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In conclusion 2 …

As promised in a previous post, here are a few slides from the second block of EWASS 2017 software presentations.

Reproducibility in Era of Data-Driven Science, Kai Polsterer (slides: PDF)

Conclusion: publications should be open access. Data should include all raw, test, training, and reference data in addition to detailed results. Software should be put into repositories and registries, and parameters, configuration, and environment needed to run the software should be saved as much as possible.


Should short codes used for astronomy research be made public?, Robert Nemiroff (slides: PDF)

Summary and key points. Short codes can be vitally important, yet we never see them, making science less falsifiable. Let's reverse this. Submit your important short codes with your papers, like Figures, OR to the ASCL (at Science, on the whole, will be stronger.


Giving credit where credit is due: the role of ADS in discovering and citing software in scholarly publications, Sergi Blanco-Cuaresma (slides: PDF)

SAO/NASA ADS. Identification: What software version? Preservation: Is that version still available? Attribution: Is the right set of authors receiving the credit?


Fifteen years of WISE technology software development and operations, Gijs Verdoes Kleijn (slides: PDF)

The future: (Big) Data Science and Education. University of Groningen astronomy student admissions tripled since 2010. Strategy: grow a new generation of data scientists


CDS reference services supporting astronomy research, Mark Allen (slides: PDF)

Challenges and Opportunities. Multi-wavelength, multi-messenger and time-domain astrophysics. Changing modes of publication -- data associated with publications. Responding to the change in scale - Big Data. New technologies - not too soon, not too late. Bringing the code to the data. Continued adaptation to meet community needs.

In conclusion 1…

Here are a few slides from presentations mentioned in a previous blog post; slides from more of the talks at EWASS will be covered in another post.

Software development best practices from Astropy, Thomas Robitaille (slides: PDF)

All contributions are made in GitHub repositor(ies). All contributions are reviewed via pull requests. Test suite run using pytest. Docs written in Sphinx, hosted on ReadTheDocs. Continuous integration on Travis AppVeyor, Circle CI.

A Computer Science Perspective on the Astronomy Research Software Process by John Wenskovitch (slides: PDF)

Summary: 1. Acknowledgement of strengths. 2. Version control. a. Use it. b. Commit often. 3. Frequent communication. 4. Manage feature requests. 5. Collaborate with an expert.

TARDIS: A radiative transfer code, an open source community, and an interdisciplinary collaboration by Wolfgang Kerzendorf (slides: PDF)

Developing simulation codes. Science discovery needs to be the key driver (everything else is secondary). Only write code that doesn't exist anywhere else. Many of the software engineering techniques are geared towards team development -- not always applicable.

Research software best practices: Transparency, credit, and citation by yours truly (slides: PDF, PPTX)

You can change the world! Or at least a little piece of it. Release your code. Specify how you want your code to be cited. License your code. Register your code. Archive your code.

Dagstuhl Manifesto on Citation: I will make explicit how to cite my software. I will cite the software I used to produce my research results. When reviewing, I will encourage others to cite the software they have used.

ASCL projects at the EWASS Hack Together Day

The European Astronomical Society (EAS) European Week of Astronomy and Space Science (EWASS) meeting, held June 26-30 in Prague, had its first Hack Together Day, coordinated by Abigail Stevens (U Amsterdam), Amruta Jaodand (ASTRON), and Matteo Bachetti (INAF-Osservatorio Astronomico di Cagliari).

The projects were varied and some participants worked on more than one. I proposed two ASCL-related projects for this, both of which had willing participants. Daniel Evans (Keele U) worked on creating a dataset of keywords for ASCL entries based on their associated papers, and Jessica Kirkby-Kent (Keele U), Eleonora Alei (INAF – Astronomical Observatory of Padua) and I worked on finding preferred citation information for codes that didn’t have it. Since we were working from an open Google spreadsheet, the link to the spreadsheet was tweeted out several times during the Hack Together Day and later, allowing others not at EWASS to participate in this Hack Together Day project that day and in subsequent days, to good effect.

Kirkby-Kent, Alei, and I looked for preferred citation info for at least 184 codes and found this information for 45 codes, so we have a yield of 24.5% — we found citation information on 24.5% of the code sites we looked at. Another two codes had citation information added to them by unknown users during the Hack event, and later, citation information was added for several more codes. I spent last weekend with the data Kirkby-Kent, Alei, mostly anonymous others, and I gathered and adding the collected preferred citations to ASCL entries, editing a total of 52 entries to add this important information. I still have a bit of information to go through and get clarification on, and will soon add that, too, and then will go back through the Google spreadsheet again, as I see someone — I suspect Kirkby-Kent! — has been methodically adding more information. (Thank you!!)

Evans continued to build the dataset after EWASS and found a few bibcode anomalies along the way, which I’ll share with ADS at a later time. He has sent me email to let me know his searching is complete and he is getting the results into reasonable shape so this information can be added to the ASCL, too. Having this information will be very useful to anyone who uses the ASCL to find software. (Thank you!!)

I am so glad I participated in the Hack Together Day, and am grateful to Evans, Kirkby-Kent,  Alei, and all others who gathered information for the ASCL, and to Jaodand, Stevens, and Bachetti for planning it. Thank you!

Developments and Practices in Astronomy Research Software at EWASS 2017

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 review

The 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:

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 presenting at EWASS

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, NL

Interactive 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.

ASCL at the 2017 European Week of Astronomy and Space Science (EWASS) meeting

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

Program page for software talks
Image by Amruta Jaodand

This 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!

June additions to the ASCL

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 exoplanets

GenPK: Power spectrum generator
KeplerSolver: Kepler equations solver
LMC: Logarithmantic Monte Carlo
PyPulse: PSRFITS handler
rtpipe: Searching for Fast Radio Transients in Interferometric Data

sick: Spectroscopic inference crank
the-wizz: Clustering redshift estimation code

May additions to the ASCL

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 Images

fd3: 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 2

NPTFit: Non-Poissonian Template Fitting
PCAT: Probabilistic Cataloger
PROFILER: 1D galaxy light profile decomposition
PSOAP: Precision Spectroscopic Orbits A-Parametrically
SPTCLASS: SPecTral CLASSificator code

supernovae: Photometric classification of supernovae
WeirdestGalaxies: Outlier Detection Algorithm on Galaxy Spectra

April additions to the ASCL

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 Python

PySM: 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 atmospheres

UDAT: A multi-purpose data analysis tool
VaST: Variability Search Toolkit
VULCAN: Chemical Kinetics For Exoplanetary Atmospheres
XID+: Next generation XID development

March additions to the ASCL

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 Properties

ICICLE: 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 Python

QtClassify: 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

January and February additions to the ASCL

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 waveforms

KAULAKYS: 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 calculator

The Joker: A custom Monte Carlo sampler for binary-star and exoplanet radial velocity data
Vizic: Jupyter-based interactive visualization tool for astronomical catalogs

And 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 KM3NeT

JetCurry: 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 interactions

streamgap-pepper: Effects of peppering streams with many small impacts
Validation: Codes to compare simulation data to various observations