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Category Archives: codes
Omar Laurino joins panel for AAS splinter meeting “Astrophysics Code Sharing?”
Omar Laurino (Harvard-Smithsonian Center for Astrophysics) has joined the panel for the ASCL-sponsored splinter meeting “Astrophysics Code Sharing?” at the upcoming AAS meeting in Long Beach. The topic of his short presentation is What do we want to accomplish?
Session date/time/location:
Wednesday, January 9
2:00 PM – 3:00 PM
Regency Ballroom D (Downtown Hyatt Long Beach)
Peter Teuben (Astronomy Department, UMD) will discuss the results of sessions on code release and discoverability from earlier conferences; he will also moderate the discussion. Robert Hanisch (STScI/VAO) will talk on Integrity in the publication process and Bruce Berriman (IPAC, Caltech) will cover Code repositories in other disciplines. ASCL editor Alice Allen will share a little information about (surprise!) the ASCL. The floor will be open for discussion and sharing after the five-minute presentations. And we’ll have glow-in-the-dark pencils to give away, too!
A preferred reference method seems to be evolving
Looking recently at references to code entries, I see most are in the format:
- author, year, in Astrophysics Source Code Library, record ascl ID
For example: Barnes, J. E., 2011, Astrophysics Source Code Library, record ascl:1102.027
Using the entire ascl ID (ascl:xxxx.xxx) in the reference enables ADS to more easily pick up the citation. It may be helpful to the reader to include the name of the code as well:
- Barnes, J. E., 2011, ZENO, Astrophysics Source Code Library, record ascl:1102.027
The ascl ID number can be used to provide a link to a particular entry. For the example above, typing ascl.net/1102.027 into your browser brings up the entry for the code ZENO.
ADS BibTeX records for citing ASCL entries
ADS is currently generating incorrect BibTeX records for citations to code entries in the ASCL. This will be fixed, but in the meantime, here’s an example of what is being generated and how to fix it, courtesy of Mark Taylor and Alberto Accomazzi.
Hitting the “Bibtex entry for this abstract” button on the ADS page for the ASCL Sherpa entry gives:
@ARTICLE{2011ascl.soft07005F,
author = {{Freeman}, P. and {Nguyen}, D. and {Doe}, S. and {Siemiginowska}, A.
},
title = “{Sherpa: CIAO Modeling and Fitting Package}”,
journal = {Astrophysics Source Code Library},
year = 2011,
month = jul,
pages = {7005},
adsurl = {http://adsabs.harvard.edu/abs/2011ascl.soft07005F},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
The identifier that should be in “pages” is “1107.005” as ASCL IDs are all of the form yymm.nnn. However, a better Bibtex entry format is:
@ARTICLE{2011ascl.soft07005F,
author = {{Freeman}, P. and {Nguyen}, D. and {Doe}, S. and {Siemiginowska}, A.
},
title = “{Sherpa: CIAO Modeling and Fitting Package}”,
journal = {Astrophysics Source Code Library},
year = 2011,
month = jul,
eprint = {ascl:1107.005},
adsurl = {http://adsabs.harvard.edu/abs/2011ascl.soft07005F},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
Note the removal of “page” and the addition of the “eprint” field.
After running LaTeX and BibTeX on it, it should generate an entry in the .bbl file that looks like this:
bibitem[{{Freeman et al.}(2011)]{2011ascl.soft07005F}
{Freeman}, P., {Nguyen}, D., {Doe}, S., and {Siemiginowska}, A. 2011
Astrophysics Source Code Library, eprint{ascl:1107.005}
My thanks to Dr. Accomazzi and Dr. Taylor for their work on this!
October 2012 additions
Thirty-one codes were added to the ASCL in October; on October 31, there were 546 codes in the library.
BOOTTRAN: Error Bars for Keplerian Orbital Parameters
CALCLENS: Curved-sky grAvitational Lensing for Cosmological Light conE simulatioNS
Consistent Trees: Gravitationally Consistent Halo Catalogs and Merger Trees for Precision Cosmology
ConvPhot: A profile-matching algorithm for precision photometry
EZ: A Tool For Automatic Redshift Measurement
FLUKA: Fully integrated particle physics Monte Carlo simulation package
GASGANO: Data File Organizer
GOSSIP: SED fitting code
GP2PCF: Brute-force computation of 2-point correlation functions
HAM2D: 2D Shearing Box Model
inf_solv: Kerr inflow solver
McPHAC: McGill Planar Hydrogen Atmosphere Code
ORBADV: ORBital ADVection by interpolation
PAHFIT: Properties of PAH Emission
pPXF: Penalized Pixel-Fitting stellar kinematics extraction
PVS-GRMHD: Conservative GRMHD Primitive Variable Solvers
PyCosmic: Detecting cosmics in CALIFA and other fiber-fed integral-field spectroscopy datasets
QFitsView: FITS file viewer
QYMSYM: A GPU-accelerated hybrid symplectic integrator
Rockstar: Phase-space halo finder
RVLIN: Fitting Keplerian curves to radial velocity data
Sapporo: N-body simulation library for GPUs
SearchCal: The JMMC Evolutive Search Calibrator Tool
SGNAPS: Software for Graphical Navigation, Analysis and Plotting of Spectra
SMART: Spectroscopic Modeling Analysis and Reduction Tool
Specview: 1-D spectral visualization and analysis of astronomical spectrograms
Systemic Console: Advanced analysis of exoplanetary data
TA-DA: A Tool for Astrophysical Data Analysis
Tempo2: Pulsar Timing Package
TRIP: General computer algebra system for celestial mechanics
Papers to read
Best Practices for Scientific Computing. What can I say? Good reading! Please don’t let not following its recommendations stop you from making your code(s) public or from submitting it/them to the ASCL, however. Offer them up with the CRAPL license; make your codes available no matter how messy they are. After all, Astronomical Software Wants To Be Free. And really, science requires it.
September 2012 additions
Fifteen codes were added to the ASCL in September, bringing the number to 515.
ANNz: Artificial Neural Networks for estimating photometric redshifts
Aspects: Probabilistic/positional association of catalogs of sources
Bayesian Blocks: Detecting and characterizing local variability in time series
CHORIZOS: CHi-square cOde for parameterRized modeling and characterIZation of phOtometry and Spectrophotmetry
DiskFit: Modeling Asymmetries in Disk Galaxies
FAMIAS: Frequency Analysis and Mode Identification for AsteroSeismology
HARM: A Numerical Scheme for General Relativistic Magnetohydrodynamics
IRACproc: IRAC Post-BCD Processing
JAGS: Just Another Gibbs Sampler
LSD: Large Survey Database framework
macula: Rotational modulations in the photometry of spotted stars
MeqTrees: Software package for implementing Measurement Equations
Phantom-GRAPE: SIMD accelerated numerical library for N-body simulations
Scanamorphos: Maps from scan observations made with bolometer arrays
TMCalc: Fast estimation of stellar metallicity [Fe/H]
NEMO 3D has been released (updated code, not the fish)
Peter Teuben, main developer of the code NEMO (and ASCL Advisory Committee chair) released a new version of the code, dubbed NEMO 3D, yesterday. Nothing fishy about this code! It offers improved 3D applications, notably glnemo2.
Codes added in August 2012
Twenty-five codes were added to the ASCL in August; we ended the month with 500 codes.
APLpy: Astronomical Plotting Library in Python
APT: Aperture Photometry Tool
Astrometry.net: Astrometric calibration of images
BASE: Bayesian Astrometric and Spectroscopic Exoplanet Detection and Characterization Tool
Big MACS: Accurate photometric calibration
BINSYN: Simulating Spectra and Light Curves of Binary Systems with or without Accretion Disks
BLOBCAT: Software to Catalog Blobs
BLOCK: A Bayesian block method to analyze structure in photon counting data
BSGMODEL: The Bahcall-Soneira Galaxy Model
ccogs: Cosmological Calculations on the GPU
CUBEP3M: High performance P3M N-body code
EXTINCT: A computerized model of large-scale visual interstellar extinction
EzGal: A Flexible Interface for Stellar Population Synthesis Models
Fewbody: Numerical toolkit for simulating small-N gravitational dynamics
Lare3d: Lagrangian-Eulerian remap scheme for MHD
MPFIT: Robust non-linear least squares curve fitting
MPI-AMRVAC: MPI-Adaptive Mesh Refinement-Versatile Advection Code
ParselTongue: AIPS Python Interface
PSM: Planck Sky Model
PyKE: Reduction and analysis of Kepler Simple Aperture Photometry data
RADPACK: A RADical compression analysis PACKage for fitting to the CMB
SolarSoft: Programming and data analysis environment for solar physics
Swarm-NG: Parallel n-body Integrations
TiRiFiC: Tilted Ring Fitting Code
VARTOOLS: Light Curve Analysis Program
Codes added in July 2012
Fourteen codes were added to the ASCL in July; there are now 475 codes in the library.
Astropysics: Astrophysics utilities for python
dcr: Cosmic Ray Removal
EXOFAST: Fast transit and/or RV fitter for single exoplanet
HiGPUs: Hermite’s N-body integrator running on Graphic Processing Units
Hyperion: Parallelized 3D Dust Continuum Radiative Transfer Code
JKTEBOP: Analyzing light curves of detached eclipsing binaries
L.A.Cosmic: Laplacian Cosmic Ray Identification
PCA: Principal Component Analysis for spectra modeling
PyFITS: Python FITS Module
PyRAF: Python alternative for IRAF
PySALT: SALT science pipeline
VAC: Versatile Advection Code
wvrgcal: Correction of atmospheric phase fluctuations in ALMA observations
xSonify: Sonification software