Category Archives: presentations

Understanding data: Visualisation, machine learning, and reproducibility

The ASCL has once again partnered with others on a Special Session at EWASS. This year’s Special Session (SS34) is titled Understanding data: Visualisation, machine learning, and reproducibility, and will be held on Tuesday, 25 June, in Room 3. Not at EWASS? Follow the session on Twitter at #ewass19ss34.

Full information, including abstracts for the presentations listed below, can be found in the detailed interactive program; look for the sessions in yellow and labeled SS34a, SS34b, and SS34c.

Tuesday, 25 June, 9:00 in Room 3, chaired by Rein Warmels
Reproducibility in computer-aided research by Konrad Hinsen
Publishing associated data: Challenges & opportunities by Pierre Ocvirk
FAIR data in astronomy by Mark Allen
Template for reproducible, shareable & achievable research by Mohammad Akhlaghi
These talks are followed by an open discussion moderated by David Valls-Gabaud.

Tuesday, 25 June, 14:30 in Room 3, chaired by Amruta Jaodand
High-performance machine learning in Astrophysics by Simon Portegies Zwart
Machine learning for the SKA by Anna Scaife
SuperNNova: Open-source, deep learning photometric time-series classifier by Anais Möller
Transfer learning for radio galaxy classification by Hongming Tang
Unsupervised classification of galaxy spectra and interpretability by Didier Fraix-burnet

Tuesday, 25 June, 16:30 in Room 3, chaired by John Wenskovitch
Visual Analytics of Data in Astronomy by Johanna Schmidt
Visual analytics algorithms for multidimensional astronomical data by Dany Vohl
Pulsar to Person (P2P): Data Visualization & Sonification to Experience the Universe by John Wenskovitch
Lightning talks for e-Posters
These talks are followed by an open discussion moderated by the session chair.

This Special Session was organized by:
Rachael Ainsworth (UManchester)
Mohammad Akhlaghi (Instituto De Astrofísica De Canarias)
Amruta Jaodand (ASTRON)
David Valls-Gabaud (Observatoire de Paris)
Rein Warmels (ESO)
John Wenskovitch (Virginia Tech)
Alice Allen (ASCL/UMD)

Open Digital Infrastructure in Astrophysics

I spent two days last week at the Open Digital Infrastructure in Astrophysics meeting at the Kavli Institute for Theoretical Physics (KITP) at UC Santa Barbara. This meeting featured presentations on open-knowledge digital infrastructure projects, the communities around them, their metrics for success, funding, diversity efforts, and plans for sustainability. Yeah, we’re talking code, a lot of code, and code projects, too, from AstroPy to yt, and data, and efforts that support openness and research transparency.

Open data presentations were given on:

STScI data, which includes JWST, Hubble, and PanSTARRS data, and the discovery and analysis software for these archives, by Arfon Smith
SDSS Data Infrastructure, by Joel Brownstein
LSST Transients data, by Federica Bianco
Open gravitational wave data and software tools for these data, by Duncan Brown

These software projects were represented at the meeting:

photograph of the Kavli Institute for Theoretical PhysicsAstropy, by Kelle Cruz
ATHENA++, by Jim Stone
Einstein Toolkit, by Philipp Mösta
emcee, by Daniel Foreman-Mackey
GYRE, by Rich Townsend
JETFIT, by Andrew Macfadyen
MESA Project, by Frank Timmes
TOM Toolkit and the AEON Network, by Rachel Street
yt, by Matt Turk

Other open digital resources presented were:

Journal of Open Source Software, by Arfon Smith
R astrostatistics, by Gwendolyn Eadie
Astrophysics Source Code Library, by yours truly

The meeting hashtag was #OpenAstroInfra, and many of the presentations were live tweeted. They were also video recorded and the podcasts are available on the KITP media page for the meeting, as are most of the slide decks. Participants of the co-located “Better Stars, Better Planets: Exploiting the Stellar-Exoplanetary Synergy” and “The New Era of Gravitational-Wave Physics and Astrophysics” programs were encouraged to attend, and we had a raven or two trying to have lunch with us as well.

Each of the presentations had about 15 minutes devoted to questions and discussion about the project highlighted. In two of these discussion sessions, the presenters were asked whether they were concerned about “improper use” of a code; sometimes people who are not well-schooled in the theory or science underlying a software package will use the code incorrectly, arriving at results that are dodgy, or downright wrong, and in a few cases (I know of only one), have then claimed the software is in error. This fear has been given as the reason some software authors do not release their code. I was cheering in my head with Jim Stone’s response to this question the first time it came up; he stated that there is so much benefit to making the code available that a potential improper use should not stop release. (YES!!!) He further went on to say, as did others in the room, that science will correct the record (YES!!!!!). I could not agree more with these replies, and it was great to hear these sentiments from others.

This was my first visit to KITP, and what a wonderful introduction to the institution it was! So many excellent projects, and so much exciting work being done in the open! My thanks to organizers Frank Timmes, Lars Bildsten, and Rich Townsend for inviting the ASCL to participate, and to the Sloan and Ford Foundations for funding the meeting.

ASCL presentation slides

Research Data Alliance Plenary 13 presentation

The ASCL is participating in the Research Data Alliance (RDA) meeting currently underway in Philadelphia, PA. The Plenary 13 meeting motto is “With Data Comes Responsibility.” Indeed! Among the sessions of special interest for software folks was yesterday’s Interest Group meeting on Software Source Code and today’s first meeting of a new Working Group on Software Source Code Identification. The Working Group is led by Roberto Di Cosmo, who is a founder of Software Heritage, Martin Fenner from DataCite, and Daniel Katz from the University of Illinois. This initial meeting is titled “Identifying, referencing and citing the source code of research software: a state of the art.” The ASCL is doing a short presentation that focuses on a few of our practices, how we do them, and the rationale for them; this includes what we do when we process a submission, what metadata for software we do and don’t have and why, and some of our curation practices. Our slides for this presentation are available below.

Photograph of Alice presenting a slide

Photo courtesy of @StephvandeSandt

Our attendance at this meeting was made possible with support from Software Heritage; our thanks to that organization!

Slides (PDF)

A visit to NASA’s Goddard Space Flight Center

Photo showing slide of new journals friendly to astro computing articles started since 2012

At the podium

Although I was born in Washington, DC and have spent most of my life in its Maryland suburbs, yesterday was my first time on the Goddard campus (aside from its Visitor Center, which I’ve been to many times), this despite having two family members and many friends who used to1 or do work there. I was excited! And I had a great reason for going: I was presenting a talk to the Astrophysics Science Division titled “Make your research software famous! (or at least discoverable).” The talk, broadcast on a NASA UStream channel and recorded for future viewing,2 covered a bit about our research on source code availability in astronomy, and also covered our current project to make NASA astro research software more discoverable, what the Astrophysics Source Code Library is and how it improves research transparency, software citation, and recent changes in publishing with regard to software that, combined with other changes in the community and science in general, make it easier than ever before to make one’s astro research software discoverable. The slides I presented are available for download (PDF), and links to different resources, journals, and organizations that I mentioned in the talk are also available.

Kristin Rutkowski, along with Tess Jaffe and Alex Reustle, hosted my visit to GSFC; I had met both Kristin and Tess at last year’s ADASS conference in College Park, where we had our first conversation about my visiting the site to talk about the ASCL. Yesterday’s audience was great; they were involved and asked a lot of excellent questions, about copyright, code authors not receiving credit for the software they write, how we handle dead links, mutable author lists, NASA policies regarding software release, and how the ASCL is funded. Some of the questions came from people attending remotely and were asked online; Alex made sure these were covered, too. Alex is also involved in making the video of the talk available online, and when it is available, I’ll update this post with its link.

Photo of NASA's Space Environment Simulator

Space Environment Simulator

After my presentation, Kristin and Tess took me to see some of the NASA labs and equipment, including the Space Environment Simulator Facility, the JWST/OTIS Vibration Test System, the currently out-of-service High Capacity Centrifuge, and the Acoustic Test Cell. We went through doors marked “Authorized Personnel Only”!! This is one of the perqs of working on the ASCL — I become “Authorized Personnel” when visiting telescopes and labs and such, which, to me, is very cool and exciting! Sure, it’s only for a few minutes and always in the company of others who have far more business being there than I do, but still: very cool and exciting!! After looking at these labs and equipment, Kristin and I said goodbye to Tess, and then drove over to see dinosaur footprints that had been found on the Goddard campus. (Could a visit anywhere be any cooler?!?!)

Dinosaur and small mammal tracks

Science science everywhere! I had a great time at Goddard, and thank Alex and Tess and especially Kristin for hosting my visit!

 

 

 

 

 

 

 

1 Happy retirement day, Janie!
2 No, that’s not nerve-wracking at all, so long as one doesn’t think about it.

Resources mentioned in NASA GSFC presentation on making research software more discoverable

Presentation slides (PDF)

Journals

Journal of Open Source Software (JORS)

Astronomy and Computing (A&C)

Computational Astrophysics and Cosmology (ComAC)

SoftwareX

Journal of Open Source Software (JOSS)

Research Notes of the AAS

Change leaders and guidelines

Force11/Force11 Software Citation Principles

CodeMeta

Working toward Sustainable Software for Science: Practice and Experiences (WSSSPE)

FAIR principles

Social coding sites and archival services

Bitbucket

GitHub

Figshare

Zenodo

Other resources

Asclepias

arXiv/arXiv Next Generation

DataCite

Research poster at AAS 233

URLs have often been used as proxy citations for software and data. We extracted URLs from one journal’s 2015 research articles, removed those from certain long-term reliable domains, and tested the remainder to determine what percentage of these URLs were accessible in September and October 2017. We repeated this test a year later to determine what percentage of these links were still accessible. We will present what we learned about URL accessibility in astronomy.

P. Wesley Ryan, Astrophysics Source Code Library

Download poster

ASCL poster at AAS #233

Software is the most used instrument in astronomy, and organizations such as NASA and the Heidelberg Institute for Theoretical Physics (HITS) fund, develop, and release research software. NASA, for example, has created sites such as code.nasa.gov and software.nasa.gov to share its software with the world, but how easy is it to see what NASA has? Until recently, searching NASA’s Astrophysics Data System (ADS) for NASA’s astronomy software has not been fruitful; NASA has funded the Astrophysics Source Code Library (ASCL ascl.net) to improve the discoverability of these codes. The ASCL, now celebrating its 20th anniversary, is a free online registry of software used in astronomy research and is indexed by ADS, Web of Science, and other resources. Adding NASA and HITS astronomy research codes to the ASCL with appropriate tags enables finding this software easily not only in the ASCL but also in ADS and other services that index the ASCL. This poster presentation covers the changes the ASCL has made to enable discovery of NASA software in ADS and the results of this work.

Alice Allen, Astrophysics Source Code Library/University of Maryland, College Park
Peter Teuben, University of Maryland, College Park
Judy Schmidt, Astrophysics Source Code Library
Robert Nemiroff, Michigan Technological University

Download poster

Software activities at AAS 233 in Seattle, Jan 2019

It’s that time of year again when software folks — users and authors alike — dream of all the software activities at the winter AAS meeting. So here is the ASCL’s (abbreviated*) annual round-up to jumpstart your dreams and warm your code-loving heart! If you have items you want added, please let me know in the comments below or send an email to editor@ascl.net. Thank you!

All rooms are in the Washington State Convention Center unless otherwise specified.


SATURDAY, 5 JANUARY 2019
Workshops
Introduction to Software Carpentry (Day 1), 9:00 AM – 5:00 PM; 211
The AAS Chandra/CIAO Workshop, 9:00 AM – 6:00 PM; 204
Using Python to Search NASA’s Astrophysics Archives, 10:00 AM – 11:30 AM; 213


SUNDAY, 6 JANUARY 2019
Workshops
SOFIA Workshop for FORCAST and HAWC+ Data Analysis, 8:30 AM – 5:15 PM; 201
Adding LISA to your Astronomy Tool Box, 9:00 AM – 5:00 PM; 213
Introduction to Software Carpentry (Day 2), 9:00 AM – 5:00 PM; 211
Using Python and Astropy for Astronomical Data Analysis, 9:00 AM – 5:00 PM; 4C-4
The AAS Chandra/CIAO Workshop, 9:00 AM – 6:00 PM; 204
Advanced Searching in the New ADS: On the Web and Using the API, 3:00 PM – 4:30 PM; 304


MONDAY, 7 JANUARY 2019
Splinter meetings
Data Science, 8:00 AM – 6:00 PM, 4C-1
Updates on Implementing Software Citation in Astronomy, 12:30 PM – 2:00 PM; 203
An Open Discussion on Astronomy Software, 2:00 PM – 3:30 PM; 4C-4

Open event
AAS WorldWide Telescope presents: Advances in Astronomical Visualization, 10:00 AM – 11:30 AM; 214

Oral presentations
Session 126. Machine Learning in Astronomical Data Analysis, 2:00 PM – 3:30 PM; 607 (5 presentations)

Also:
112.01. Constraining BH formation with 2M05215658+4359220, 10:00 AM – 10:10 AM, 612
109.03. Real-time data reduction pipeline and image analysis software for FIREBall-2: first flight with a δ-doped UV-EMCCDs operating in counting mode, 10:30 AM – 10:40 AM, 608
175.06. Python, Unix, Observing, and LaTeX: Introducing First Year Undergraduates to Astronomical Research, 10:50 AM – 11:00 AM, 620
109.08. TESS Data Analysis using the community-developed Lightkurve Python Package, 11:20 AM – 11:30 AM, 608
123.02D. A Uniform Analysis of Exoplanet Atmosphere Spectra Observed by HST WFC3 Is Consistent with Watery Worlds, 2:10 PM – 2:30 PM, 6C
129.06. Reconstructing the Orphan Stream Progenitor with MilkyWay@home Volunteer Computing, 3:00 PM – 3:10 PM, 611

Selected posters
144.25. Identifying and Comparing Centrally Star-Forming Galaxies Using MaNGA
144.29. Deriving star formation histories from photometric spectral energy distributions with diffusion k-means
144.30. Using Convolutional Neural Networks to predict Galaxy Metallicity from Three-Color Images
144.35. Automatic Detection and Analysis of Debris from Galactic Accretion Events
145.05. Galaxy Gradients Across Simulations
145.07. Reduction and Analysis of GMOS Spectroscopy for Herschel Sources in CANDELS
145.25. Comparison of the HI Signal Extraction Algorithms of SoFiA and ALFALFA
140.02. Tracking the TESS Pipeline
140.12. Undergraduates Can Find Planets Too
140.16. Identifying Transiting Exoplanets in with Deep Learning in K2 Data
140.20. The Impact of Small Statistics on Identifying Background False Positives in Kepler Data
140.23. AutoRegressive Planet Search for Ground-Based Transit Surveys
140.29. Getting to Know Your Star: A comparison of analytic techniques for deriving stellar parameters and abundances
149.18. NANOGrav: Data Accessibility, Analysis and Automation using Python
150.01. Revised Simulations of the Planetary Nebulae Luminosity Function
150.15. Identifying Binary Central Stars of Planetary Nebulae with PSF Fitting
158.02. HaloSat: X-Ray Calibration and Spectral Analysis for a NASA CubeSat
162.04. The Starchive

Selected iPosters
167.02. Modeling circumstellar dust around low-mass-loss rate carbon-rich AGB stars
167.04. The response of optical Fe II emission in AGNs to changes in the ionizing continuum, I: photoionization modelling
164.02. A Maximum Likelihood Approach to Extracting Photon-Starved Spectra of Directly Imaged Exoplanets
166.02. Smoothed Particle Inference Analysis of SNR DEM L71
171.03. The State of Software Tools for the Space Telescope Imaging Spectrograph

Other activities of possible interest
Monday, January 7: Data Science Splinter Meeting, 8:00 AM – 6:00 PM, 4C-1


TUESDAY, 8 JANUARY 2019
Workshop
LSST Science Pipelines Stack Tutorial for AAS, 9:00 AM – 5:00 PM; 310

Splinter meeting
Cafe SCiMMA: Conceptualizing an NSF Center for Scalable Cyberinfrastructure for Multimessenger Astrophysics, 3:15 PM – 5:15 PM; Redwood (Sheraton Seattle Hotel)

Oral presentations
Session 225. Computation, Data Science, and Image Analysis, 2:00 PM – 3:30 PM, 6E (6 presentations)

Also:
218.05. A Uniform Analysis of Kepler/K2 Exoplanet Transit Parameters, 10:40 AM – 10:50 AM, 603
206.05D. High Resolution spatial analysis of z ~2 lensed galaxy using pixelated source-reconstruction algorithm, 10:50 AM – 11:10 AM, 605/610
203.05. Atmosphere Retrieval of Planetary Mass Companions with the APOLLO Code: A Case Study of HD 106906b and Prospects for JWST, 11:00 AM – 11:10 AM, 6B
207.10. astroquery: An Astronomical Web-Querying Package in Python, 11:03 AM – 11:10 AM, 606
239.04D. Kinematics of Circumgalactic Gas and Cold Gas Accretion at Redshift z=0.2, 2:40 PM – 3:00 PM, 609
227.07. Mu and You: Public Microlensing Analysis Tools and Survey Data, 3:12 PM – 3:24 PM, 606

Poster presentations
Session 245. Computation, Data Science, and Image Analysis posters (31 posters!)

Selected posters
243.08. Utilizing Independent Component Analysis to Explore the Diversity of Quasars
245.01. Making organizational research software more discoverable
245.27. The MAESTROeX low Mach number stellar hydrodynamics code
245.29. The Castro Adaptive Mesh Refinement Hydrodynamics Code: Applications, Algorithm Development, and Performance Portability
247.30. Chemical Analysis of Tabby’s Star (KIC 8462852)
247.35. VPLanet: The VIrtual Planet Simulator
249.11. Know Your Neighbors: New Catalogs and Analysis of Star Clusters in the LMC, SMC, & M33
250.02. X-Ray Source Analysis In The Globular Clusters NGC 6341 and NGC 6541
253.06. Structure Function Analysis of Turbulent Properties in the Small and Large Magellanic Clouds
259.05. Forward-Modeling Analysis of Late-T Dwarf Atmospheres
259.15. Finding age relations for low mass stars using magnetic activity and kinematics
259.24. A Uniform Retrieval Analysis on a Sample of 16 T-dwarfs
258.25. SuperNovae Analysis aPplication (SNAP): Identifing and Understanding the Physics of Supernovae

Selected iPosters
268.02. Towards 3D Parameter Space Studies of CCSNe With Grey, Two-Moment Neutrino Transport
261.12. Using Machine Learning to Predict the Masses of Galaxy Clusters
261.15. Mapping Galaxy Cluster Orientations from Cosmo-OWLS Simulations
261.16. A Hydrodynamical Simulation of the Off-Axis Cluster Merger Abell 115


WEDNESDAY, 9 JANUARY 2019
Open meeting
AAS WorldWide Telescope with Python and Astropy, 10:00 AM – 11:30 AM; 214

Oral presentations
316.04D. Feedback and Chemical Enrichment in Low Mass Dwarf Galaxies: Insights from Simulations Tracking Individual Stars, 10:30 AM – 10:50 AM, 617
304.03. Recent upgrades to the pyLIMA software for microlensing modeling and analysis of two binary events, 10:10 AM – 10:20 AM, 6E
311.05. Quantifying the effects of spatial resolution and noise on galaxy metallicity gradients, 11:00 AM – 11:10 AM, 612
313.05D. Probabilistic data analysis methods for large photometric surveys, 10:50 AM – 11:10 AM, 614
336.04D. Simultaneous modelling of X-rays emission and optical polarization of intermediate polars using the CYCLOPS code: the case of V405 Aurigae, 2:40 PM – 3:00 PM, 614
342.06. On Open Cluster Disruption, 3:00 PM – 3:10 PM, 620
341.01. Reproducing Stellar Rotation Periods in the Kepler Field via Magnetic Braking and Tidal Torques

Selected posters
346.04. Designing a Python Module for the Calculation of Molecular Parameters and Production Rates in Comets
347.01. Hyperlink preservation in astrophysics papers
348.19. The COBAIN code. Basic principles and geometrical considerations
348.27. Considerations and Design Principles for the 2.1 Release of the PHOEBE Eclipsing Binary Modeling Code
356.06. Analysis of a large number of spiral galaxies shows asymmetry between clockwise and counterclockwise galaxies

Session 381. Computation, Data Science, and Image Analysis session (8 iPosters)

Selected iPosters
381.03. ASTROstream: Automated claSsification of Transient astRonomical phenOmena in the streaming mode
381.05. Understanding and using the Fermitools
381.07. Polarization Calibration Post-Pipeline in CASA: Pilot Implementation
381.08. Transitioning from ADS Classic to the new ADS search platform


THURSDAY, 10 JANUARY 2019
Hack Together Day
8:30 AM – 7:00 PM; 4C-2

Oral presentations
413.06. The Radio Astronomy Software Group: Foundational Tools for 21 cm Cosmology and Beyond, 11:10 AM – 11:20 AM, 614
408.07D. Hundreds of New Planet Candidates from K2, 11:00 AM – 11:20 AM, 608
411.05D. AzTEC Survey of the Central Molecular Zone: Modeling Dust SEDs and N-PDF with Hierarchical Bayesian Analysis, 10:40 AM – 11:00 AM, 612
405.05. How can new data analysis methods get more out of Kepler/K2 data?, 10:40 AM – 10:50 AM, 605/610
425.01. The Dedalus project: open source science in astrophysics with examples in convection and stellar dynamos, 2:00 PM – 2:22 PM, 606
430.02D. Analysis of the spatially-resolved V-3.6μm colors and dust extinction within 257 nearby NGC and IC galaxies, 2:20 PM – 2:40 PM, 612

Selected posters
443.11. WFC3 PSF Database and Analysis Tools
457.02. The Stak Notebooks: Transitioning From IRAF to Python
442.01. ExoPhotons: Exoplanet Monte Carlo Radiative Transfer
442.02. Quantifying inhomogeneities in the HI distributions of simulated galaxies
445.01. Lightkurve v1.0: Kepler, K2, and TESS time series analysis in Python
445.05. Using Kepler DR25 Products to Compute Exoplanet Ocurrence Rates
465.07. Distribution of stellar rotation periods using light curve analysis of second phase Kepler data


* abbreviated as in I haven’t listed all the posters that could be listed here, as the list was getting very very long…

ASCL research poster at ADASS XXVIII


Astronomers use software for their research, but how many of the codes they use are available as source code? We examined a sample of 166 papers from 2015 for clearly identified software use, then searched for source code for the software packages mentioned in these research papers. We categorized the software to indicate whether source code is available for download and whether there are restrictions to accessing it, and if source code was not available, whether some other form of the software, such as a binary, was. Over 40% of the source code for the software used in our sample was not available for download. As URLs have often been used as proxy citations for software and data, we also extracted URLs from one journal’s 2015 research articles, removed those from certain long-term reliable domains, and tested the remainder to determine what percentage of these URLs were accessible in September and October, 2017. We repeated this test a year later to determine what percentage of these links were still accessible. This poster will present what we learned about software availability and URL accessibility in astronomy.

P. Wesley Ryan, Astrophysics Source Code Library
Alice Allen, Astrophysics Source Code Library/University of Maryland
Peter Teuben, University of Maryland

Download poster

Seminar at Centre de Recherche Astrophysique de Lyon

I gave a seminar at the Centre de Recherche Astrophysique de Lyon on Friday, September 14, at the invitation of Mohammad Akhlaghi, a post-doc there. Mohammad is very interested and has done a lot of work on reproducibility, ensuring that his work is reproducible and developing a reproducibility framework that can be adopted by others. The seminar took place on CRAL’s lovely historic campus at the Observatoire de Lyon in Saint-Genis-Laval. The title, abstract, and link to the slides are below.


Title: Make your code famous! (or at least discoverable).

Abstract: Source codes are increasingly important for the advancement of science in general and astrophysics in particular. Journal articles detail the general logic behind new results and ideas, but often the source codes that enable these results remain hidden from public view. In this presentation, I will discuss our recent study on the availability of source codes used for published research and how this affects the transparency and reproducibility of astro research. I will cover what the Astrophysics Source Code Library (ASCL, ascl.net) is, how to submit software to the resource, and the benefits of doing so. I will share what happens after software is submitted, how ASCL entries are indexed by ADS, the links between literature and software entries, and how an ASCL ID can be used for citing your code. I will cover good and bad ways to cite software, avenues for publishing software, and how journals are changing to include and recognize the contribution software makes to our discipline.

Slides (PDF)