Category Archives: codes

Even more data play: Social media and the rest

The pie below shows what percentage of codes in the ASCL have social coding links in their entries, and the Starlink caveat still holds: all the Starlink codes are in one Github repo, so that repo is represented only once in the pie below. These numbers are somewhat low, as some codes offer a webpage/site to which the ASCL links, with that webpage then directing people to a repostitory. If someone does a better analysis, please send it over; I’d love to include it!

socialvseverythingelse

As before, the data are here.

Related posts:
Data play: Social coding sites
More data play: Common domains

February 2015 additions to the ASCL

Twenty-three codes were added in February, 2015:

ADAM: All-Data Asteroid Modeling
AMIsurvey: Calibration and imaging pipeline for radio data
AstroLines: Astrophysical line list generator in the H-band
Camelus: Counts of Amplified Mass Elevations from Lensing with Ultrafast Simulations
HDS: Hierarchical Data System

KAPPA: Optically thin spectra synthesis for non-Maxwellian kappa-distributions
ketu: Exoplanet candidate search code
libnova: Celestial mechanics, astrometry and astrodynamics library
Magnetron: Fitting bursts from magnetars
MaLTPyNT: Quick look timing analysis for NuSTAR data

Montblanc: GPU accelerated Radio Interferometer Measurement Equations in support of Bayesian Inference for Radio Observations
nbody6tt: Tidal tensors in N-body simulations
NGenIC: Cosmological structure initial conditions
OpenOrb: Open-source asteroid orbit computation software
PARSEC: PARametrized Simulation Engine for Cosmic rays

PolyChord: Nested sampling for cosmology
PyBDSM: Python Blob Detection and Source Measurement
Rabacus: Analytic Cosmological Radiative Transfer Calculations
RH 1.5D: Polarized multi-level radiative transfer with partial frequency distribution
ROBOSPECT: Width fitting program

SPHGR: Smoothed-Particle Hydrodynamics Galaxy Reduction
XFGLENSES: Gravitational lens visualizer
XPCell: Convective plasma cells simulator

Data play: Social coding sites

I’ve posted before about where the codes are; here’s a pie that shows the relative use of Github, Google Code, Bitbucket, and Sourceforge. Please note that because all the Starlink codes are in one Github repo, that repo is represented only once in the pie below. Want to do your own analysis? The site links (1080 of them at the moment, as some codes have more than one) are available here.

socialcodingsitepercentages

January 2015 additions to the ASCL

December 2014 additions to the ASCL

Fourteen codes were added to the ASCL in December 2014:

BRUCE/KYLIE: Pulsating star spectra synthesizer
Cheetah: Starspot modeling code
CRPropa: Numerical tool for the propagation of UHE cosmic rays, gamma-rays and neutrinos
DAMIT: Database of Asteroid Models from Inversion Techniques
GeoTOA: Geocentric TOA tools

HMF: Halo Mass Function calculator
Hrothgar: MCMC model fitting toolkit
MMAS: Make Me A Star
PIAO: Python spherIcAl Overdensity code
SoFiA: Source Finding Application

SOPHIA: Simulations Of Photo Hadronic Interactions in Astrophysics
TraP: Transients discovery pipeline for image-plane surveys
URCHIN: Reverse ray tracer
UTM: Universal Transit Modeller

 

Update: Where the codes are; also, a bit about citing software

This is an update on figures I’ve previously shared (most recently here). Currently, the ASCL indexes 977 codes. The percentage of these codes housed on social coding sites are:

GitHub: 8.1%
SourceForge: 4.2%
Code.Google: 2.8%
Bitbucket: 1.3%

This gives us 16.4% of codes listed on the ASCL housed on a public social coding site, an increase since February of 5.4%, most of this from GitHub (up from 4.2% in February), though the percentages of four sites have increased.

As I said in February, I expect the percentage of codes on social coding sites will continue to grow, especially since GitHub’s use is increasing quickly in the community. One factor some credit for this increase is that GitHub has made it easy to push code to Zenodo for archiving and DOI minting, and providing another way to cite code.*

As mentioned in my previous post, how codes are cited vary. Software citation will be the main topic at Tuesday’s inaugural Software Publishing Special Interest Group meeting at AAS225, which will be held at 3:45 PM in 615 of the Convention Center. If you are at AAS this week, you are welcome to attend and I hope to see you there!

 

*It was reported at .Astronomy6 that “some astro journals won’t even accept a DOI as a citation.” I don’t know which journals and hope someone will enlighten me; I would like to know the rationale for that stance and would gladly take this up with publishers.

Astro software citation examples

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:

Other: MNRAS citation for yt
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:

Other: URL for CAMB in Classical and Quantum GravityOther: link for CAMB
Conference proceedings are cited in some cases, as the citation below for WCSTools in an The Astrophysical Journal paper demonstrates:

Other: citation from ApJ for conference proceedings for WCStools

ASCL entries can be cited, too, as shown in this citation for pynbody in a paper published in Physical Review D:

ASCL: pynbody citation in PhysRevDSomeone — 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 Pacific

Additional screenshots of software citations:

ASCL: Citation to PyKE in A&AOther: citation for astrometry.net in ApJGasoline citation in PhysRevDScreen Shot 2014-12-28 at 10.18.28 PMScreen Shot 2015-01-01 at 1.54.20 PMScreen Shot 2015-01-01 at 2.04.07 PMScreen Shot 2015-01-01 at 11.35.47 PMScreen Shot 2015-01-01 at 1.40.11 PM

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.

Screen Shot 2014-12-28 at 10.12.30 PMScreen Shot 2015-01-01 at 1.31.14 PM