Author Archives: Alice Allen

ASCL poster at AAS #229

With 1,400 codes, the Astrophysics Source Code Library (ASCL, ascl.net) is the largest indexed resource for codes used in astronomy research in existence. This free online registry was established in 1999, is indexed by Web of Science and ADS, and is citable, with citations to its entries tracked by ADS. Registering your code with the ASCL is easy with our online submissions system. Making your software available for examination shows confidence in your research and makes your research more transparent, reproducible, and falsifiable. ASCL registration allows your software to be cited on its own merits and provides a citation that is trackable and accepted by all astronomy journals and journals such as Science and Nature. Registration also allows others to find your code more easily. This presentation covers the benefits of registering astronomy research software with the ASCL.

Alice Allen, Astrophysics Source Code Library
Kimberly DuPrie, Space Telescope Science Institute
G. Bruce Berriman, IPAC, Caltech
Jessica D. Mink, Smithsonian Astrophysical Observatory
Robert J. Nemiroff, Michigan Technological University
Thomas Robitaille, Freelance
Judy Schmidt, Astrophysics Source Code Library
Lior Shamir, Lawrence Technological University
Keith Shortridge, Knave and Varlet
Peter J. Teuben, University of Maryland
John F. Wallin, Middle Tennessee State University
Rein Warmels, European Southern Observatory

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December 2016 additions to the ASCL

Twenty-two codes were added to the ASCL in December 2016:

AUTOSTRUCTURE: General program for calculation of atomic and ionic properties
BaTMAn: Bayesian Technique for Multi-image Analysis
CELib: Software library for simulations of chemical evolution
CRETE: Comet RadiativE Transfer and Excitation
dacapo_calibration: Photometric calibration code

Earthshine simulator: Idealized images of the Moon
flexCE: Flexible one-zone chemical evolution code
GAMER: GPU-accelerated Adaptive MEsh Refinement code
Grackle: Chemistry and radiative cooling library for astrophysical simulations
InversionKit: Linear inversions from frequency data

libprofit: Image creation from luminosity profiles
LSDCat: Line Source Detection and Cataloguing Tool
Meso-NH: Non-hydrostatic mesoscale atmospheric model
ProFit: Bayesian galaxy fitting tool
pylightcurve: Exoplanet lightcurve model

PyORBIT: Exoplanet orbital parameters and stellar activity
PyProfit: Wrapper for libprofit
Python-CPL: Python interface for the ESO Common Pipeline Library
QSFit: Quasar Spectral FITting
REPS: REscaled Power Spectra for initial conditions with massive neutrinos

Superplot: Graphical interface for plotting and analyzing data
Trident: Synthetic spectrum generator

November 2016 additions to the ASCL

Twenty-two codes were added to the ASCL in November 2016:

AIMS: Asteroseismic Inference on a Massive Scale
Carpet: Adaptive Mesh Refinement for the Cactus Framework
CMCIRSED: Far-infrared spectral energy distribution fitting for galaxies near and far
EarthShadow: Calculator for dark matter particle velocity distribution after Earth-scattering
Exo-Transmit: Radiative transfer code for calculating exoplanet transmission spectra

GalPot: Galaxy potential code
GRASP2K: Relativistic Atomic Structure Package
Icarus: Stellar binary light curve synthesis tool
Kapteyn Package: Tools for developing astronomical applications
MPDAF: MUSE Python Data Analysis Framework

OXAF: Ionizing spectra of Seyfert galaxies for photoionization modeling
phase_space_cosmo_fisher: Fisher matrix 2D contours
Pippi: Parse and plot MCMC chains
PRECESSION: Python toolbox for dynamics of spinning black-hole binaries
proEQUIB: IDL/GDL library for atomic level populations and line emissivities in statistical equilibrium

pyGMMis: Mixtures-of-Gaussians density estimation method
RHOCUBE: 3D density distributions modeling code
SlicerAstro: Astronomy (HI) extension for 3D Slicer
SNCosmo: Python library for supernova cosmology
tf_unet: Generic convolutional neural network U-Net implementation in Tensorflow

Transit Clairvoyance: Predicting multiple-planet systems for TESS
UltraNest: Pythonic Nested Sampling Development Framework and UltraNest

Perspectives in Research Software Special Session at AAS 229

FRIDAY, 6 JANUARY 2017
Special Session: Perspectives in Research Software: Education, Funding, Reproducibility, Citation, and Impact
10:00 am – 11:30 am
Grapevine 2

The Moore-Sloan Data Science Environment at NYU and the ASCL have organized a Special Session at January’s AAS. The session, Perspectives in Research Software: Education, Funding, Reproducibility, Citation, and Impact, will be moderated by Bruce Berriman (IPAC, Caltech/Astronomy Computing Today). The session will feature short presentations and will include a discussion period with the floor open for questions and comments, and maybe even a few answers, too. The topics and presenters are :

Tracy Teal (Data Carpentry), Software not as a service
Michael Hucka (Caltech), Finding the right wheel when you don’t want to reinvent it
Lior Shamir (LTU), Reproducibility and reusability of scientific software
Ivelina Momcheva (STScI), Funding research software development
Heather Piwowar (ImpactStory), Capturing the impact of software
David W. Hogg (NYU), The relationships between software publications and software systems
Alice Allen (ASCL), Update on research software citation efforts

That last speaker looks a wee bit dodgy, but the moderator and other panelists are aces! And you, software authors and users, are as always important participants in the discussion. I hope to see you there!

Software events at AAS 229, Grapevine

And here it is: the Big List o’ Software Stuff at next month’s AAS meeting. If I missed anything, please let me know in the comments below; thanks!

TUESDAY, 3 JANUARY 2017
Workshops
Introduction to Software Carpentry, 8:00 am ‐ 5:30 pm, Appaloosa 1
Using Python for Astronomical Data Analysis, 8:30 am ‐ 5:00 pm, Texas C

WEDNESDAY, 4 JANUARY 2017
Splinter meeting: Flexible Multi‐dimensional Modeling of Complex Data in Astronomy, 9:30 am ‐ 11:30 am, Grapevine 4

Poster presentations
146.04 Gemini Planet Imager Calibrations, Pipeline Updates, and Campaign Data Process
146.07 Reprocessing of Archival Direct Imaging Data of Herbig Ae/Be Stars
146.13 Finding Planets in K2: A New Method of Cleaning the Data
146.17. Searching for Wide, Planetary-Mass Companions in Archival Spitzer/IRAC Data
154.25 Automated Detection of Dwarf Galaxies and Star Clusters in SMASH through the NOAO Data Lab
154.27 On the Quantification of Incertitude in Astrophysical Simulation Codes
155.13 Spectro-spatial reconstruction of Wide Field Imaging Interferometry Testbed (WIIT) data

Oral presentations
Testing SMBH scaling relations using cosmological simulations and optical/near-IR imaging data, 10:00 am – 10:20 am, Grapevine C
An Empirical Examination of the NEOWISE Results and Data analysis, 10:50 am – 11:00 am, Texas 4
Data Simulation for 21 cm Cosmology Experiments, 2:40 pm – 2:50 pm, Grapevine C

THURSDAY, 5 JANUARY 2017
Poster presentations
Session 236: Computation, Data Handling, Image Analysis & Light Pollution (21 posters)

239.03, The era of synoptic galactic archeology: using HST and Chandra observations to constrain the evolution of elliptical galaxies through the spatial distribution of globular clusters and X-ray binaries
244.05, Three-Dimensional Simulations of the Convective Urca Process in Pre-Supernova White Dwarfs

Oral presentations
Mind the Gap when Data Mining the Ritter-Kolb Cataclysmic Variable Catalogue, 10:00 am – 10:10 am, Fort Worth 6
What drives the kinematic evolution of star-forming galaxies? 10:20 am – 10:30 am, Grapevine 2
Simulating Galactic Winds on Supercomputers, 2:50 pm – 3:10 pm, Grapevine A
Photometric Redshifts for High Resolution Radio Galaxies in the SuperCLASS Field, 3:10 pm – 3:20 PM, Grapevine A

FRIDAY, 6 JANUARY 2017
Special Session: Perspectives in Research Software: Education, Funding, Reproducibility, Citation, and Impact, 10:00 am – 11:30 am, Grapevine 2

Poster presentations
335.05, When Will It Be …?: U.S. Naval Observatory Religious Calendar Computers Expanded
336.09, Variable Stars as an Introduction to Computational Research
345.03, An ALMA Survey of Planet Forming Disks in Rho Ophiuchus
345.19, Chemistry of protostellar envelopes and disks: computational testing of 2D abundances
348.06, Computing Architecture for the ngVLA

Oral presentations
K2 red giant asteroseismology using Bayesian Asteroseismology data Modeling (BAM), 10:24 am – 10:36 am, Grapevine B
Upgrades to MINERVA control software, 2:00 pm – 2:10 pm, Texas D

SATURDAY, 7 JANUARY 2017
Special Session: Statistical, Mathematical and Computational Methods for Astronomy (ASTRO): SAMSI 2016-17, 10:00 am – 11:30 am, Grapevine 2

Workshop: Hack Together Day, 10:00 am ‐ 7:00 pm, Grapevine 4 (Info and registration)

Also of likely interest is the Special Session on The Value of Astronomical Data and Long Term Preservation that will take place on Thursday, 4 January from 10:00 am – 11:30 am in Texas 3.

 

OpenCon2016 Day 0

I’m attending OpenCon2016 (#OpenCon) in Washington, DC this weekend; this is a meeting of people from around the world who are improving access to data, software, and educational materials for better science, research, and education.

Tonight was an informal reception at the conference hotel. I picked up my badge from Nicole Allen and Brady Yano, and immediately got into conversation with Cody Taylor from the University of Oklahoma Libraries, where he is an Emerging Technologies Librarian. His work includes working with professors to make textbooks open access to reduce costs. Kristofferson Culmer, a PhD student in computer science at the University of Missouri and also President of the National Association of Graduate-Professional Students (NAGPS) joined us. This is Kristofferson’s third OpenCon; as Cody and I are both OpenCon newbies, our conversation included a bit of Q&A about the conference itself.

After leaving Cody and Kristofferson, I walked over to a small group of people that included Erin McKiernan, a physics professor at the National Autonomous University of Mexico and whose tweets frequently appear in my Twitter feed, and my target for walking in that direction, Peter Murray-Rust, a chemist at the University of Cambridge. Peter and I had exchanged tweets when we were both in Portland at Force2016 this past April — not that I remembered that initially — and I’ve been following him ever since. I had a reason for seeking him out tonight, as in my earlier conversation, I learned that Peter has a content mining tools that might help the ASCL: ContentMine. Yes! I cannot wait to start using it! We also talked about the state of data representation in chemistry and astrophysics and how closed chemistry is, with theses embargoed in some universities for five (!!) years. (Wow!)

I had a great conversation next with Thomas Hervé Mboa Nkoudou; he is studying Scholarly Communication at Université Laval and is from Cameroon, where he started a school. He’s very interested in science and in promoting research done in Africa and Haiti, and in the maker movement in education. We also talked about astronomy education. After that, I met Daniel Himmelstein from the University of Pennsylvania and Vinodh Ilangovan from the Max Planck Institute for Biophysical Chemistry, with whom I lamented my apparent inability to find Jon Tennant, the one person I actually expected to meet tonight!

This is a conference of mostly young people — grad students and early career — who have amazing (quite daunting!) accomplishments and are working hard to make knowledge more accessible. I am really looking forward to the next two days! I’m participating, too, with a two-minute presentation on Saturday on the ASCL, and an unconference session on Sunday on encouraging software release and citation.

October 2016 additions to the ASCL

Sixteen codes were added to the ASCL in October 2016:

BurnMan: Lower mantle mineral physics toolkit
BXA: Bayesian X-ray Analysis
C3: Command-line Catalogue Crossmatch for modern astronomical surveys
CERES: Collection of Extraction Routines for Echelle Spectra

cluster-in-a-box: Statistical model of sub-millimeter emission from embedded protostellar clusters
DSDEPROJ: Direct Spectral Deprojection
Fourierdimredn: Fourier dimensionality reduction model for interferometric imaging
Freddi: Fast Rise Exponential Decay accretion Disk model Implementation

gatspy: General tools for Astronomical Time Series in Python
GSGS: In-Focus Phase Retrieval Using Non-Redundant Mask Data
MC3: Multi-core Markov-chain Monte Carlo code
MUSE-DRP: MUSE Data Reduction Pipeline

NuPyCEE: NuGrid Python Chemical Evolution Environment
Piccard: Pulsar timing data analysis package
PyMC3: Python probabilistic programming framework
velbin: radial velocity corrected for binary orbital motions

ADASS BoF: Implementing Ideas for Improving Software Citation and Credit

On Tuesday at ADASS, ASCL Advisory Committee Chair Peter Teuben led a Birds of a Feather session intended as a working session to have people put some of the ideas for improving software citation and credit into practice.

ADS now has a doc type called software

Slide from Peter’s opening presentation

He opened the session with a few remarks about last year’s BoF, similar efforts elsewhere, and examples of progress since last year. Yes, there has been progress! He then showed a list of actionable items and asked people to work on them, adding their work to a common Google doc. His slides are here.

And they did! It was the quietest BoF ever, I believe, as Keith Shortridge, Bruce Berriman, and Jessica Mink wrote about their experiences in releasing software; Renato Callado Borges and Greg Sleap provided guidance on the types of software contributions that add value to science; Alberto Accomazzi, Nuria Lorente, and Kai Polsterer listed ways one can publish and take credit for software; Peter Teuben, Steven Crawford, and possibly others pulled together a list of organization web pages about software created at the institutions, this as a way to highlight and recognize scientific software contributions; Maurizio Tomasi added a suggestion for gathering licensing information; and Thomas Robitaille, Ole Streicher, Tim Jenness, Kimberly DuPrie, and I discussed exactly what should be in the “Preferred citation field” of the ASCL and various people listed about a dozen preferred citations to be added to the ASCL and others used the Suggest a change or addition link for several software packages to provide preferred citation information.

Though Peter had asked that people work for about 30 minutes, he monitored contributions to the Google doc and saw work was still being done so did not call us back together until only 15 minutes or so were left in the session. Instead of having people report back on what they had done as originally plan, he asked for other feedback instead, as progress made was evident in the shared document, and after a bit of discussion on licensing and a few other comments, closed the session.

Though the session is over, the next phase is to put this information to use or disseminate it in some way so it can do some good and be the changes we want to see for software!

 

ADASS XXVI poster: Decoupling the Archive

Decoupling the archive posterThe James Webb Space Telescope (JWST) archive will store numerous metadata for the various files that it contains: at the time of this writing a single FITS file can have up to 250 different metadata fields in the archive, most of which map to keywords in the primary header or header extensions. One of the goals of the archive design is to allow for changes to the fields stored in the database without having to change the ingest code. We have found this to be very helpful during the code development phase of the mission when the FITS file definitions are frequently changing. We also anticipate it will be advantageous during the lifetime of the mission as changes to processing will likely result in changes to the keywords but should not require changes to the ingest code. This poster describes the methods we use to decouple the archive from the ingest process.

Kimberly DuPrie, Space Telescope Science Institute
Lisa Gardner, Space Telescope Science Institute
Michael Gough, Space Telescope Science Institute
Richard C. Kidwell Jr., Space Telescope Science Institute