Author Archives: Alice Allen

SciCodes.net: Experiment with building your own software registry/repository

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.

October and November 2015 additions to the ASCL

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 calculations

DEBiL: 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 code

George: Gaussian Process regression
GGADT: Generalized Geometry Anomalous Diffraction Theory
HumVI: Human Viewable Image creation
JKTLD: Limb darkening coefficients
JSPAM: Interacting galaxies modeller

LCD3: 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 datasets

Pangloss: 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 Telescope

SparsePZ: 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

Software activities at AAS 227, Kissimmee

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 Harrington

10:10 AM – 10:20 AM; 212.02. Bayesian Atmospheric Radiative Transfer (BART) Code and Application to WASP-43b
Presenter: Jasmina Blecic

Topics 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. Elhoussieny

243.37. Bayesian and Profile Likelihood Approaches to Time Delay Estimation for Stochastic Time Series of Gravitationally Lensed Quasars
Presenter: Hyungsuk Tak

Majors 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-Hamilton

342.05. Machine Learning and Cosmological Simulations
Presenter: Harshil Kamdar

342.07. 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.

Looking before Leaping: Creating a Software Registry

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

Improving Software Citation and Credit BoF session slides

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.

Some of the posters, some of the codes

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]
lephareCIGALE
PySALT [ascl:1207.010]
pysalt
SoFiA [ascl:1412.001]
sofia
Splotch [ascl: 1103.005]
Splotch
TOPCAT [ascl:1101.010]
topcat
Vissage [ascl:1402.001]
Vissage

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.

Resources for ADASS Birds of a Feather session: Improving software citation and credit

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.

ASCL poster at ADASS XXV

ASCL poster for ADASS XXVThe 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

Download poster (PDF)

ASCL Advisory Committee changes

Earlier this month, Robert Hanisch stepped down as an adviser on the ASCL’s Advisory Committee (AC); we are grateful for his service to the ASCL and thank him for his assistance.

Thomas Robitaille from the Max Planck Institute for Astronomy (MPIA) has joined the AC. He brings with him a wealth of experience as a software author, having developed Hyperion and APLpy; he’s also work on Glue and AstroPy and other astronomy software. We are delighted to have his input!

Suggest a change or addition to a record

Have you found an error in an ASCL entry? Is there a paper using your code you’d like to add? Would you like to specify right in an ASCL entry how your code should be cited?

We have added a “Suggest a change or addition” link to every code entry in the ASCL. This link brings up a form that is similar to the Submissions form and allows you to not only request changes to fields currently displayed, but also enter information for fields we are considering adding.

For example, we would like to disambiguate the URLs for refereed papers into those that describe a code and those that use a code; we’d also like to add categories to make searching for codes easier.Fields for described in and used in

 

 

 

 

Something that’s been on our wish list for a while is a “see also” feature, one that identifies, for a particular code, codes having a similar function or that someone looking at that code would likely be interested in, too. All we need to do this are the data!

Last update: July 20, 2021