Author Archives: Alice Allen

January 2019 additions to the ASCL

Twelve codes were added to the ASCL in January, 2019:

bettermoments: Line-of-sight velocity calculation
Bilby: Bayesian inference library
CCL: Core Cosmology Library
cFE: Core Flight Executive

eddy: Extracting Disk DYnamics
Galaxia_wrap: Galaxia wrapper for generating mock stellar surveys
OCFit: Python package for fitting of O-C diagrams
Photon: Python tool for data plotting

SEDobs: Observational spectral energy distribution simulation
ssos: Solar system objects detection pipeline
stellarWakes: Dark matter subhalo searches using stellar kinematic data
unwise_psf: PSF models for unWISE coadds

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

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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

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December 2018 additions to the ASCL

Eighteen codes were added to the ASCL in December 2018:

aesop: ARC Echelle Spectroscopic Observation Pipeline
AUTOSPEC: Automated Spectral Extraction Software for integral field unit data cubes
distlink: Minimum orbital intersection distance (MOID) computation library
easyaccess: SQL command line interpreter for astronomical surveys
ExoGAN: Exoplanets Generative Adversarial Network

Fermipy: Fermi-LAT data analysis package
galclassify: Stellar classifications using a galactic population synthesis model
GENGA: Gravitational ENcounters with Gpu Acceleration
GLADIS: GLobal Accretion Disk Instability Simulation
GRAND-HOD: GeneRalized ANd Differentiable Halo Occupation Distribution

Juliet: Transiting and non-transiting exoplanetary systems modelling tool
Lightkurve: Kepler and TESS time series analysis in Python
OctApps: Octave functions for continuous gravitational-wave data analysis
PFANT: Stellar spectral synthesis code
psrqpy: Python module to query the ATNF pulsar catalogue

PynPoint 0.6.0: Pipeline for processing and analysis of high-contrast imaging data
SPAMCART: Smoothed PArticle Monte CArlo Radiative Transfer
WISP: Wenger Interferometry Software Package

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…

An Open Discussion on Astronomy Software Splinter Meeting at AAS 233

MONDAY, 7 JANUARY 2019
Splinter Meeting: An Open Discussion on Astronomy Software
2:00 pm – 3:30 pm
Room 4C-4, Washington State Convention Center

The Astrophysics Source Code Library (ASCL) has organized a Splinter Meeting at January’s AAS  meeting. The session, An Open Discussion on Astronomy Software, is offered in recognition of the ASCL’s 20th anniversary.

Though progress has been made on various fronts, there is still work to be done to improve how astronomers (and other scientists) design, write, share, publish, maintain, archive, and receive credit, recognition, and steady positions for software. This open discussion on software will cover issues, topics, and questions attendees would like addressed, with a panel of software authors to reflect on the topics along with attendees. The session could potentially cover topics such as the sustainability of core astronomical software, whether astronomy should have a Decadal Plan for software and whether publishing need to change, and if so, how? Please submit the issues and questions you would like to see addressed this Google document (https://tinyurl.com/AAS233SWDiscussion). The panel members are:

Megan Ansdell, University of California Berkeley
Rory Barnes, University of Washington
C.E. Brasseur, Space Telescope Science Institute (@cebrasseur)
Tess Jaffe, University of Maryland/NASA Goddard Space Flight Center
Mario Juric, University of Washington (@mjuric)
Amanda Kepley, National Radio Astronomy Observatory (@aakepley)
Rocio Kiman, City University of New York (@rociokiman)

The meeting will be moderated by Alice Allen (ASCL/UMD) and will end with celebratory food (yes, there will be cake!!) for the ASCL’s 20th anniversary.

ASCL tags and finding software in ADS

The ASCL makes it easy to cite the software astro research depends on. Every astronomy journal and many others such as Science and Nature accept ASCL references; ADS shows citations to ASCL entries from nearly 90 journals. Citations to ASCL entries are tracked by ADS, Web of Science, and other indices.

bar chart showing citations to ASCL entries per year as of December 5, 2018, with the 2018 bar labeled with 1,161 citations
Citations to ASCL entries from ADS as of 12/05/2018

ADS makes it easy to search for software in its holdings through the use of the “software” doctype.
Image of the ADS Bumblebee query box with the search term doctype:software in it

ASCL has started tagging NASA software among its entries, allowing you to search ASCL and ADS for this software.
ADS bumblebee query field showing search terms doctype:software keyword:nasa
Screenshot showing entries in ASCL with the NASA keyword

You can find the tags on an entry below the “Discuss” button.Partial screenshot of Kadenza code entry with a red arrow indication the location of the keywords

Citation information and other statistics, such as the number of site links we most recently checked, when we checked them, and how many are healthy, appear on our dashboard, which is updated on Tuesdays and Fridays.
Partial screenshot of dashboard showing 3382 site links (96.77%) are working as of 2018-12-04 03:57:42. Statistics: There are 1833 codes in the ASCL, and 24 submitted. There are 2847 citations to ASCL entries in ADS. 1833 (100.00%) ASCL codes are in ADS. 584 (31.86%) have ADS citations. Bar charts of code additions by year and citations by year
If you have any questions about citing ASCL entries, we’re happy to help! Email editor@ascl.net or tweet to @asclnet.

November 2018 additions to the ASCL

Twenty codes were added to the ASCL in November 2018:

binaryBHexp: On-the-fly visualizations of precessing binary black holes
DiskSim: Modeling Accretion Disk Dynamics with SPH
DRAGONS: Gemini Observatory data reduction platform
Flame: Near-infrared and optical spectroscopy data reduction pipeline
gdr2_completeness: GaiaDR2 data retrieval and manipulation

MillCgs: Searching for Compact Groups in the Millennium Simulation
muLAn: gravitational MICROlensing Analysis Software
PENTACLE: Large-scale particle simulations code for planet formation
PulsarHunter: Searching for and confirming pulsars
pygad: Analysing Gadget Simulations with Python

Pylians: Python libraries for the analysis of numerical simulations
QuickSip: Project survey image properties onto the sky into Healpix maps
radon: Streak detection using the Fast Radon Transform
RLOS: Time-resolved imaging of model astrophysical jets
SEP: Source Extraction and Photometry

Shark: Flexible semi-analytic galaxy formation model
SIM5: Library for ray-tracing and radiation transport in general relativity
synphot: Synthetic photometry using Astropy
VoigtFit: Absorption line fitting for Voigt profiles
Vplanet: Virtual planet simulator

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

Resources mentioned in ADASS 2018 presentation on receiving credit for research software

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