February 2021 additions to the ASCL

Thirty codes were added to the ASCL in February:

BALRoGO: Bayesian Astrometric Likelihood Recovery of Galactic Objects
binaryoffset: Detecting and correcting the binary offset effect in CCDs
CMasher: Scientific colormaps for making accessible, informative plots
DaMaSCUS-SUN: Dark Matter Simulation Code for Underground Scatterings – Sun Edition
EqTide: Equilibrium Tide calculations

extinction: Dust extinction laws
ForwardDiff: Forward mode automatic differentiation for Julia
GalRotpy: Parametrize the rotation curve and gravitational potential of disk-like galaxies
GLEAM: Galaxy Line Emission and Absorption Modeling
hardCORE: Exoplanet core radius fractions calculator

HUAYNO: Hierarchically split-Up AstrophYsical N-body sOlver N-body code
lensingGW: Lensing of gravitational waves
Lightbeam: Simulate light through weakly-guiding waveguides
mirkwood: SED modeling using machine learning
MOSAIC: Multipole operator generator for Fast Multipole Method operators

MST: Minimum Spanning Tree algorithm for identifying large-scale filaments
Multi_CLASS: Cross-tracer angular power spectra of number counts using CLASS
MUSE-PSFR: PSF reconstruction for MUSE WFM-AO mode
nway: Bayesian cross-matching of astronomical catalogs
OPUS: Interoperable access to analysis and simulation codes

Piff: PSFs In the Full FOV
Pixell: Rectangular pixel map manipulation and harmonic analysis library
polgraw-allsky: All-sky almost-monochromatic gravitational-wave pipeline
PyAutoFit: Classy probabilistic programming
PyFstat: Continuous gravitational-wave data analysis

RASSINE: Normalizing 1D stellar spectra
spinOS: SPectroscopic and INterferometric Orbital Solution finder
ThumbStack: Map and profile stacking pipeline
viscm: Analyzing colormaps and creating new colormaps
X-PSI: X-ray Pulse Simulation and Inference

Resources for SIAM CSE21 presentation on Schrödinger’s Code

I am giving a presentation at the SIAM (virtual) Conference on Computational Science and Engineering today in a Minisymposium on Data-Driven Analysis of Scientific Software Quality, Availability, and Development Productivity to discuss research we published in 2018 and the relevance of our findings to scientific software availability. A link to the slides from the presentation is below, along with links to additional information.


Slides (PDF)

Paper: Schroedinger’s Code: A Preliminary Study on Research Source Code Availability and Link Persistence in Astrophysics
Data and code

Other studies mentioned:
Collberg C., Proebsting T. and Warren A. M. 2014 Repeatability and Benefaction in Computer Systems Research: A Study and a Modest Proposal, Tech. Rep. TR 14-04 (http://repeatability.cs.arizona.edu/v2/RepeatabilityTR.pdf)

Howison J. and Bullard J. 2016 Software in the scientific literature: Problems with seeing, finding, and using software mentioned in the biology literature, Journal of the Association for Information Science and Technology 67 2137

Mangul, S., Mosqueiro, T., Duong, D., Mitchell, K., Sarwal, V., Hill, B., Brito, J., Littman, R., Statz, B., Lam, A., Dayama, G., Grieneisen, L., Martin, L., Flint, J., Eskin, E., & Blekhman, R. 2018, A comprehensive analysis of the usability and archival stability of omics computational tools and resources, bioRxiv

Rewarding the effort involved

Funding
How to fund research software development
Essential Open Source Software for Science
DOE to Provide $12 Million for Research on Adapting Scientific Software to Run on Next-Generation Supercomputers

Recognition
Citations for software
FORCE11 Software Citation Principles
FORCE11 Software Citation Implementation Working Group
Software must be recognised as an important output of scholarly research

Career path
The Society of Research Software Engineering
US Research Software Engineer Association

Training

Better Scientific Software (BSSw)
SciCoder
Software Sustainability Institute
How to Professionally Develop Reusable Scientific Software—And When Not To

Changes in journal practices

In which journals should I publish my software?
Software with impact
An empirical analysis of journal policy effectiveness for computational reproducibility

Better support through technology

Tools for working with CITATION.cff files
Create a CodeMeta file
Getting a DOI for your code

January 2021 additions to the ASCL

Eighteen codes were added to the ASCL in January:

3LPT-init: Initial conditions with third-order Lagrangian perturbation for cosmological N-body simulations
apogee: Tools for APOGEE data
Avocado: Photometric classification of astronomical transients and variables with biased spectroscopic samples
BAYES-LOSVD: Bayesian framework for non-parametric extraction of the LOSVD
cFS: core Flight System

Curvit: Create light curves from UVIT data
DarpanX: X-ray reflectivity of multilayer mirrors
Eigentools: Tools for studying linear eigenvalue problems
EphemMatch: Ephemeris matching of DR25 TCEs, KOIs, and EBs for false positive identification
Mask galaxy: Machine learning pipeline for morphological segmentation of galaxies

Nigraha: Find and evaluate planet candidates from TESS light curves
Octo-Tiger: HPX parallelized 3-D hydrodynamic code for stellar mergers
ptemcee: A parallel-tempered version of emcee
pyUPMASK: Unsupervised clustering method for stellar clusters
PyXspec: Python interface to XSPEC spectral-fitting program

radiowinds: Radio Emission from Stellar Winds
stratsi: Stratified streaming instability
whereistheplanet: Predicting positions of directly imaged companions

The ASCL at the 237th meeting of the American Astronomical Society

It’s that time of year again, when astronomers’ hearts and wings turn to AAS for the winter AAS meeting. This year, however, the wings are virtual; like other conferences in this time of pandemic, the 237th meeting of the AAS is online. I’m very impressed with the online meeting space, which includes a conference center with different locations to visit, a virtual exhibit hall, an iPoster gallery, and many opportunities through Slack and thoughtfully-planned activities to enable and encourage interaction between attendees, exhibitors, and presenters, including the always great Open Mic event, a highlight of the winter meeting, on Wednesday evening.

Members of the ASCL are presenting two iPosters + (the “plus” is a short Zoom session about  the poster) and an oral presentation at this meeting.

On Monday, Siddha Mavuram, an UMD student hired to do development work for the ASCL for our NASA ADAP project, is doing an iPoster + presentation titled Come search the ASCL with our new API! I also have an iPoster + presentation on Monday called Life, the Universe and Everything… you ever wanted to know about the Astrophysics Source Code Library. Though our short talks, using our posters only as our visual aids, are on Monday, our posters are available all week.

On Tuesday, Peter Teuben is presenting results of our NASA ADAP project. Though Siddha is presenting part of the development work done for this project, Peter is sharing the overall results in his oral presentation Increasing the visibility of NASA astrophysics software through the ASCL, showing how this project has made it possible to search the ASCL and ADS for NASA software through the use of keywords and, on ADS, the doctype value software. You can see these results yourself on the ASCL and with an ADS search.

Because I very cleverly failed to realize that all the links I added to the slides for my iPoster wouldn’t work once I made those slides images (doh!), I provide a PDF of these slides for download below in which most, but alas not all, of the links work. Later this week, I’ll provide a full list of links in another post that will contain all of the resources and links the ASCL is presenting this week.

Slides for Alice’s ASCL iPoster slideshow (PDF)

December 2020 additions to the ASCL

Twenty-six codes were added to the ASCL in December:

BinaryStarSolver: Orbital elements of binary stars solver
BlackHawk: Black hole evaporation calculator
dolphin: Automated pipeline for lens modeling
DRAGraces: Reduction pipeline for GRACES spectra

EinsteinPy: General Relativity and gravitational physics problems solver
EOS: Equation of State for planetary impacts
getsf: Multi-scale, multi-wavelength sources and filaments extraction
HCGrid: Mapping non-uniform radio astronomy data onto a uniformly distributed grid

HydroCode1D: 1D finite volume code
LALSuite: LIGO Scientific Collaboration Algorithm Library Suite
LIFELINE: LIne proFiles in massivE coLliding wInd biNariEs
MADLens: Differentiable lensing simulator

Magritte: 3D radiative transfer library
MLC_ELGs: Machine Learning Classifiers for intermediate redshift Emission Line Galaxies
NSCG: NOIRLab Source Catalog Generator
Pomegranate: Probabilistic model builder

PyXel: Astronomical X-ray imaging data modeling
Robovetter: Automatic vetting of Threshold Crossing Events (TCEs)
seaborn: Statistical data visualization
sedop: Optimize discrete versions of common SEDs

Sengi: Interactive viewer for spectral outputs from stellar population synthesis models
SimCADO: Observations simulator for infrared telescopes and instruments
Skye: Excess clustering of transit times detection
SLIT: Sparse Lens Inversion Technique

SWIGLAL: Access LALSuite libraries with Python and Octave scripts
TRAN_K2: Planetary transit search

November 2020 additions to the ASCL

Thirty codes were added to the ASCL in November 2020:

ACStools: Python tools for Hubble Space Telescope Advanced Camera for Surveys data
AdaMet: Adaptive Metropolis for Bayesian analysis
ARES: Accelerated Reionization Era Simulations
CAPTURE: Interferometric pipeline for image creation from GMRT data
Clustering: Code for clustering single pulse events

CWITools: Tools for Cosmic Web Imager data
DarkBit: Dark matter constraints calculator
DarkCapPy: Dark Matter Capture and Annihilation
DDCalc: Dark matter direct detection phenomenology package
DeepShadows: Finding low-surface-brightness galaxies in survey images

DYNAMITE: DYnamics, Age and Metallicity Indicators Tracing Evolution
EvapMass: Minimum mass of planets predictor
frbcat: Fast Radio Burst CATalog querying package
GoFish: Molecular line detections in protoplanetary disks
GOTHIC : Double nuclei galaxy detector

GPCAL: Instrumental polarization calibration in VLBI data
HaloGen: Modular halo model code
HSTCosmicrays: Analyzing cosmic rays in HST calibration data
Kalkayotl: Inferring distances to stellar clusters from Gaia parallaxes
kīauhōkū: Stellar model grid interpolation

MCMCDiagnostics: Markov Chain Monte Carlo convergence diagnostics
PNICER: Extinction estimater
REBOUNDx: Adding effects in REBOUND N-body integrations
reproject: Python-based astronomical image reprojection
RRATtrap: Rotating Radio Transient identifier

Scintools: Pulsar scintillation data tools
SEDkit: Spectral energy distribution construction and analysis tools
TLC: Tidally Locked Coordinates
tlpipe: Data processing pipeline for the Tianlai experiment
wobble: Time-series spectra analyzer

October 2020 additions to the ASCL

Fifteen codes were added to the ASCL in October 2020:

Astronomaly: Flexible framework for anomaly detection in astronomy
Exo-DMC: Exoplanet Detection Map Calculator
grapus: GRavitational instability PopUlation Synthesis
GSpec: Gamma-ray Burst Monitor analyzer
LaSSI: Large-Scale Structure Information

Legolas: Large Eigensystem Generator for One-dimensional pLASmas
lenspyx: Curved-sky python lensed CMB maps simulation package
MBF: MOLSCAT 2020, BOUND, and FIELD for atomic and molecular collisions
Pix2Prof: Deep learning for textraction of useful sequential information from galaxy imagery
plancklens: Planck 2018 lensing pipeline

relxill: Reflection models of black hole accretion disks
ROGER: Automatic classification of galaxies using phase-space information
stella: Stellar flares identifier
stsynphot: synphot for HST and JWST
TACHE: TensoriAl Classification of Hydrodynamic Elements

Lightning talk at ADASS XXX: Making organizational software easier to find

The excellent ADASS XXX conference concluded yesterday. I missed meeting ADASS attendees face-to-face, but was delighted to spend time with them safely online, to learn about their projects and research, to talk about software and data, to share what the ASCL has been doing, and to meet old and new friends. The all-virtual conference was just about perfect; the technology set-up was excellent, providing opportunities to see sessions as they happened or at a later time on video, ask questions, comment on and discuss what was presented, and have one-on-one or small group video calls. The schedule was easy to keep track of, as one could subscribe to the schedule and get updates to it (mostly additions) immediately. Support was extremely responsive; an online Help Desk provided answers to queries almost immediately. There was even a conference photo!

Poster presenters were invited to record and upload a lightning talk — no more than three minutes — for their posters; two-minute lightning talks via Zoom were also arranged at the conference. The ASCL presented a poster on Making organizational software easier to find in ASCL and ADS; the hastily-put-together lightning talk presented at the conference for this poster is below.

ADASS attendee Simón Torres offered to download all the pre-recorded lightning talks and stream them during the conference, so a Poster Video Watching Party was scheduled for Wednesday afternoon. The stream was great fun to watch! It was interesting, too, to see all the different ways people presented their lightning talks.

What a great conference this was! I look forward to next year’s!

ASCL poster on NASA software project at ADASS XXX


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. Through its ADAP program, NASA has funded the Astrophysics Source Code Library (ASCL ascl.net) to improve the discoverability of these codes. Adding institutional tags to ASCL entries makes it easy to find this software 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 as a result of this funding and how you can use the results of this work to better find organizational software in ASCL and ADS.

Download poster (PDF)

ASCL API poster at ADASS XXX

Poster about ASCL API
We have developed an API for the Astrophysics Source Code Library (ASCL) that enhances the ability of users to conduct complex and automated queries on ASCL indexed codes. The API is public and allows anyone to programmatically search and filter the ASCL software database via an HTTP request. For example, the search https://ascl.net/api/search/?q=%22supernova%22&fl=credit returns a list of authors with ASCL-indexed codes involving supernovae in JSON format. We will demonstrate the API and show its use in answering a researcher’s questions regarding the growth and usage of both interpreted and compiled languages in the database, gaining a more nuanced understanding of trends in astrophysics software development. Our findings confirmed a piece of conventional wisdom: that Python is growing in market share, while low level programming languages like C and C++ remain very popular. Further documentation for the API is available at https://github.com/teuben/ascl-tools/tree/master/API.

Siddha Mavuram (UMD), Alice Allen (ASCL/UMD), Robert J. Nemiroff (MTU), Judy Schmidt (ASCL), Peter J. Teuben (UMD)

Download poster (PDF)