ASCL News
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Twenty codes were added to the ASCL in December, 2015:
ALFA: Automated Line Fitting Algorithm
AstroBlend: Visualization package for use with Blender
Bisous model: Detecting filamentary pattern in point processes
CounterPoint: Zeeman-split absorption lines
CubeIndexer: Indexer for regions of interest in data cubesDiffuseModel: Modeling the diffuse ultraviolet background
DRACULA: Dimensionality Reduction And Clustering for Unsupervised Learning in Astronomy
EDRS: Electronography Data Reduction System
EDRSX: Extensions to the EDRS package
ExoData: Open Exoplanet Catalogue exploration and analysis toolFFTLog: Fast Fourier or Hankel transform
GetData: A filesystem-based, column-oriented database format for time-ordered binary data
GPC: General Polygon Clipper library
growl: Growth factor and growth rate of expanding universes
IRACpm: Distortion correction for IRAC astrometric dataSpirality: Spiral arm pitch angle measurement
TACT: The Action Computation Tool
TM: Torus Mapper
UPSILoN: AUtomated Classification of Periodic Variable Stars using MachIne LearNing
ZeldovichRecon: Halo correlation function using the Zeldovich approximation -
Posters! Sessions! Meetings! The upcoming AAS meeting in Kissimmee, Florida is shaping up to be the busiest ever! Here are the formal meeting activities the ASCL is participating in.
Special Session: Tools and Tips for Better Software (aka Pain Reduction for Code Authors)
Tuesday, January 05, 2:00 PM - 3:30 PM; Sanibel
Organizers: Astrophysics Source Code Library (ASCL)/Moore-Sloan Data Science Environment at NYUResearch in astronomy is increasingly dependent on software methods and astronomers are increasingly called upon to write, collaborate on, release, and archive research quality software, but how can these be more easily accomplished? Building on comments and questions from previous AAS special sessions, this session, organized by the Astrophysics Source Code Library (ASCL) and the Moore-Sloan Data Science Environment at NYU, explores methods for improving software by using available tools and best practices to ease the burden and increase the reward of doing so. With version control software such as git and svn and companion online sites such as GitHub and Bitbucket, documentation generators such as Doxygen and Sphinx, and Travis CI, Intern, and Jenkins available to aid in testing software, it is now far easier to write, document and test code. Presentations cover best practices, tools, and tips for managing the life cycle of software, testing software and creating documentation, managing releases, and easing software production and sharing. After the presentations, the floor will be open for discussion and questions.
The topics and panelists are:
Source code management with version control software, Kenza S. Arraki
Software testing, Adrian M. Price-Whelan
The importance of documenting code, and how you might make yourself do it, Erik J. Tollerud
Best practices for code release, G. Bruce Berriman
Community building and its impact on sustainable scientific software, Matthew Turk
What to do with a dead research code, Robert J. Nemiroff
Poster 247.07: Astronomy education and the Astrophysics Source Code Library
Wednesday, January 06, Exhibit Hall AThe Astrophysics Source Code Library (ASCL) is an online registry of source codes used in refereed astrophysics research. It currently lists nearly 1,200 codes and covers all aspects of computational astrophysics. How can this resource be of use to educators and to the graduate students they mentor? The ASCL serves as a discovery tool for codes that can be used for one’s own research. Graduate students can also investigate existing codes to see how common astronomical problems are approached numerically in practice, and use these codes as benchmarks for their own solutions to these problems. Further, they can deepen their knowledge of software practices and techniques through examination of others’ codes.
Poster 348.01: Making your code citable with the Astrophysics Source Code Library
Thursday, January 07, Exhibit Hall AThe Astrophysics Source Code Library (ASCL, ascl.net) is a free online registry of codes used in astronomy research. With nearly 1,200 codes, it is the largest indexed resource for astronomy codes in existence. Established in 1999, it offers software authors a path to citation of their research codes even without publication of a paper describing the software, and offers scientists a way to find codes used in refereed publications, thus improving the transparency of the research. Citations using ASCL IDs are accepted by major astronomy journals and if formatted properly are tracked by ADS and other indexing services. The number of citations to ASCL entries increased sharply from 110 citations in January 2014 to 456 citations in September 2015. The percentage of code entries in ASCL that were cited at least once rose from 7.5% in January 2014 to 17.4% in September 2015. The ASCL’s mid-2014 infrastructure upgrade added an easy entry submission form, more flexible browsing, search capabilities, and an RSS feeder for updates. A Changes/Additions form added this past fall lets authors submit links for papers that use their codes for addition to the ASCL entry even if those papers don’t formally cite the codes, thus increasing the transparency of that research and capturing the value of their software to the community.
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The ASCL is offering clones of its infrastructure for any group or discipline wanting to build a code registry or repository of its own, with control of the new resource residing with the requesting parties. If you would like to build your own software resource, you can take our infrastructure, configure it as you like, and use it.
Specifically, we’re offering to:
- clone the ASCL infrastructure to your domain name
- host the infrastructure for at least three years (if you’d like) at MTU
- share innovations on ASCL with those who accept this offer
- maintain the host
- let you move your site elsewhere with data intact
We would expect you to:
- pay for/provide a domain name
- have control over the site and configure it for your own use
- use the site for a software repository/registry
- gather ye codes as ye may
- share innovations on the site with the ASCL and others who accept this offer
- not do anything harmful to MTU’s computing environment
ASCL.net is built using these open source tools:
- mySQL
- WordPress
- phpbb
- CodeIgniter
Interested? Let us know at editor@ascl.net or comment below.
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Thirty codes were added to the ASCL in October and November 2015:
ASPIC: STARLINK image processing package
batman: BAsic Transit Model cAlculatioN in Python
ccdproc: CCD data reduction software
CCDtoRGB: RGB image production from three-band atronomical images
CosmoBolognaLib: Open source C++ libraries for cosmological calculationsDEBiL: Detached Eclipsing Binary Light curve fitter
DES exposure checker: Dark Energy Survey image quality control crowdsourcer
EPIC: E-field Parallel Imaging Correlator
GALFORM: Galactic modeling
Galileon-Solver: N-body codeGeorge: Gaussian Process regression
GGADT: Generalized Geometry Anomalous Diffraction Theory
HumVI: Human Viewable Image creation
JKTLD: Limb darkening coefficients
JSPAM: Interacting galaxies modellerLCD3: Three-parameter limb darkening coefficient sampling
MCAL: M dwarf metallicity and temperature calculator
Mercury-T: Tidally evolving multi-planet systems code
MHF: MLAPM Halo Finder
milkywayproject_triggering: Correlation functions for two catalog datasetsPangloss: Reconstructing lensing mass
PromptNuFlux: Prompt atmospheric neutrino flux calculator
pyhrs: Spectroscopic data reduction package for SALT
PyLDTk: Python toolkit for calculating stellar limb darkening profiles and model-specific coefficients for arbitrary filters
SkyView Virtual TelescopeSparsePZ: Sparse Representation of Photometric Redshift PDFs
SuperFreq: Numerical determination of fundamental frequencies of an orbit
T-Matrix: Codes for Computing Electromagnetic Scattering by Nonspherical and Aggregated Particles
Xgremlin: Interferograms and spectra from Fourier transform spectrometers analysis
ZInCo: Zoomed Initial Conditions -
As promised in a previous post, here is the list of software activities at the upcoming January AAS meeting in Kissimmee; I hope to add a Software Publishing Special Interest Group meeting to the list, but other than that, the list should be complete. If I missed anything that should be here, please (please!) let me know. Thank you, and see you there!
SUNDAY, JANUARY 03, 2016
Introduction to Software Carpentry 2 Day Workshop (day 1 of 2)
Organizer: Software Carpentry
9:00 AM - 5:30 PM; St. George 106 (Gaylord Palms Resort and Convention Center)
MONDAY, JANUARY 04, 2016
Introduction to Software Carpentry 2 Day Workshop (day 2 of 2)
Organizer: Software Carpentry
8:00 AM - 5:30 PM; St. George 106 (Gaylord Palms Resort and Convention Center)Astrostatistics and R
Organizer: Eric D. Feigelson (Penn State University) and two assistants
9:00 AM - 6:00 PM; Emerald 8 (Gaylord Palms Resort and Convention Center)Using Python for Astronomical Data Analysis
Organizer: Perry Greenfield
9:00 AM - 4:30 PM; St. George 114 (Gaylord Palms Resort and Convention Center)SciCoder Presents: Developing Larger Software Projects
Organizer: Demitri Muna
10:00 AM - 6:00 PM; Emerald 6 (Gaylord Palms Resort and Convention Center)Bayesian Methods in Astronomy: Hands-on Statistics
Organizer: Jake VanderPlas (U. Washington) and two assistants
1:00 PM - 6:00 PM; Emerald 2 (Gaylord Palms Resort and Convention Center)
TUESDAY, JANUARY 05, 2016
Tools and Tips for Better Software (aka Pain Reduction for Code Authors)
Organizers: Astrophysics Source Code Library (ASCL)/Moore-Sloan Data Science Environment at NYU
2:00 PM - 3:30 PM; Sanibel (Gaylord Palms Resort and Convention Center)
WEDNESDAY, JANUARY 06, 2016
Lectures in AstroStatistics
10:00 AM - 11:30 AM; Osceola 5 (Gaylord Palms Resort and Convention Center)Extrasolar Planet Atmospheres: BART Atmospheric Modelling Code and Applications
10:00 AM - 10:10 AM; 212.01. A Random Walk on WASP-12b with the Bayesian Atmospheric Radiative Transfer (BART) Code
Presenter: Joseph Harrington10:10 AM - 10:20 AM; 212.02. Bayesian Atmospheric Radiative Transfer (BART) Code and Application to WASP-43b
Presenter: Jasmina BlecicTopics in Astrostatistics
1:30 PM - 3:30 PM; St. George 106 (Gaylord Palms Resort and Convention Center)AGN, QSO, Blazars Poster Session
243.46 Time-dependent Photoionization of Gaseous Nebulae: TD_XSTAR Code
Presenter: Ehab E. Elhoussieny243.37. Bayesian and Profile Likelihood Approaches to Time Delay Estimation for Stochastic Time Series of Gravitationally Lensed Quasars
Presenter: Hyungsuk TakMajors and Graduate Student Education and Professional Development Poster Session
247.07 Astronomy education and the Astrophysics Source Code Library
Presenter: Alice Allen
THURSDAY, JANUARY 07, 2016
Catalogs, Surveys, and Data Viewing
2:00 PM - 2:10 PM; 324.01. Introducing Nightlight: A New, Modern FITS Viewer
Presenter: Demitri Muna
Tampa (Gaylord Palms Resort and Convention Center)2:10 PM - 2:20 PM; 324.02. Synthesizing Understanding from Data with yt
Presenter: Matthew Turk
Tampa (Gaylord Palms Resort and Convention Center)Cosmological Simulations of Galaxies
3:00 PM - 3:10 PM; 316.05. The Non-parametric Concentration of Dark Matter Halos in Cosmological N-body Simulations
Presenter: Meagan Lang
Sun A (Gaylord Palms Resort and Convention Center)3:10 PM - 3:20 PM; 316.06. The Scylla Multi-Code Comparison Project
Presenter: Ariyeh Maller
Sun A (Gaylord Palms Resort and Convention Center)348. Computation, Data Handling, Image Analysis Poster Session
Posters in other sections:
338.17. Simulating magnetospheres with numerical relativity: The GiRaFFE code
Presenter: Maria Babiuc-Hamilton342.05. Machine Learning and Cosmological Simulations
Presenter: Harshil Kamdar342.07. SurveySim: a new MCMC code to explore the evolution of the IR luminosity function
Presenter: Matteo Bonato
FRIDAY, JANUARY 08, 2016
Beyond the Academy: Showcasing Astronomy Alumni in Non-Academic Careers
413.01. Astronomers as Software Developers
Presenter: Rachel A. Pildis
10:00 AM - 10:25 AM; Osceola 4 (Gaylord Palms Resort and Convention Center)Hack Day
Organizer: Kelle Cruz (Hunter College/CUNY and AMNH)
10:00 AM - 5:00 PM; Tallahassee (Gaylord Palms Resort and Convention Center)
To participate in Hack Day, please register at http://www.astrobetter.com/wiki/AASHackDay. -
Judy Schmidt, our designer/developer, and I have a new paper, "Looking before Leaping: Creating a Software Registry," in the Journal of Open Research Software. The article is open access and can be found here: http://doi.org/10.5334/jors.bv
When I started work on the ASCL in 2010, I wanted to understand why the original ASCL -- started in 1999 -- and other previous similar resources had not reached critical mass. I looked at these resources, what they offered, and how they were structured, and for some of them, talked with the people who had started them, to see what I could learn from their experiences. In addition, Robert Nemiroff and I have had many conversations about the early days of the ASCL, and I also talked with researchers who used some of these services. The lessons from this look back has informed our work on the ASCL. My background in change management has also been helpful in determining the ASCL's path forward. In the paper, we share not only some of what was learned, but also specific steps we've taken, why we've taken them, how the ASCL has changed over time, and some of our future plans.
The first version of this paper was accepted for the 2nd Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE2), which took place in New Orleans in November 2014, and was later revised for publication.
WSSSPE2 blog post
3rd Workshop on Sustainable Software for Science: Practice and Experiences -
On Tuesday, October 27, the ASCL held a Birds of a Feather session at ADASS on Improving Software Citation and Credit. The session was opened with a brief presentation by Bruce Berriman, who reported on a Software Publishing Special Interest Group meeting held at the January 2015 AAS meeting and the ongoing work that has come out of that. I followed with a quick overview of other efforts to improve software credit and citation, not just in astronomy but across disciplines, after which Keith Shortridge moderated a lively discussion among the forty people present. The slides Bruce and I presented are now available online.
Previously, we shared resources for the session and the Google doc created during the session to capture some of the main points from the discussion.
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I used to read ADASS posters in part to find new codes to register. I still do that, but it's harder these days, for reasons that make me very happy: many of the codes are already in the ASCL! Here is a sampling from a quick and definitely not thorough perusal of posters.
CIGALE [ascl:1111.004] and LePHARE [ascl:1108.009]
PySALT [ascl:1207.010]
SoFiA [ascl:1412.001]
Splotch [ascl: 1103.005]
TOPCAT [ascl:1101.010]
Vissage [ascl:1402.001]
It's lovely to see ADASS folks I've met before, and lovely to see codes I already know. It's also great to meet new people and run across new codes, and I'll be highlighting some of the new codes added as a result of this ADASS in a future blog post.
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The ASCL has organized a Birds of a Feather session (BoF) at ADASS to discuss improving software citation and credit to be held on Tuesday, October 27; the following links may be helpful for the discussion.
Astronomy-specific
Astronomy software citation examples and ideas (working [Google] document arising from AAS SPSIG discussion)Astronomy software indexing workshop
Cross-disciplinary
Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE)
Force11 Software Citation Working Group (Mission statement, member list, timeline, communications plan, etc. on GitHub)Center for Open Science's Transparency and Openness Promotion (TOP) Guidelines
Google doc created during the BoF session; anyone with the link can comment.
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The Astrophysics Source Code Library, started in 1999, moved to a new infrastructure in 2014 with enhancements developed in response to feedback from users and publishers. With one-click author search, flexible browsing options, and a simple form-based submission process, the ASCL offers a better experience for users. Since the introduction of the new platform in mid-2014, users have submitted nearly 100 codes, more than in all previous years combined. Data sharing options, including the ability to pull all of the resource’s public data in JSON and XML, provide new ways to collaborate with the resource. The ASCL now houses information on more than 1000 codes and its entries are increasingly used for citation, with over 15% of its entries cited, up from 7.5% in January of last year. Exciting opportunities to collaborate have been presented to the ASCL, including participation in the 2nd Workshop on Sustainable Software for Science: Practice and Experiences and a request from the AAS to form a special interest group on software publishing. This presentation will demonstrate the new capabilities of the ASCL and discuss its growth and recent outreach and collaborations.Alice Allen, Astrophysics Source Code Library; G. Bruce Berriman, Infrared Processing and Analysis Center, California Institute of Technology; Kimberly DuPrie, Space Telescope Science Institute/Astrophysics Source Code Library; Jessica Mink, Harvard-Smithsonian Center for Astrophysics; Robert Nemiroff, Michigan Technological University; Judy Schmidt, Astrophysics Source Code Library; Lior Shamir, Lawrence Technological University; Keith Shortridge, Australian Astronomical Observatory; Mark Taylor, University of Bristol; Peter Teuben, Astronomy Department, University of Maryland; John Wallin, Middle Tennessee State University
