Category Archives: codes

March 2013 additions to the ASCL

Thirty codes were added to the ASCL in March:

2MASS Kit: 2MASS Catalog Server Kit
ACORNS-ADI: Algorithms for Calibration, Optimized Registration and Nulling the Star in Angular Differential Imaging
ATLAS12: Opacity sampling model atmosphere program
BSE: Binary Star Evolution
CADRE: CArma Data REduction pipeline

CosmoHammer: Cosmological parameter estimation with the MCMC Hammer
DPUSER: Interactive language for image analysis
emcee: The MCMC Hammer
Galactus: Modeling and fitting of galaxies from neutral hydrogen (HI) cubes
GaPP: Gaussian Processes in Python

GBTIDL: Reduction and Analysis of GBT Spectral Line Data
Ginga: Flexible FITS viewer
idistort: CMB spectral distortions templates and code
ionFR: Ionospheric Faraday rotation
iSAP: Interactive Sparse Astronomical Data Analysis Packages

MAGIX: Modeling and Analysis Generic Interface for eXternal numerical codes
micrOMEGAs: Calculation of dark matter properties
MOPSIC: Extended Version of MOPSI
pysynphot: Synthetic photometry software package
SMMOL: Spherical Multi-level MOLecular line radiative transfer

SSE: Single Star Evolution
Stellarics: Inverse Compton scattering from stellar heliospheres
Sunrise: Radiation transfer through interstellar dust
SWIFT: A solar system integration software package
TAC-maker: Transit Analytical Curve maker

TGCat: Chandra Transmission Grating Catalog and Archive
TYCHO: Stellar evolution code
UCL_CHEM: time and depth dependent gas-grain chemical model
UCL_PDR: Time dependent photon-dissociation regions model
Xmatch: GPU Enhanced Astronomic Catalog Cross-Matching

Finding codes and Russian nesting dolls

As those familiar with the ASCL know, those working on it take an active approach to sharing astrophysical source code, ferreting out codes, looking for their download sites, and creating entries for them in the ASCL. We welcome and indeed (enthusiastically!) encourage code authors to create entries for their codes, but most of the indexing of codes is currently done by ASCL associate editor Kim DuPrie and me.

I regularly read through pre-prints looking for mention of codes not yet indexed by the ASCL; Advisory Committee Chairman Peter Teuben does the same. He has access to publications I cannot get to, such as MNRAS, and looks there for codes as well. A paper may yield a code new to the ASCL, and sometimes, a paper will reveal what Peter and I refer to as Russian dolls: the deeper we get into a paper, the more codes it reveals. One paper he sent to me recently revealed 37 (!) codes, only 5 of which the ASCL had indexed. Thirty-two new codes to try to find!

Other times, a paper will mention two or three or more codes which lead us to other papers which mention yet more codes, which lead us to papers which mention even more codes… and though the ASCL indexes over 600 codes, there are still hundreds, probably thousands, out there it hasn’t indexed, so some of these more more MORE codes that we come across also need to be found. Like Russian nesting dolls, the codes go on and on and on.

It’s times like that — finding 32 new codes in just one paper! peeling back layers and layers of new codes! — I wish I could work on the ASCL full-time. Well, also the times I look at the list we’d already compiled (a list I stopped adding to over a year ago) of ~ 200 codes to find. Also the times I look at the list of things still to be done for/on/about the ASCL beyond indexing new codes.

So many codes, so little time to spend on them, alas!

Where do they come from? ASCL pageviews by country

Idly browsing through Google Analytics statistics on the ASCL, I pulled out pageviews by country, these just of the ASCL forum on Asterisk for this month so far. Of the 4,843 pageviews, 1,939 (40%) are from the US, which means of course that 60% are not. People from eighty-three countries have accessed the code entries forum; I’ve tagged the pie slices below of the ten countries with at least 2% of the total pageviews. Click on the pie to see the chart at full size.

March pageviews by country, as of 3/25/2013

March pageviews by Country, as of 3/25/2013

 

Updated codes

Gyula Józsa has been updating TiRiFiC and fixing minor bugs, and has added features and made the code standalone software, no longer requiring GIPSY; instead, input files are in FITS format now. You can be alerted to updates by subscribing to the TiRiFiC thread on the ASCL.

Peter Teuben reported on the ASCL that an updated version of ZEUS-MP (V1.5) has been made public by the U.Maryland group. Please find the updated version here: http://www.netpurgatory.com/zeusmp.html

He also provided an additional download site for new code GRID-core.

If you would like to receive an email whenever a new post is made on the ASCL forum which houses the code entries, instructions for subscribing to the forum are available.

February 2013 additions to the ASCL

Seventeen codes were added to the ASCL in February:

ACS: ALMA Common Software
DisPerSE: Discrete Persistent Structures Extractor
EPICS: Experimental Physics and Industrial Control System
ESO-MIDAS: General tools for image processing and data reduction
FASTPHOT: A simple and quick IDL PSF-fitting routine

GALA: Stellar atmospheric parameters and chemical abundances
GRID-core: Gravitational Potential Identification of Cores
IAS Stacking Library in IDL
ICORE: Image Co-addition with Optional Resolution Enhancement
ISIS: Interactive Spectral Interpretation System for High Resolution X-Ray Spectroscopy

MARX: Model of AXAF Response to X-rays
ME(SSY)**2: Monte Carlo Code for Star Cluster Simulations
Minerva: Cylindrical coordinate extension for Athena
NIFTY: A versatile Python library for signal inference
pNbody: A python parallelized N-body reduction toolbox

SYNMAG Photometry: Catalog-level Matched Colors of Extended Sources
XDQSO: Photometic quasar probabilities and redshifts

We also added CSCview: A Graphical User Interface to the Chandra Source Catalog to our web tools page, and pyro: hydro by example — A simple python-based tutorial on computational methods for hydrodynamics to our list of online resources. As of February 28, there were 585 codes in the ASCL.

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!