ASCL News
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The annual meeting of the European Astronomical Society (EAS), the European Week of Astronomy and Space Science (EWASS), was held June 26-30 in beautiful Prague. As mentioned in a previous blog post, Abigail Stevens (U Amsterdam), Amruta Jaodand (ASTRON), Matteo Bachetti (INAF-Osservatorio Astronomico di Cagliari), Rein Warmels (ESO), and I organized a Special Session titled Developments and Practices in Astronomy Research Software. Special Sessions at EWASS can be from one to three 90-minute blocks; we organized three blocks, each with its own focus and all scheduled on Wednesday, June 28, which were:
Best practices for code development and management
Perspectives in research software
Astronomy software packages reviewThe first two sessions opened with review talks, then had a series of slightly shorter presentations, each with a particular focus. Each of these sessions concluded with a 30-minute period in which the floor was open to all to ask questions of the speakers and discuss the issues and information that had been shared during the 90 minutes. The third session offered talks on specific popular software packages and concluded with lightning talks on the software posters submitted to this Special Session. In addition to this series of talks, a Hack Together Day was organized collaboratively that offered more information on and assistance with installing and/or using many of the software packages presented.
Session titles and presenters for the software sessions that Abigail Stevens (U Amsterdam), Amruta Jaodand (ASTRON), Matteo Bachietti (INAF-Osservatorio Astronomico di Cagliari), Rein Warmels (ESO), and I organize are listed below, and if you want to read through the Storify of session tweets, compiled by Stevens as a Hack Together Day project, that’s here: https://storify.com/abigailstev/developments-and-practices-in-astronomy-research-s
Best practices for code development and management
Moderator: Rein Warmels, ESO, Germany
This session opened with a talk by Simon Portegies Zwart (Leiden University, NL), author of AMUSE and other astro codes, on Reproducible science in scientific computing. He laid the groundwork for this block of talks by presenting the difficulties of reproducibility in simulation software, the best practices his group uses, and the philosophy behind AMUSE, which includes standardizing interfaces and automating as much as possible. His talk included simulations that made for an extremely large presentation file, so a partial set of his slides is provided.
(slides: PDF)
Simon Portegies Zwart In the interest of time, I will not summarize the other talks in this block, but will say you should have been there! These were excellent presentations with many great practices and ideas shared. In the discussion, moderated by Warmels, someone asked about "short codes," and as luck would have it, the next block had a talk on just that topic. There was disagreement on some voiced opinions, and many ideas shared that warrant greater discussion.
The other talks in this block were:
Software development best practices from Astropy
Thomas Robitaille, Freelance, UK (slides: PDF)A Computer Science Perspective on the Astronomy Research Software Process
John Wenskovitch, Virginia Tech & Allegheny College, US (slides: PDF)TARDIS: A radiative transfer code, an open source community, and an interdisciplinary collaboration
Wolfgang Kerzendorf, ESO, DE (slides: PDF)Research software best practices: Transparency, credit, and citation
Alice Allen, ASCL, US (slides: PDF, PPTX)
Perspectives in research software
Moderator: Alice Allen, ASCL, USA/
Kai Polsterer (Heidelberg Institute for Theoretical Studies, DE) set the stage for the second block in the Special Session with his presentation Reproducibility in Era of Data-Driven Science. He also highlighted the difficulties of reproducibility, among them that different computing environments can produce different results from the same code, and though he acknowledged the difficulties in doing so, advocates that publications, datasets (including raw and training data), codes, component and software configuration, and computing environments need to be shared for full reproducibility. Or as John Wenskovitch summarized in a tweet during this presentation, "Publish everything. EVERYTHING. Architecture, model, code, data, parameters, ..." We are not there yet, but must share what we can when we can to increase reproducibility.
(slides: PDF)
Kai Polsterer, image by @K_Bonson The other talks in this second of three blocks were:
Should short codes used for astronomy research be made public?
Robert Nemiroff, Michigan Technological University, US (slides: PDF, PPTX)Giving credit where credit is due: the role of ADS in discovering and citing software in scholarly publications
Sergi Blanco-Cuaresma, Harvard-Smithsonian Center for Astrophysics, US (slides: PDF)Fifteen years of WISE technology software development and operations
Gijs Verdoes Kleijn, University of Groningen, NL (slides: PDF)CDS reference services supporting astronomy research
Mark Allen, CDS, Observatoire Astronomique De Strasbourg, FR (slides: PDF)
Astronomy software packages review
Moderator: Amruta Jaodand, ASTRON, NL
The third block of talks in this Special Session presented software packages useful for software research, from the well-established AstroPy to, in the short poster presentations, newly-developed software such as SPARTAN. The talks in this 90-minute block were:The Astropy Project
Thomas Robitaille, Freelance, UK (slides: PDF)Stingray and Dave: Spectral timing for all
Matteo Bachetti, INAF-Osservatorio Astronomico di Cagliari, IT (slides: PDF)Living on the fringe: Making CASA ready for VLBI
Ilse van Bemmel, JIVE, NLInteractive widgets for the Jupyter notebook
Maarten Breddels, Kapteyn Astronomical Institute, NL (Jupyter notebook, ipywidgets demo (PDF), poster)Lightning poster talks
Again, you should have been there! One blog post cannot possibly convey everything shared in this Special Session, but the slides the presenters have shared captures some of the great goodness in these talks. My thanks to all the presenters, to my co-organizers, and to the attendees who made this session so interesting and excellent, to EWASS for accepting our proposals, and to HITS for providing the ASCL with funding that allowed us to participate.
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The European Week of Astronomy and Space Science (EWASS) was held June 26-30 in Prague and attended by over 1,100 people, and the ASCL was there! This post is an overview of the ASCL's participation in the event; a subsequent post (or two) will provide more detailed information and links to slide decks for sessions the ASCL was involved in organizing.
Program page for software talks
Image by Amruta JaodandThis was my first time attending EWASS, which was initially brought to my attention by Keith Smith (Science). It was also my first time in Prague. My activities since the meeting have included submitting proposals (with others) for EWASS 2018, which will be in Liverpool, and pricing short-term apartment rentals in Prague; clearly, I liked both the meeting and the city very much! My thanks to Keith for cluing me in to this fine meeting.
ASCL Advisory Committee member Rein Warmels (ESO) and I partnered with Abigail Stevens (U Amsterdam), Amruta Jaodand (ASTRON), and Matteo Bachetti (INAF-Osservatorio Astronomico di Cagliari) on software-related sessions for EWASS 2017; our collaboration resulted in a day of talks on Wednesday called Developments and Practices in Astronomy Research Software and a Hack Together Day on Thursday, this latter coordinated by Stevens, Jaodand, and Bachetti.
The ASCL was well represented, with ASCL co-founder Robert Nemiroff (MTU) giving a talk on short codes and Warmels and I each moderating 90-minute sessions on software, both with a discussion period; I also gave a presentation on the ASCL and participated in the Hack Together Day.
The Hack Together Day had numerous exciting projects; the ASCL's projects were less glamorous than most others but yielded really useful information, some of which has already been added to ASCL entries.
Our collective efforts went very well, despite a few worrisome moments along the way. The room our Special Session presentations were in had 98 seats; perhaps 90% were filled for these sessions, and there were people also standing in the room. The presenters/presentations were great and the discussions were lively, and more information about these sessions will be posted soon.There was of course much much more to EWASS than our efforts; notable for those software-inclined were the astrometry, big data, and astroinformatics sessions and associated posters for all of these sessions. In all, an excellent conference!
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Twelve codes were added to the ASCL in June 2017:
DaMaSCUS: Dark Matter Simulation Code for Underground Scatterings
Dark Sage: Semi-analytic model of galaxy evolution
encube: Large-scale comparative visualization and analysis of sets of multidimensional data
EXOSIMS: Exoplanet Open-Source Imaging Mission Simulator
Exotrending: Fast and easy-to-use light curve detrending software for exoplanetsGenPK: Power spectrum generator
KeplerSolver: Kepler equations solver
LMC: Logarithmantic Monte Carlo
PyPulse: PSRFITS handler
rtpipe: Searching for Fast Radio Transients in Interferometric Datasick: Spectroscopic inference crank
the-wizz: Clustering redshift estimation code -
It's come up in Twitter, so here are CSV files for codes that have and do not have preferred citation information in their ASCL records.
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Seventeen codes were added to the ASCL in May 2017:
astroABC: Approximate Bayesian Computation Sequential Monte Carlo sampler
COSMOS: Carnegie Observatories System for MultiObject Spectroscopy
DMATIS: Dark Matter ATtenuation Importance Sampling
demc2: Differential evolution Markov chain Monte Carlo parameter estimator
f3: Full Frame Fotometry for Kepler Full Frame Imagesfd3: Spectral disentangling of double-lined spectroscopic binary stars
FDBinary: A tool for spectral disentangling of double-lined spectroscopic binary stars
getimages: Background derivation and image flattening method
LensPop: Galaxy-galaxy strong lensing population simulation
MBProj2: Multi-Band x-ray surface brightness PROJector 2NPTFit: Non-Poissonian Template Fitting
PCAT: Probabilistic Cataloger
PROFILER: 1D galaxy light profile decomposition
PSOAP: Precision Spectroscopic Orbits A-Parametrically
SPTCLASS: SPecTral CLASSificator codesupernovae: Photometric classification of supernovae
WeirdestGalaxies: Outlier Detection Algorithm on Galaxy Spectra -
Fourteen codes were added to the ASCL in April 2017:
A-Track: Detecting Moving Objects in FITS images
Difference-smoothing: Measuring time delay from light curves
Multipoles: Potential gain for binary lens estimation
Photo-z-SQL: Photometric redshift estimation framework
pwkit: Astronomical utilities in PythonPySM: Python Sky Model
Quickclump: Identify clumps within a 3D FITS datacube
Shwirl: Meaningful coloring of spectral cube data with volume rendering
STATCONT: Statistical continuum level determination method for line-rich sources
Transit: Radiative-transfer code for planetary atmospheresUDAT: A multi-purpose data analysis tool
VaST: Variability Search Toolkit
VULCAN: Chemical Kinetics For Exoplanetary Atmospheres
XID+: Next generation XID development -
Fifteen codes were added to the ASCL in March 2017:
Atmospheric Athena: 3D Atmospheric escape model with ionizing radiative transfer
Charm: Cosmic history agnostic reconstruction method
COCOA: Simulating Observations of Star Cluster Simulations
Corrfunc: Blazing fast correlation functions on the CPU
exorings: Exoring Transit PropertiesICICLE: Initial Conditions for Isolated CoLlisionless systEms
Larch: X-ray Analysis for Synchrotron Applications using Python
MC-SPAM: Monte-Carlo Synthetic-Photometry/Atmosphere-Model
PHOTOMETRYPIPELINE: Automated photometry pipeline
PyMVPA: MultiVariate Pattern Analysis in PythonQtClassify: IFS data emission line candidates classifier
sidm-nbody: Monte Carlo N-body Simulation for Self-Interacting Dark Matter
SNRPy: Supernova remnant evolution modeling
starsense_algorithms: Performance evaluation of various star sensors
TransitSOM: Self-Organizing Map for Kepler and K2 transits -
Twelve codes were added to the ASCL in January 2017:
CosmoSlik: Cosmology sampler of likelihoods
Forecaster: Mass and radii of planets predictor
GrayStar: Web-based pedagogical stellar modeling
GrayStarServer: Stellar atmospheric modeling and spectrum synthesis
GWFrames: Manipulate gravitational waveformsKAULAKYS: Inelastic collisions between hydrogen atoms and Rydberg atoms
kcorrect: Calculate K-corrections between observed and desired bandpasses
MSWAVEF: Momentum-Space Wavefunctions
SONG: Second Order Non-Gaussianity
Spectra: Time series power spectrum calculatorThe Joker: A custom Monte Carlo sampler for binary-star and exoplanet radial velocity data
Vizic: Jupyter-based interactive visualization tool for astronomical catalogsAnd twelve codes were added to the ASCL in February 2017:
Chempy: A flexible chemical evolution model for abundance fitting
corner: Corner plots
GalaxyGAN: Generative Adversarial Networks for recovery of galaxy features
GRIM: General Relativistic Implicit Magnetohydrodynamics
HOURS: Simulation and analysis software for the KM3NeTJetCurry: Modeling 3D geometry of AGN jets from 2D images
juwvid: Julia code for time-frequency analysis
KEPLER: General purpose 1D multizone hydrodynamics code
ORBE: Orbital integrator for educational purposes
stream-stream: Stellar and dark-matter streams interactionsstreamgap-pepper: Effects of peppering streams with many small impacts
Validation: Codes to compare simulation data to various observations -
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 -
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 codeEarthshine 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 datalibprofit: 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 modelPyORBIT: 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 neutrinosSuperplot: Graphical interface for plotting and analyzing data
Trident: Synthetic spectrum generator
