Bruce Berriman is blogging about ADASS on his Astronomy Computing Today site; his first installment is already available. And Peter Teuben is posting photos from the event (and Calgary). You can also follow the events on Twitter, hashtag #astroADASS.
Category Archives: news
ASCL poster at ADASS
Abstract: The Astrophysics Source Code Library (ASCL) is a free online registry of codes used in astronomy research; it currently contains over 900 codes and is indexed by ADS. The ASCL has recently moved a new infrastructure into production. The new site provides a true database for the code entries and integrates the WordPress news and information pages and the discussion forum into one site. Previous capabilities are retained and permalinks to ascl.net continue to work. The site offers more functionality and flexibility than the previous site, is easier to maintain, and offers new possibilities for collaboration. This presentation covers these recent changes to the ASCL.
Authors: Robert Hanisch (National Institute of Standards and Technology)
Alice Allen (Astrophysics Source Code Library)
Bruce Berriman (Infrared Processing and Analysis Center, California Institute of Technology)
Kimberly Duprie (Space Telescope Science Institute)
Jessica Mink (Harvard-Smithsonian Center for Astrophysics)
Robert Nemiroff (Michigan Technological University)
Lior Shamir (Lawrence Technological University)
Keith Shortridge (Australian Astronomical Observatory)
Mark Taylor (University of Bristol)
Peter Teuben (University of Maryland)
John Wallin (Middle Tennessee State University)
Working towards Sustainable Software for Science: Practice and Experiences
The 2nd Working towards Sustainable Software for Science: Practice and Experiences workshop (WSSSPE) will be held in New Orleans on Sunday, November 16. The community was invited to submit short actionable papers for use in designing the workshop.
Getting a community to adopt better practices doesn’t usually happen overnight. The ASCL has looked at previous efforts to create code libraries or registries to try to find common barriers that may have inhibited widespread use of these services; the ASCL also has looked to specific management techniques adapted from business practice to encourage change. These findings and change management strategies are discussed in our #WSSSPE 2 paper.
The WSSSPE site lists all of the freely downloadable accepted papers.
ASCL in Computer
The cover feature this month of the IEEE’s flagship journal Computer is Computing in Astronomy. Its “Applications and Examples” includes a short article (behind a paywall) describing the ASCL.
A new site for the ASCL!
On Thursday, July 10, the ASCL’s new site, designed and developed by Judy Schmidt, was moved into production. Code entries are in a new, more flexible database; as a result, browsing is much more flexible, and back-end processing is greatly improved. We have retained WordPress for related content management and this blog, and the phpbb — the discussion forum — for announcements and discussion of individual codes.
I’ve embedded a presentation that highlights the major changes to the ASCL, but hope you will explore the site and click through it rather than click through the slides! Regardless of which you do, I hope you will click Leave a reply below to post your feedback and questions; please let us know what you think!
Thanks!
March and April 2014 code additions
Twenty-six codes were added to the ASCL in March:
ASTERIX: X-ray Data Processing System
BAOlab: Image processing program
CCDPACK: CCD Data Reduction Package
CHIMERA: Core-collapse supernovae simulation code
computePk: Power spectrum computation
disc2vel: Tangential and radial velocity components derivation
GAIA: Graphical Astronomy and Image Analysis Tool
GPU-D: Generating cosmological microlensing magnification maps
GRay: Massive parallel ODE integrator
Inverse Beta: Inverse cumulative density function (CDF) of a Beta distribution
ISAP: ISO Spectral Analysis Package
JAM: Jeans Anisotropic MGE modeling method
KAPPA: Kernel Applications Package
KINEMETRY: Analysis of 2D maps of kinematic moments of LOSVD
Lightcone: Light-cone generating script
MGE_FIT_SECTORS: Multi-Gaussian Expansion fits to galaxy images
MLZ: Machine Learning for photo-Z
pyExtinction: Atmospheric extinction
RMHB: Hierarchical Reverberation Mapping
SLALIB: A Positional Astronomy Library
SOFA: Standards of Fundamental Astronomy
SURF: Submm User Reduction Facility
T(dust) as a function of sSFR
Unified EOS for neutron stars
Viewpoints: Fast interactive linked plotting of large multivariate data sets
YNOGKM: Time-like geodesics in the Kerr-Newmann Spacetime calculations
And seventeen codes were added to the ASCL in April:
AMBIG: Automated Ambiguity-Resolution Code
AST: World Coordinate Systems in Astronomy
CAP_LOESS_1D & CAP_LOESS_2D: Recover mean trends from noisy data
carma_pack: MCMC sampler for Bayesian inference
Comet: Multifunction VOEvent broker
LTS_LINEFIT & LTS_PLANEFIT: LTS fit of lines or planes
macula: Model of rotational modulations of a spotted star
RegPT: Regularized cosmological power spectrum
SAS: Science Analysis System for XMM-Newton observatory
SER: Subpixel Event Repositioning Algorithms
SpecPro: Astronomical spectra viewer and analyzer
Spextool: Spectral EXtraction tool
TORUS: Radiation transport and hydrodynamics code
TTVFast: Transit timing inversion
VictoriaReginaModels: Stellar evolutionary tracks
WFC3UV_GC: WFC3 UVIS geometric-distortion correction
ZDCF: Z-Transformed Discrete Correlation Function
Changes to the ASCL
Improvements are coming to the ASCL; we don’t have a firm timeline yet but expect to have the majority of changes made well before the end of the year. The presentation below shows screenshots of the changes; we hope you like what you see.
The biggest changes are that code entries will move from the APOD discussion forum and will be housed in a new database. We have been running the new database in parallel with the existing ASCL and are getting closer to putting the new database into production. We are integrating our current technologies — this WordPress site for our general information and blog and the phpbb for announcements and discussion for individual codes — into our new infrastructure as well.
Current URLs for code entries will continue to work after implementation of the new system. We will likely be making changes in several phases, and will announce them before and after here and on our social media sites.
Please let us know what you think; thanks!
Code citation news, info, and commentary
Mozilla Science Lab, GitHub and Figshare team up to fix the citation of code in academia
The Mozilla Science Lab, GitHub and Figshare – a repository where academics can upload, share and cite their research materials – is starting to tackle the problem. The trio have developed a system so researchers can easily sync their GitHub releases with a Figshare account. It creates a Digital Object Identifier (DOI) automatically, which can then be referenced and checked by other people.
Discussion of the above article on YCombinator
…it always make me cringe when privately held companies want to define an “open standard” for scientific citations that (surprise!) relies completely on their proprietary infrastructure. I still remember the case of Mendeley, which promised to build an open repository for research documents, and which is now a subsidiary of Elsevier, an organization that does not really embrace “open science”, to put it mildly.
Tool developed at CERN makes software citation easier
Researchers working at CERN have developed a tool that allows source code from the popular software development site GitHub to be preserved and cited through the CERN-hosted online repository Zenodo….
Now, people working on software in GitHub will be able to ensure that their code is not only preserved through Zenodo, but is also provided with a unique digital object identifier (DOI), just like an academic paper.
Webcite
WebCite is an on-demand archiving system for webreferences (cited webpages and websites, or other kinds of Internet-accessible digital objects), which can be used by authors, editors, and publishers of scholarly papers and books, to ensure that cited webmaterial will remain available to readers in the future.
DOIs unambiguously and persistently identify published, trustworthy, citable online scholarly literature. Right?
So DOIs unambiguously and persistently identify published, trustworthy, citable online scholarly literature. Right? Wrong.
The examples above are useful because they help elucidate some misconceptions about the DOI itself, the nature of the DOI registration agencies and, in particular issues being raised by new RAs and new DOI allocation models.
February 2014 code additions
Thirty-five codes were added to the ASCL in February:
Aladin Lite: Lightweight sky atlas for browsers
ANAigm: Analytic model for attenuation by the intergalactic medium
ARTIST: Adaptable Radiative Transfer Innovations for Submillimeter Telescopes
astroplotlib: Astronomical library of plots
athena: Tree code for second-order correlation functions
BAOlab: Baryon Acoustic Oscillations software
BF_dist: Busy Function fitting
CASSIS: Interactive spectrum analyzer
Commander 2: Bayesian CMB component separation and analysis
CPL: Common Pipeline Library
Darth Fader: Galaxy catalog cleaning method for redshift estimation
DexM: Semi-numerical simulations for very large scales
FAMA: Fast Automatic MOOG Analysis
GalSim: Modular galaxy image simulation toolkit
Glue: Linked data visualizations across multiple files
gyrfalcON: N-body code
HALOFIT: Nonlinear distribution of cosmological mass and galaxies
HydraLens: Gravitational lens model generator
KROME: Chemistry package for astrophysical simulations
libsharp: Library for spherical harmonic transforms
MGHalofit: Modified Gravity extension of Halofit
Munipack: General astronomical image processing software
P2SAD: Particle Phase Space Average Density
PyGFit: Python Galaxy Fitter
PyVO: Python access to the Virtual Observatory
PyWiFeS: Wide Field Spectrograph data reduction pipeline
QUICKCV: Cosmic variance calculator
QuickReduce: Data reduction pipeline for the WIYN One Degree Imager
SPLAT-VO: Spectral Analysis Tool for the Virtual Observatory
SPLAT: Spectral Analysis Tool
TARDIS: Temperature And Radiative Diffusion In Supernovae
UVMULTIFIT: Fitting astronomical radio interferometric data
Vissage: ALMA VO Desktop Viewer
wssa_utils: WSSA 12 micron dust map utilities
XNS: Axisymmetric equilibrium configuration of neutron stars
Licensing your code
“Each developer holds copyright in his or her code the moment it is written, and because all the world’s major copyright systems—including the US after 1976—do not require notices, publishing code without a copyright notice doesn’t change this.”1
In the recent code sharing session at the AAS 223 meeting, both Alberto Accomazzi and David Hogg mentioned the difficulty of dealing with code that did not carry any license, copyright notice, nor sometimes even author information with it. Such code is difficult to share for transparency, reuse, or expansion. Letting people know whether and how they can use your code and/or share it is a kindness not just to them, but to the community and even yourself, whether you want to retain copyright on the code, choose one of the copyleft licenses, or make your code public domain.
Just beginning to think about licensing and trying to wrap your head around it? TechSoup offers a good introduction on licensing in Making Sense of Software Licensing, and I’ve previously mentioned A Quick Guide to Software Licensing for the Scientist-Programmer from PLoS in our list of general articles that may be of interest to astronomical software users.
If you already know you want an open source license for your open source software (OSS) but don’t know which to choose, the Choose a license site describes different popular open source licenses; it is a good resource for getting an overview of each of them. The Open Source Initiative also offers information on licenses and has a FAQ that is useful for clarifying such terms as copyleft, public domain, open source, and free software in addition to others one runs across when considering licensing.
Interested in retaining copyright within a collaborative free software project? This white paper from the Software Freedom Law Center identifies best practices for doing so. And if you’re thinking about changing a code’s license, you may want to read Bruce Berriman’s informative post, with plenty of resources in it, on his Astronomy Computing Today blog.
What resources have you found helpful for licensing? I am very interested in knowing, and hope you will please share them; thank you!
1 http://softwarefreedom.org/resources/2012/ManagingCopyrightInformation.html