ASCL News
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I've recently learned that some citations to ASCL (and arXiv) entries are not caught by ADS because some BibTeX styles (.bst) don't support the eprint field, which ADS uses when generating the BibTeX for ASCL and arXiv entries. The lack of support for the eprint field results in a citation that formats the ascl ID incorrectly; for ADS to be able to find and count the citation, the ascl ID needs to be formatted just as it appears in the code entry, e.g. ascl:1010.051 for NEMO. The arXiv site has a list of BibTeX styles that have been updated to support the eprint field, and Norman Gray's nice urlbst code can add this functionality to existing .bst files.
(This information has been added to the Citing ASCL code entries page.)
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The ASCL, along with the AAS’s Working Group on Astronomical Software (WGAS), is coordinating a Special Session at the January 2014 AAS meeting. This session is scheduled for 2:00 PM on January 7, and will feature case studies on code release for AstroPy, Montage, and Cloudy in addition to talks on the state of code sharing and funding agencies’ policies.
The session will be moderated by Peter Teuben and Robert Hanisch; the speakers for this session are:
G. Bruce Berriman, NExScI, PAC, Caltech
Gary J. Ferland, University of Kentucky
David W. Hogg, New York University
Daniel S. Katz, National Science Foundation
Erik J. Tollerud, Yale University
Benjamin J. Weiner, University of ArizonaAfter the presentations, the floor will be opened for discussion on ways to encourage code sharing to improve the transparency and efficiency of research and mitigate the negative aspects of releasing code.
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Twenty codes were added to the ASCL in July, and eighteen in August.
July:
AstroTaverna: Tool for Scientific Workflows in Astronomy
cosmoxi2d: Two-point galaxy correlation function calculation
CTI Correction Code
DustEM: Dust extinction and emission modelling
ETC++: Advanced Exposure-Time CalculationsFieldInf: Field Inflation exact integration routines
im2shape: Bayesian Galaxy Shape Estimation
ITERA: IDL Tool for Emission-line Ratio Analysis
K3Match: Point matching in 3D space
LENSVIEW: Resolved gravitational lens images modelingMAH: Minimum Atmospheric Height
Monte Python: Monte Carlo code for CLASS in Python
NEST: Noble Element Simulation Technique
Obit: Radio Astronomy Data Handling
orbfit: Orbit fitting softwarephoSim: Photon Simulator
PURIFY: Tools for radio-interferometric imaging
Shapelets: Image Modelling
SIMX: Event simulator
SOPT: Sparse OPTimisationAugust:
APPSPACK: Asynchronous Parallel Pattern Search
BASIN: Beowulf Analysis Symbolic INterface
Ceph_code: Cepheid light-curves fitting
ChiantiPy: Python package for the CHIANTI atomic database
CReSyPS: Stellar population synthesis codeCRUSH: Comprehensive Reduction Utility for SHARC-2 (and more...)
GYRE: Stellar oscillation code
JHelioviewer: Visualization software for solar physics data
LensEnt2: Maximum-entropy weak lens reconstruction
LOSSCONE: Capture rates of stars by a supermassive black holeMapCurvature: Map Projections
MoogStokes: Zeeman polarized radiative transfer
RADLite: Raytracer for infrared line spectra
SMILE: Orbital analysis and Schwarzschild modeling of triaxial stellar systems
SPEX: High-resolution cosmic X-ray spectra analysisSYN++: Standalone SN spectrum synthesis
SYNAPPS: Forward-modeling of supernova spectroscopy data sets
THELI GUI: Optical, near- & mid-infrared imaging data reductionAlso in August, we added one very cool web resource, the NASA Exoplanet Archive.
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The AAS's Working Group on Astronomical Software (WGAS) and the ASCL are coordinating a Special Session on software at the January 2014 AAS meeting. It will feature several case studies by code authors in addition to broader issues in the development, use, and sharing of software. Watch this space for more information!
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I'm currently working on a report for the Preserving.exe: Toward a National Strategy for Preserving Software summit held at the Library of Congress in May. My head is filled with the reasons and ways (and lack of ways) to save software discussed at the meeting, and by software, I don't mean necessarily astrophysics codes, oh no! All kinds of software: mainframe HR software and VisiCalc and Doom and old browsers and dBASE and ... well, everything.
This has dovetailed nicely, or perhaps alarmingly, with recent readings, including a blog post by Kristin Briney titled How Long Should You Keep Data? and the Retraction Watch post which inspired it, JCI paper retracted for duplicated panels after authors can’t provide original data, about a 2007 paper which recently had one figure retracted because the authors could not provide the data from which it was generated.
Jon Ippolito of the University of Maine was at the summit and wrote about it in his blog post The Ex-files: how long will our software last?
How long indeed? And if you wanted to retrieve data from 2007, would you be able to even if you had the data files? Would you still have the tools available to get into them? In astronomy, probably so; with FITS, astronomy is better off than many sciences. Elsewhere, maybe not.
How long will astronomy software last? That might be unknowable; perhaps a better question, then, is how long should it last?
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Today I was reading the draft of an upcoming thesis defense in our library, and noted the student in question had been using a nice number of codes to support her research. All properly referenced via footnotes, and even some routine names in a "typewriter" font to make them stand out.
Later that afternoon after the weekly graduate un-journal club talk she gave, we and another graduate student got to talking about the ASCL, and explaining to them the triad of paper/data/code that one can view as the three ways our research is now peer review published. In fact, if you look at some recent publications, just after the Acknowledgements, you can find a "Facilities:" line, in which the various facilities (read: observatory/instrument pairs) are listed from which the data in this particular paper were used. We in ASCL have been suggesting that one should add a "Codes:" line as well, with (ASCL) codes used in the paper. Now that ASCL entries are searchable via ADS, there is no reason not to make searching for codes in papers easier. In fact, if you look at the next ADASS conference proceedings, you will find a separate ASCL index in the back of the book!
What do people think, should we ask the editors of journals to make this "Codes:" line a standard feature of papers?
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Sixteen codes were added to the ASCL in June:
BEHR: Bayesian Estimation of Hardness Ratios
Bessel: Fast Bessel Function Jn(z) Routine for Large n,z
grmonty: Relativistic radiative transport Monte Carlo code
Harmony: Synchrotron Emission Coefficients
LRG DR7 Likelihood SoftwareMADCOW: Microwave Anisotropy Dataset Computational softWare
MAPPINGS III: Modelling And Prediction in PhotoIonized Nebulae and Gasdynamical Shocks
Pico: Parameters for the Impatient Cosmologist
PROM4: 1D isothermal and isobaric modeler for solar prominences
PROS: Multi-mission X-ray analysis software systemSAC: Sheffield Advanced Code
STF: Structure Finder
Tapir: A web interface for transit/eclipse observability
VHD: Viscous pseudo-Newtonian accretion
Yaxx: Yet another X-ray extractor -
I'm behind and am glad my next weekend starts on Thursday and runs for four days; perhaps I'll get caught up! Eight codes added in June are now available and more are coming. Watch
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Photo credit: Peter Teuben On May 20 and 21, the Library of Congress's Digital Preservation program held Preserving.exe: Toward a National Strategy for Preserving Software, which focused on preserving software as digital artifacts of life in the late 20th-early 21st century. Robert Hanisch, Peter Teuben, and Alice Allen attended, and Peter, chair of our Advisory Committee, presented a talk on the ASCL. The slides from Peter's talk are now available online.
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Fifteen codes were added to the ASCL in May:
AdaptaHOP: Subclump finder
ESTER: Evolution STEllaire en Rotation
FITDisk: Cataclysmic Variable Accretion Disk Demonstration Tool
GaussFit: Solving least squares and robust estimation problems
GILDAS: Grenoble Image and Line Data Analysis SoftwareMapCUMBA: Multi-grid map-making algorithm for CMB experiments
Merger Trees: Formation history of dark matter haloes
Non-Gaussian Realisations
PINOCCHIO: PINpointing Orbit-Crossing Collapsed HIerarchical Objects
PkdGRAV2: Parallel fast-multipole cosmological codePressure-Entropy SPH: Pressure-entropy smooth-particle hydrodynamics
pynbody: N-Body/SPH analysis for python
TAU: 1D radiative transfer code for transmission spectroscopy of extrasolar planet atmospheres
TPM: Tree-Particle-Mesh code
YNOGK: Calculating null geodesics in the Kerr spacetimeWe also added ExoVis to our web resources and tools page.