Author Archives: Alice Allen

Birds of a Feather session at ADASS on software citation and credit

The Implementing Ideas for Improving Software Citation and Credit BoF is intended to be a working session to put ideas already generated into action! Everyone in the community has a role in improving it. We have listed a lot of ideas in the previous post about this BoF, have slides online here, and a Google doc to which you can contribute here.

Montage poster at ADASS 2016

We want to share some of the posters that are appearing at ADASS this week (with permission of their authors). Montage is in the ASCL; we love this poster for several reasons, but especially because it makes clear that sustainability of the software is important!
Image of paper on the software Montagle

Abstract: The Montage toolkit is finding exceptional breadth of usage, far beyond its intended application as a mosaic engine for astronomy. New uses include:
– Visualization of complex images with data overlays: e.g. as a re-projection engine integrated into the server-side architecture of a Gbit visualization system supporting investigations of 3D printing with the X3D protocol creation of sky coverage maps for missions and projects bulk creation of sub-images of multiband photometry data creation of plots in the APLPy library.
– Creation of new data products at scale: mosaics of Gemini AO images from the Gemini Multi-Conjugate Adaptive Optics System/Gemini South Adaptive Optics Imager (GEMS/GSAOI) instrument, from the VISTA VIDEO and the UKIDSS DXS surveys welding the Herschel infrared Galactic plane (Hi-GAL) far-infrared Survey into a set of large-scale mosaics, for planetarium shows at a digital as well as for research
– As a re-projection engine to support discovery of 86 Near Earth Asteroids (a U.S. congressional mandate) in the Lincoln Near-Earth Asteroid Research Program (LINEAR).
– Integration into data processing environments: integration of the 4D image cutout tool into the VO-compliant CSIRO ASKAP Science Data Archive (CASDA) as a re-projection engine for the Dark Energy Survey (DES) pipeline.
– Discovery of imaging data at scale: use of memory mapped R-tree indices to support searches for spatially extended data, in use in Spitzer and WISE image searches and in spatial and temporal searches for WISE and KOA.
It has been cited as an exemplar application for development of next generation cyber-infrastructure in 238 papers between 2014 and 2016 to date. What has enabled this broad take-up is that Montage has been built and managed as a scalable toolkit, written in C and portable across all common *nix platforms, with minimal dependencies on third-party software, such that it can be built with a simple “make” command. All the components have proven powerful general-purpose tools in their own right, even those first developed to support mosaic creation, such as discovery of images for input to the engine and for management of mosaics. We describe how Montage is managed to assure that the benefits of the architecture are retained, and how we ensure that new development is driven by the needs of the community.

ASCL poster at ADASS XXVI

ASCL poster for ADASS XXVIThe Astrophysics Source Code Library (ASCL) is a free online registry of codes used in research; it is indexed by ADS and Web of Science and has over 1300 code entries. Its entries are increasingly used to cite software; citations have been at least doubling each year since 2012, and every major astronomy journal accepts citations to the ASCL. Codes in the resource cover all aspects of astrophysics research and many programming languages are represented. In the past year, the ASCL has added dashboards for users and administrators, started minting DOIs for codes it houses, and added metadata fields requested by users. This presentation covers the ASCL’s growth in the past year and the opportunities afforded to it as one of the few domain libraries for science research codes, and will solicit ideas for new features.

Alice Allen, Astrophysics Source Code Library
G. Bruce Berriman, Infrared Processing and Analysis Center, California Institute of Technology
Kimberly DuPrie, Space Telescope Science Institute/ASCL
Jessica Mink, Harvard-Smithsonian Center for Astrophysics
Robert Nemiroff, Michigan Technological University
Thomas Robitaille, Freelance
Judy Schmidt, Astrophysics Source Code Library
Lior Shamir, Lawrence Technological University
Keith Shortridge, Australian Astronomical Observatory
Mark Taylor, University of Bristol
Peter Teuben, Astronomy Department, University of Maryland
John Wallin, Middle Tennessee State University

Download poster

ADASS!

The Astronomical Data Analysis Software and Systems (ADASS) conference starts today in Trieste, Italy with two tutorials, Everything you’ve heard about Agile development is wrong by Simon O’Toole and Multi-dimensional linked data exploration with glue by Thomas Robitaille, and then the opening reception.

The ASCL has two activities at ADASS this year. I’m presenting a poster on the ASCL’s growth over the past year; the poster will be featured in a separate blog post tomorrow. On Tuesday, Peter Teuben, chair of the ASCL Advisory Committee, and other ASCLers here are running a Birds of a Feather session on Implementing Ideas for Improving Software Citation and Credit; this is a follow-up of last year’s session on Improving Software Citation and Credit. This year, we will look at some of the ideas that came out of last year’s session along with ideas generated at the Engineering Academic Software seminar held in June, 2016 and WSSSPE4, held last month at the University of Manchester, and work to implement them. These ideas include:

  • collecting and publishing stories from people who have released their software to share their experience with doing so
  • updating software sites you own to explicit state how your software should be cited
  • emailing code authors who don’t have clear citation instructions on their repos/code sites to suggest they make clear how their codes should be cited
  • adding preferred citation methods to ASCL entries via the “Suggest a change or addition” link or sending them to associate editor Kimberly duPrie or me to add directly
  • looking at your organization’s annual research activity report and suggesting ways it can specifically request software activities
  • writing a document that provides guidance about the types of software contributions that add value to science
  • developing guidelines for recognizing software contributions in hiring and promotion
  • gathering representative research software engineering job descriptions and adding them to the AstroBetter wiki, and suggesting other ways they can be shared for use them as examples

We look forward to an interesting and productive BoF, and an interesting and productive ADASS overall. And gelato, too!

First look at software activities at AAS 229

Though we have a way to go before January’s AAS meeting (and ADASS and OpenCon on the ASCL’s schedule coming up sooner), a look at the schedule for the AAS meeting already shows multiple options for the computationally-inclined astronomer. I’m very excited about the Special Session we’ve organized with the Moore-Sloan DSE, called Perspectives in Research Software. Bruce Berriman (IPAC, Caltech/Astronomy Computing Today) will moderate the session. In keeping with previous sessions, the session will include a discussion period with the floor open for questions and comments; we want to hear what you have to say. We have a panel of seven speakers; the presenters and topics are:

Tracy Teal (Data Carpentry), Software not as a service
Michael Hucka (Caltech), Finding the right wheel when you don’t want to reinvent it
Lior Shamir (LTU), Reproducibility and reusability of scientific software
Ivelina Momcheva (STScI), Funding research software development
Heather Piwowar (ImpactStory), Capturing the impact of software
David W. Hogg (NYU), The relationships between software publications and software systems
And me, Update on research software citation efforts

I hope to see you there!

Other software events that have shown up so far on the AAS schedule are listed below. Good times coming!

Tuesday, 3 January 2017
Workshop: Introduction to Software Carpentry, 8:00 am ‐ 5:30 pm
Workshop: Using Python for Astronomical Data Analysis, 8:00 am ‐ 4:30 pm

Wednesday, 4 January 2017
Splinter Meeting: Flexible Multi‐dimensional Modeling of Complex Data in Astronomy, 9:30 am ‐ 11:30 am

Friday, 6 January 2017
Special Session: Perspectives in Research Software: Education, Funding, Reproducibility, Citation, and Impact, 10:00 am – 11:30 am

Saturday, 7 January 2017
Special Session: Statistical, Mathematical and Computational Methods for Astronomy (ASTRO): SAMSI 2016-17, 10:00 am – 11:30 am
Workshop: Hack Together Day, 10:00 am ‐ 7:00 pm

Also of likely interest is the Special Session on The Value of Astronomical Data and Long Term Preservation that will take place on Thursday, 4 January from 10:00 am – 11:30 am.

 

September 2016 additions to the ASCL

Twenty-five codes were added to the ASCL in September 2016:

21cmSense: Calculating the sensitivity of 21cm experiments to the EoR power spectrum
AdaptiveBin: Adaptive Binning
AIPY: Astronomical Interferometry in PYthon
Askaryan Module: Askaryan electric fields predictor
contbin: Contour binning and accumulative smoothing

CuBANz: Photometric redshift estimator
FISHPACK: Efficient FORTRAN Subprograms for the Solution of Separable Elliptic Partial Differential Equations
FISHPACK90: Efficient FORTRAN Subprograms for the Solution of Separable Elliptic Partial Differential Equations
FIT3D: Fitting optical spectra
GRASP: General-purpose Relativistic Atomic Structure Package

Kranc: Cactus modules from Mathematica equations
NSCool: Neutron star cooling code
Photutils: Photometry tools
PKDGRAV3: Parallel gravity code
PYESSENCE: Generalized Coupled Quintessence Linear Perturbation Python Code

PyPHER: Python-based PSF Homogenization kERnels
SCIMES: Spectral Clustering for Interstellar Molecular Emission Segmentation
SIP: Systematics-Insensitive Periodograms
Sky3D: Time-dependent Hartree-Fock equation solver
spectral-cube: Read and analyze astrophysical spectral data cubes

StarPy: Quenched star formation history parameters of a galaxy using MCMC
SuperBoL: Module for calculating the bolometric luminosities of supernovae
T-PHOT: PSF-matched, prior-based, multiwavelength extragalactic deconfusion photometry
TIDEV: Tidal Evolution package
Weighted EMPCA: Weighted Expectation Maximization Principal Component Analysis

August 2016 additions to the ASCL

Twenty codes were added to the ASCL in August 2016:

21CMMC: Parallelized Monte Carlo Markov Chain analysis tool for the epoch of reionization (EoR)
2DFFT: Measuring Galactic Spiral Arm Pitch Angle
appaloosa: Python-based flare finding code for Kepler light curves
AstroVis: Visualizing astronomical data cubes
BART: Bayesian Atmospheric Radiative Transfer fitting code

BASE-9: Bayesian Analysis for Stellar Evolution with nine variables
Cuba: Multidimensional numerical integration library
DOLPHOT: Stellar photometry
FilFinder: Filamentary structure in molecular clouds
Gemini IRAF: Data reduction software for the Gemini telescopes

gevolution: General Relativity Cosmological N-body code for evolution of large scale structures
LORENE: Spectral methods differential equations solver
NEBULAR: Spectrum synthesis for mixed hydrogen-helium gas in ionization equilibrium
NICIL: Non-Ideal magnetohydrodynamics Coefficients and Ionisation Library
OBERON: OBliquity and Energy balance Run on N-body systems

PROFFIT: Analysis of X-ray surface-brightness profiles
pvextractor: Position-Velocity Diagram Extractor
pyXSIM: Synthetic X-ray observations generator
SPIDERz: SuPport vector classification for IDEntifying Redshifts
Stingray: Spectral-timing software

Upcoming events and sessions, Fall-Winter 2016/7

I’ll be representing the ASCL at next month’s WSSSPE4 meeting in Manchester, and in October, the ASCL will be at ADASS XXVI and will hold an Advisory Committee (AC) meeting while there. Peter Teuben, chair of the ASCL AC, will moderate a Birds of a Feather session at ADASS on Implementing Ideas for Improving Software Citation and Credit; this is a follow-up on the discussion at last year’s BoF Improving Software Citation and Creditwith a goal of taking action on some of the ideas generated at last year’s BoF. Watch this space in October for more!

For January’s American Astronomy Society meeting in Texas, the Moore-Sloan Data Science Environment at NYU and the ASCL have organized another Special Session, Perspectives in Research Software. This will follow the format of previous sessions, with presentations in the first half of the session and discussion open to all for the second half. Bruce Berriman from the Infrared Processing and Analysis Center at Caltech will moderate; the presenters include Ivelina Momcheva (Space Telescope Science Institute),  Tracy Teal (Data Carpentry), Lior Shamir (Lawrence Technological University), and Michael Hucka (Caltech). I’m rationally exuberant about this session!

July 2016 additions to the ASCL

Twenty codes were added to the ASCL in July 2016:

AGNfitter: SED-fitting code for AGN and galaxies from a MCMC approach
astLib: Tools for research astronomers
Atlas2bgeneral: Two-body resonance calculator
Atlas3bgeneral: Three-body resonance calculator
BLS: Box-fitting Least Squares

BoxRemap: Volume and local structure preserving mapping of periodic boxes
Cholla: 3D GPU-based hydrodynamics code for astrophysical simulation
DICE: Disk Initial Conditions Environment
HfS: Hyperfine Structure fitting tool
HIDE: HI Data Emulator

JUDE: An Utraviolet Imaging Telescope pipeline
K2PS: K2 Planet search
Kālī: Time series data modeler
LZIFU: IDL emission line fitting pipeline for integral field spectroscopy data
PICsar: Particle in cell pulsar magnetosphere simulator

Planetary3br: Three massive body resonance calculator
RT1D: 1D code for Rayleigh-Taylor instability
SEEK: Signal Extraction and Emission Kartographer
SOPIE: Sequential Off-Pulse Interval Estimation
ZASPE: Zonal Atmospheric Stellar Parameters Estimator

Engineering Academic Software, Schloss Dagstuhl Day 0 and 1

Now that I’ve written extensively about days 2-4, I am cycling back to give day 1 its due, but first will say the sharing started on Sunday June 19 as people arrived for both the week-long Engineering Academic Software Perspectives Workshop and the three-day Information-centric Networking and Security Seminar; cake and coffee is available upon arrival, which gives folks an opportunity to meet, and conversation between participants in both workshops flowed easily. A Workshop participants on the site of the old schlossgroup of us decided to walk to the old castle ruins on the hill — up many steps — and it was on this little jaunt that I learned firsthand about stinging nettles (having only read about them before) with Andrei Chiș providing most of the hands-on instruction. He and I experimented with different nettles to see which produced the greatest stinging/welts; oh, the things we do for science! Those who had been unwilling victims of the plants provided more data points, and our quick survey leads us to suspect that the more mature the plant, the greater its “don’t touch!” defenses.

On Monday morning, we started with lightning introductions. We had been asked to create two slides, one on our relevant background and another on our interests for future use; a list of workshop participants and intro slides are available online. Tweet: "“I’m a programmer that somebody made into a professor.” @jurgenvinjuNext came presentations; first up was Dan Katz to talk about WSSSPE (Working towards Sustainable Software for Science: Practice and Experience), pronounced “wispy.” He shared the history of the organization, noting that three large annual meetings had been held, with several smaller interim meetings also having taken place. WSSSPE’s progression was to first identify challenges regarding software and best practices for sustainability, then to discuss solutions and ways to enable change, and then at WSSSPE3, to take action and encourage people to work in groups to put into practice the identified solutions. Katz’s presentation included an overview of each of the WSSSPE working groups and the progress each group has made. Some of the working groups overlapped with efforts taking place elsewhere; the Software Credit Working Group, for example, shared much in common with Force11’s Software Citation Working Group, so the decision was made to work on combining the two groups (which was successful) and for members to work on the Software Citation Principles that were being developed (which was also successful).

Katz also shared lessons learned from WSSSPE3 — what had worked, what could have worked better, and what didn’t work. He outlined what is planned for WSSSPE4 (taking place this September in Manchester), listing two tracks for the event: Building a sustainable future for open-use research software, which will concentrate on defining the future of open-use scientific software and initiating plans to arrive at this future; and Practices and experiences in sustainable software, which will concentrate on improving current practices. Katz concluded his talk by sharing links to the reports for WSSSPE1, WSSSPE2, and WSSSPE3 and the social media sites. PDF

The next presentation, Supporting Research Software Engineering, was by Mike Croucher. His talk focused on his work as an Engineering and Physical Sciences Research Council (EPSRC) Research Software Engineering Fellow; he is one of only seven to be awarded this new fellowship. He helps scientists improve their software in various ways, such as making it faster, more reliable/robust/user friendly, and more sustainable. (Now that I’ve typed that, Harder, Better, Faster, Stronger is playing on the radio in my head.) This has to be done carefully, for as Croucher put it: Tweet: "Users are afraid I’m going to “do computer science” to them. @walkingrandomly treads carefully when repairing user code."The phrase “do computer science to them” was echoed throughout the rest of the workshop; this idea — acknowledgement of that fear — seemed to resonate with many.

Croucher shared some of the outreach and education activities he’s been involved with, one of which was a (gentle) self-paced R tutorial held in a café. Volunteer facilitators walked around to answer questions, clarify information, and unstick people who got stuck and the session was a rousing success, so much so that there are now requests and expectations that more will be held!

It was acknowledged at the beginning of the day that academic software faces many challenges; Croucher’s presentation covered some of them, and included this stark slide:

Software is not valued in academizfollowed by:

Tweet: One of the major reasons I dropped out of my PhD was because I didn't believe academia could properly value software contributionsHe also mentioned the lack of funding for software activities, that soft-money researchers are discriminated against in favor of tenure-track and tenured faculty, and other issues. Oooo, he got a great discussion going with these and other points! In the active discussion, Cecilia Aragon made the point that we need to stop calling software “infrastructure,” as software has intellectual content.
Tweet: "Comment from @craragon : stop calling software 'infrastructure' because plumbers aren't invited to coauthor science papers"Though there are challenges, it’s not all bad — things are improving. The Software Sustainability Institute is funded by several organizations, the UK’s Engineering and Physical Sciences Research Council (EPSRC) has recognized the importance of software through funding of the Research Software Engineers, and a Horizon 2020 project to provide “substantial funding” for open source maths research software. Croucher’s vision of the future includes core-funded research software engineers and a hope for tenure awarded on the basis of software contributions. He closed his excellent presentation with concrete steps for changing the perception of software engineering and leading a change in culture. Slides

After a coffee break, the last presentation of the morning was given by Christoph Becker on Sustainability design.  He covered the challenges of sustainability, and referred to the “sustainability debt” Sustainability debt model across realms and widening effectsthat is mostly unknown for most systems. The effects of sustainability (or lack thereof) can be considered from several angles; one way to look at this debt is across economic, technical social, environmental, and individual aspects, and whether it has an immediate, enabling, or structural effect. The concerns about sustainability have inspired the Karlskrona Manifesto for Sustainability Design, which seeks to address sustainability across different aspects and widening effects. The Manifesto identifies eleven “misperceptions and counterpoints”, seeks to correct or mitigate them, and educate and advocate for a constructive approach to enabling a paradigm shift. Tweet: "Software projects are full of present-future trade offs, yet SE hasn't learned from behavioral economics @ChriBecker at #dagstuhleas"Becker is particularly interested in studying how people decide on the trade-offs they make when designing software, and using the insight gleaned to develop and implement methods and tools for making better choices. PDF

After Becker’s talk, we broke for lunch, then went into four breakout sessions for a good part of the afternoon; the four selected by participants from the many that had been proposed were:

  • Academic software project typology
  • Examining sustainability for a particular project
  • Making the intellectual content of software visible
  • Empirical survey of software practices in a domain

After working in our breakout sessions, we came back together to report on our progress. Wow, was there a lot of discussion! Everyone was very engaged in listening to, commenting on, and discussing the reports from the different groups. It was a very exciting afternoon, and discussion continued right up until we were forced to break for dinner.

As previously reported, we had a discussion in the evening as well. Monday was an excellent start to an outstanding week!