ASCL News
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Tuesday started with Jeffrey Carver from the University of Alabama presenting What we have learned about using software engineering practices in scientific software. They took a multi-pronged approach to studying scientific software, from conducting surveys and workshop to direct interactions and case studies. From survey work, his team was able to group problems scientists were having with their own software into four main areas: rework, performance, regression (testing), and forgetting bugs. From this, they could see what software engineering practices might help with solving the problems.
Case studies brought numerous lessons to light; they found that the use of higher-level languages was low, performance competes with other goals, and external software use can be seen as risky. Workshops highlighted some of the differences between scientist programmers and software engineers and their domains. Scientist developers often lack formal software engineering expertise but have deep knowledge of their domains and are often the main users of their software. Quality goals are different, too; scientists would rather software not run than return an incorrect result. This project demonstrated that there is a need to eliminate the stigma associated with software engineering and that software engineers need to understand domain constraints and specific problems. PDF
Every presentation sparked lively Q&A and discussion, often throughout the presentation, and this one was no exception.
The next presentation was Engineering yt by Matthew Turk from NCSA at the University of Illinois at Urbana Champaign. He provided context and information on this well-cited community-developed project, discussed how the community was built, and its adoption of a code of conduct. YTEP, yt Enhancement Proposals, provide a method to manage suggestions for improving yt. Communication methods within the community are well thought out. The challenges of creating and managing the community sparked a lot of discussion; large software projects can have many things go wrong.
Discussion among the group made Matt's presentation run long, making it necessary to break for coffee before Matt's talk was done and then return to it after the break. The group was very engaged throughout the day; fortunately, the schedule accommodated the frequent discussions in every presention very well.
After Matt's talk, Caroline Jay (University of Manchester) and Robert Haines (Software Sustainability Institute) presented Software as academic output. They discussed software's role in research, when it can be a tool that enables research or the actual research itself, and how this is different depending on the discipline and the functionality of the software within the discipline and the role of the person using the software. They made the point that "Software isn't a separate thing -- software could exist without the paper; the paper couldn't exist without the software."
Oh, there was much more goodness in this presentation, which was interrupted by lunch, than I have time to report, including The Horror, as it was termed -- the steps necessary for someone to replicate the computational work on one of the research projects this presentation covered -- and Robert's work on making this computational work software available in Docker. It also touched on the FAIR principles for computational research and academic software, and like the other presentations, generated lots of discussion, including conversations in the group on ethical considerations. PDF
The last formal presentation of the day, before the breakout workgroups, was by Claude Kirchner (INRIA) on the Software Heritage Project. He covered the rationale for this project, which includes the inconsiderate or malicious loss of code and the desire to preserve "our technical and scientific knowledge." The Software Heritage Project has set out to preserve all the software. Yes, you read that correctly: All the software. Fortunately, a version of the slides for this presentation are online so you can see them for yourself! The site is scheduled to go live next week and I look forward to seeing it.
After Claude's presentation, we went into breakout sessions.
I joined a breakout session on getting a standing award for scientific contributions through software created. The other breakout sessions were on creating a research software engineering handbook and academic software project typology. All groups reported back before the day's session ended for dinner. Quite an informative, exciting, and productive day! -
I'm at Schloss Dagstuhl – Leibniz Center for Informatics for a week-long workshop on Engineering Academic Software. Some of the questions we are tackling have been discussed elsewhere, which we are taking into consideration as we talk about them here, and new questions were not only part of the seminar's original description, but are arising throughout the general and break-out sessions. I would say we're at the end of the first day but it continues on though it is past 10 PM, with a planned open and vibrant discussion on dogmas past and present. First up for discussion tonight was Agile project management; how do you feel about it? Is this a dogma that needs to be shot or embraced?
The hashtag to follow on Twitter is #dagstuhleas for the full-group discussions; the breakout sessions so far have been too intense for tweeting!
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Twenty-eight codes were added to the ASCL in April and May 2016:
2-DUST: Dust radiative transfer code
ASTRiDE: Automated Streak Detection for Astronomical Images
BACCHUS: Brussels Automatic Stellar Parameter
CAMELOT: Cloud Archive for MEtadata, Library and Online Toolkit
CCSNMultivar: Core-Collapse Supernova Gravitational Wavescluster-lensing: Tools for calculating properties and weak lensing profiles of galaxy clusters
DISCO: 3-D moving-mesh magnetohydrodynamics package
DNest3: Diffusive Nested Sampling
DUO: Spectra of diatomic molecules
FDPS: Framework for Developing Particle Simulatorsgrtrans: Polarized general relativistic radiative transfer via ray tracing
Halotools: Galaxy-Halo connection models
K2SC: K2 Systematics Correction
LAMBDAR: Lambda Adaptive Multi-Band Deblending Algorithm in R
libpolycomp: Compression/decompression librarymagicaxis: Pretty scientific plotting with minor-tick and log minor-tick support
MARZ: Redshifting Program
MUSCLE: MUltiscale Spherical-ColLapse Evolution
OpenMHD: Godunov-type code for ideal/resistive magnetohydrodynamics (MHD)
PDT: Photometric DeTrending Algorithm Using Machine LearningSAND: Automated VLBI imaging and analyzing pipeline
Shadowfax: Moving mesh hydrodynamical integration code
Surprise Calculator: Estimating relative entropy and Surprise between samples
The Tractor: Probabilistic astronomical source detection and measurement
TMBIDL: Single dish radio astronomy data reduction packageTRIPPy: Python-based Trailed Source Photometry
TTVFaster: First order eccentricity transit timing variations (TTVs)
zeldovich-PLT: Zel'dovich approximation initial conditions generator -
I'll be heading to Schloss Dahstuhl in June for a Perspectives Workshop on Engineering Academic Software. Questions the workshop will seek to address include:
- How is academic software different from other software? What are its most pressing dimensions of quality?
- Is the software we use and produce in an academic context sustainable? How can we ensure that the software continues to evolve and offer value after serving its initial purpose?
- How can we adapt software engineering methods for the unique academic context without losing quality?
- How can we balance domain knowledge and expertise with software engineering knowledge and expertise in an academic research team?
- Do quality aspects of academic software apply to open data as well? How can well-engineered academic software together with open data make science more reproducible?
I look forward to tackling these and other questions with the other participants, and thank Carole Goble, James Howison, Claude Kirchner, and Oscar M. Nierstrasz for organizing the workshop.
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Eighteen codes were added to the ASCL in March, 2016:
Asfgrid: Asteroseismic parameters for a star
CORBITS: Efficient Geometric Probabilities of Multi-Transiting Exoplanetary Systems
Dedalus: Flexible framework for spectrally solving differential equations
DiskJockey: Protoplanetary disk modeling for dynamical mass derivation
ellc: Light curve model for eclipsing binary stars and transiting exoplanetsEQUIB: Atomic level populations and line emissivities calculator
ExoPriors: Accounting for observational bias of transiting exoplanets
FAST-PT: Convolution integrals in cosmological perturbation theory calculator
fibmeasure: Python/Cython module to find the center of back-illuminated optical fibers in metrology images
gPhoton: Time-tagged GALEX photon events analysis toolsHIIexplorer: Detect and extract integrated spectra of HII regions
PyGSM: Python interface to the Global Sky Model
PolRadTran: Polarized Radiative Transfer Model Distribution
ROBAST: ROOT-based ray-tracing library for cosmic-ray telescopes
SILSS: SPHERE/IRDIS Long-Slit Spectroscopy pipelineSMARTIES: Spheroids Modelled Accurately with a Robust T-matrix Implementation for Electromagnetic Scattering
tpipe: Searching radio interferometry data for fast, dispersed transients
VIP: Vortex Image Processing pipeline for high-contrast direct imaging of exoplanets -
Twenty-one codes were added to the ASCL in February, 2016:
Automark: Automatic marking of marked Poisson process in astronomical high-dimensional datasets
Celestial: Common astronomical conversion routines and functions
CHIP: Caltech High-res IRS Pipeline
CLOC: Cluster Luminosity Order-Statistic Code
COLAcode: COmoving Lagrangian Acceleration codeDELightcurveSimulation: Light curve simulation code
DUSTYWAVE: Linear waves in gas and dust
FilTER: Filament Trait-Evalutated Reconstruction
GANDALF: Graphical Astrophysics code for N-body Dynamics And Lagrangian Fluids
IRSFRINGE: Interactive tool for fringe removal from Spitzer IRS spectrak2photometry: Read, reduce and detrend K2 photometry
LensTools: Weak Lensing computing tools
LIRA: LInear Regression in Astronomy
LRGS: Linear Regression by Gibbs Sampling
mbb_emcee: Modified Blackbody MCMCNuCraft: Oscillation probabilities for atmospheric neutrinos calculator
POPPY: Physical Optics Propagation in PYthon
pyraf-dbsp: Reduction pipeline for the Palomar Double Beam Spectrograph
TailZ: Redshift distributions estimator of photometric samples of galaxies
The Cannon: Data-driven method for determining stellar parameters and abundances from stellar spectra -
ASCL Editor Alice Allen (that'd be me) was interviewed by Nature Toolbox on the last day of the January AAS meeting. The Q&A appears here.
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Twenty-one codes were added to the ASCL in January, 2016:
BASCS: Bayesian Separation of Close Sources
CosmicPy: Interactive cosmology computations
ctools: Cherenkov Telescope Science Analysis Software
Fit Kinematic PA: Fit the global kinematic position-angle of galaxies
Hyper-Fit: Fitting routines for multidimensional data with multivariate Gaussian uncertaintiesImpactModel: Black Hole Accretion Disk Impact Model
ISO: Isochrone construction
K2fov: Field of view software for NASA's K2 mission
LACEwING: LocAting Constituent mEmbers In Nearby Groups
LIRA: Low-counts Image Reconstruction and AnalysisMATPHOT: Stellar photometry and astrometry with discrete point spread functions
Nulike: Neutrino telescope likelihood tools
Odyssey: Ray tracing and radiative transfer in Kerr spacetime
PARAVT: Parallel Voronoi Tessellation code
ProC: Process CoordinatorQDPHOT: Quick & Dirty PHOTometry
SAGE: Semi-Analytic Galaxy Evolution
SavGolFilterCov: Savitzky Golay filter for data with error covariance
SCOUSE: Semi-automated multi-COmponent Universal Spectral-line fitting Engine
TRADES: TRAnsits and Dynamics of Exoplanetary SystemsWzBinned: Binned and uncorrelated estimates of dark energy EOS extractor
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The Astrophysics Source Code Library (ASCL, ascl.net) is a free online registry of codes used in astronomy research. With nearly 1,200 codes, it is the largest indexed resource for astronomy codes in existence. Established in 1999, it offers software authors a path to citation of their research codes even without publication of a paper describing the software, and offers scientists a way to find codes used in refereed publications, thus improving the transparency of the research. Citations using ASCL IDs are accepted by major astronomy journals and if formatted properly are tracked by ADS and other indexing services. The number of citations to ASCL entries increased sharply from 110 citations in January 2014 to 456 citations in September 2015. The percentage of code entries in ASCL that were cited at least once rose from 7.5% in January 2014 to 17.4% in September 2015. The ASCL’s mid-2014 infrastructure upgrade added an easy entry submission form, more flexible browsing, search capabilities, and an RSS feeder for updates. A Changes/Additions form added this past fall lets authors submit links for papers that use their codes for addition to the ASCL entry even if those papers don’t formally cite the codes, thus increasing the transparency of that research and capturing the value of their software to the community.
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The Astrophysics Source Code Library (ASCL) is an online registry of source codes used in refereed astrophysics research. It currently lists nearly 1,200 codes and covers all aspects of computational astrophysics. How can this resource be of use to educators and to the graduate students they mentor? The ASCL serves as a discovery tool for codes that can be used for one’s own research. Graduate students can also investigate existing codes to see how common astronomical problems are approached numerically in practice, and use these codes as benchmarks for their own solutions to these problems. Further, they can deepen their knowledge of software practices and techniques through examination of others’ codes.
