Author Archives: Alice Allen

What to do with an astronomy code? Share it!

The poster I’m presenting at AAS 223 is below. Please stop by poster 255.25 on Tuesday; I would love to know whether you share your codes and why you do or do not.

AAS2014JanPosterFinal-20percentsize
Abstract: Now that you’ve written a useful astronomy code for your soon-to-be-published research, you have to figure out what you want to do with it. Our suggestion? Share it! This presentation highlights the means and benefits of sharing your code. Make your code citable — submit it to the Astrophysics Source Code Library and have it indexed by ADS! The Astrophysics Source Code Library (ASCL) is a free online registry of source codes of interest to astronomers and astrophysicists. With over 700 codes, it is continuing its rapid growth, with an average of 17 new codes a month. The editors seek out codes for inclusion; indexing by ADS improves the discoverability of codes and provides a way to cite codes as separate entries, especially codes without papers that describe them.

Authors: Alice Allen, Astrophysics Source Code Library
Alberto Accomazzi, Smithsonian Astrophysical Observatory
Bruce Berriman, California Institute of Technology
Kimberly DuPrie, Astrophysics Source Code Library
Robert Hanisch, Space Telescope Science Institute/Virtual Astronomical Observatory
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, UK
Peter Teuben, University of Maryland
John Wallin, Middle Tennessee State University

ASCL at AAS 223

The ASCL will be at the AAS meeting in (not quite) Washington, DC next week; I’ll be handing out (non-glowing) pens like crazy at both the ASCL poster (255.25, titled You’ve Written a Cool Astronomy Code! Now What Do You Do with It?) and the Special Session (more information below) on Tuesday, too. I hope you’ll stop by the poster to say hi, talk codes, and grab a pen!

The AAS’s Working Group on Astronomical Software (WGAS) and the ASCL are holding a Special Session on code sharing that includes presentations and an open discussion. Peter Teuben and Robert Hanisch will moderate the session, which will be held on Tuesday, January 7, 2:00 to 3:30 in National Harbor 5, Gaylord National Resort and Convention Center.

The panelists and topics for the session are:

Benjamin J. Weiner, Occupy Hard Drives: Making your work more valuable by giving it away
G. Bruce Berriman, Maintaining a user community for the Montage Image Mosaic Toolkit
Gary J. Ferland, Cloudy – the non-equilibrium microphysics of gas and dust, and its observed spectrum
Daniel S. Katz, NSF policies on software and data sharing and their implementation
Erik J. Tollerud, The Astropy Project’s self-herding cats development model
David W. Hogg, Costs and benefits of developing out in the open

After the presentations, Peter will open the floor for questions and discussion; at the end of the discussion, Bob will summarize the themes and points and will close the Special Session.

We’ll be tweeting, too, especially during the Special Session on Tuesday: @asclnet or #asclnet. See you (in person or online) next week!

ADASS BoF working documents

Peter Teuben moderated today’s BoF, which asked participants to brainstorm ideas for dealing with three categories of concerns: factors which inhibit code sharing, factors which encourage sharing, and overall community issues. The questions were in yesterday’s blog post, along with a link to the introductory slides for the session. One of the questions posed was not selected for discussion; another was proposed by participant William O’Mullane (what tools are available for sharing code?).

Each discussion group discussed one of eight questions; people were given the opportunity to move to another group for a second discussion. Scribes captured the ideas and comments of participants; the resulting documents can be found by following the links below.

My thanks to Jessica Mink, Kimberly DuPrie, Omar Laurino, Mark Taylor, Bruce Berriman, Bob Hanisch, Kai Polsterer, and William O’Mullane for scribing, to Nuria Lorente for tweeting about the session, and to Peter Teuben for his leadership!

Please feel free to add your own comments directly in the documents!

Messy code
Google doc

Expectations of support
Google doc

University policies
Google doc

Recognition by citation
Google doc

 Impact
Google doc

Journals and funding agencies
Google doc

Community at large
Google doc

Tools for sharing code
Google doc

Eight questions…

… are being posed in the Ideas for Advancing Code Sharing (or A Different Kind of Hack Day) Birds of a Feather (BoF) session at ADASS. The eight questions ask how to deal with three categories of concerns: factors which inhibit sharing, factors which encourage sharing, and overall community issues. The questions are below; do you have answers to them? Please share them if you do!

The introductory slides for the BoF are available online. We will post what comes out of the discussions shortly after the BoF.

Mitigating inhibitors
How do we encourage release even if the code is “messy”?
How do we reduce expectations of support when coders don’t want to support code and still encourage code release?
How can universities be convinced to change policies which prohibit software publication?

Increasing incentives
What can we do to encourage citations for codes?
Beyond citations, what can we do to give code authors recognition for writing and releasing their software?
How can we measure the impact of a code on research and its value to the community?

Community factors
What roles might journal publishers and funding agencies have in furthering code release, and how can the community influence them to take on that role?
What else can we do to have code release recognized as an essential part of research reproducibility

 

ASCL at ADASS

The ASCL is participating in ADASS in the following ways:

Not going to ADASS but want to participate in the BoF session? We’d love to have your input and ideas. We’ll be running a Twitter feed running throughout the BoF  (follow @asclnet). What else might work for you?

Citations redux

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.)

Astrophysics Code Sharing II: The Sequel at the January 2014 AAS meeting

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 Arizona

After 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.

 

July and August 2013 additions to the ASCL

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 Calculations

FieldInf: 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 modeling

MAH: 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 software

phoSim: Photon Simulator
PURIFY: Tools for radio-interferometric imaging
Shapelets: Image Modelling
SIMX: Event simulator
SOPT: Sparse OPTimisation

August:
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 code

CRUSH: 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 hole

MapCurvature: 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 analysis

SYN++: Standalone SN spectrum synthesis
SYNAPPS: Forward-modeling of supernova spectroscopy data sets
THELI GUI: Optical, near- & mid-infrared imaging data reduction

Also in August, we added one very cool web resource, the NASA Exoplanet Archive.