, doesn’t tell you anything about the relationship between the article and the software. ADS and the ASCL have been working to improve this. The ASCL has been disambiguating these article links into Described in and Used in. At the ADS Hack Day event last month, ASCL provided ADS with disambiguated links for over 900 entries, and Carolyn Grant had these uploaded into ADS in a matter of minutes. (ADS folks are wizards, I tell you! Wizards! They work magic!!)

Currently, ASCL records appear the same, but for those records we have provided disambiguated article links, ADS displayed them as Described in and Used in, as you can see in the 2-DUST: Dust radiative transfer code entry, for which the ASCL lists two papers:

For ASCL records in which the Appears in link(s) have not been disambiguated, there is no change in how they are displayed in ADS. We have over 700 entries with article links still to be disambiguated and we continue this work; ADS will be ingesting the changes with their regular weekly ingest of ASCL data.