July and August 2013 additions to the ASCL

Twenty codes were added to the ASCL in July, and eighteen in August.

July:
AstroTaverna: Tool for Scientific Workflows in Astronomy
cosmoxi2d: Two-point galaxy correlation function calculation
CTI Correction Code
DustEM: Dust extinction and emission modelling
ETC++: Advanced Exposure-Time Calculations

FieldInf: Field Inflation exact integration routines
im2shape: Bayesian Galaxy Shape Estimation
ITERA: IDL Tool for Emission-line Ratio Analysis
K3Match: Point matching in 3D space
LENSVIEW: Resolved gravitational lens images modeling

MAH: Minimum Atmospheric Height
Monte Python: Monte Carlo code for CLASS in Python
NEST: Noble Element Simulation Technique
Obit: Radio Astronomy Data Handling
orbfit: Orbit fitting software

phoSim: Photon Simulator
PURIFY: Tools for radio-interferometric imaging
Shapelets: Image Modelling
SIMX: Event simulator
SOPT: Sparse OPTimisation

August:
APPSPACK: Asynchronous Parallel Pattern Search
BASIN: Beowulf Analysis Symbolic INterface
Ceph_code: Cepheid light-curves fitting
ChiantiPy: Python package for the CHIANTI atomic database
CReSyPS: Stellar population synthesis code

CRUSH: Comprehensive Reduction Utility for SHARC-2 (and more…)
GYRE: Stellar oscillation code
JHelioviewer: Visualization software for solar physics data
LensEnt2: Maximum-entropy weak lens reconstruction
LOSSCONE: Capture rates of stars by a supermassive black hole

MapCurvature: Map Projections
MoogStokes: Zeeman polarized radiative transfer
RADLite: Raytracer for infrared line spectra
SMILE: Orbital analysis and Schwarzschild modeling of triaxial stellar systems
SPEX: High-resolution cosmic X-ray spectra analysis

SYN++: Standalone SN spectrum synthesis
SYNAPPS: Forward-modeling of supernova spectroscopy data sets
THELI GUI: Optical, near- & mid-infrared imaging data reduction

Also in August, we added one very cool web resource, the NASA Exoplanet Archive.

How long should you keep your codes? And your data?

I’m currently working on a report for the Preserving.exe: Toward a National Strategy for Preserving Software summit held at the Library of Congress in May. My head is filled with the reasons and ways (and lack of ways) to save software discussed at the meeting, and by software, I don’t mean necessarily astrophysics codes, oh no! All kinds of software: mainframe HR software and VisiCalc and Doom and old browsers and dBASE and … well, everything.

This has dovetailed nicely, or perhaps alarmingly, with recent readings, including a blog post by Kristin Briney titled How Long Should You Keep Data? and the Retraction Watch post which inspired it, JCI paper retracted for duplicated panels after authors can’t provide original data, about a 2007 paper which recently had one figure retracted because the authors could not provide the data from which it was generated.

Jon Ippolito of the University of Maine was at the summit and wrote about it in his blog post The Ex-files: how long will our software last?

How long indeed? And if you wanted to retrieve data from 2007, would you be able to even if you had the data files? Would you still have the tools available to get into them? In astronomy, probably so; with FITS, astronomy is better off than many sciences. Elsewhere, maybe not.

How long will astronomy software last? That might be unknowable; perhaps a better question, then, is how long should it last?

Facilities and Codes in papers?

Today I was reading the draft of an upcoming thesis defense in our library, and noted the student in question had been using a nice number of codes to support her research. All properly referenced via footnotes, and even some routine names in a “typewriter” font to make them stand out.

Later that afternoon after the weekly graduate un-journal club talk she gave, we and another graduate student got to talking about the ASCL, and explaining to them the triad of paper/data/code that one can view as the three ways our research is now peer review published. In fact, if you look at some recent publications, just after the Acknowledgements, you can find a “Facilities:” line, in which the various facilities (read: observatory/instrument pairs) are listed from which the data in this particular paper were used. We in ASCL have been suggesting that one should add a “Codes:” line as well, with (ASCL) codes used in the paper. Now that ASCL entries are searchable via ADS, there is no reason not to make searching for codes in papers easier. In fact, if you look at the next ADASS conference proceedings, you will find a separate ASCL index in the back of the book!

What do people think, should we ask the editors of journals to make this “Codes:” line a standard feature of papers?

June 2013 additions to the ASCL

Sixteen codes were added to the ASCL in June:

BEHR: Bayesian Estimation of Hardness Ratios
Bessel: Fast Bessel Function Jn(z) Routine for Large n,z
grmonty: Relativistic radiative transport Monte Carlo code
Harmony: Synchrotron Emission Coefficients
LRG DR7 Likelihood Software

MADCOW: Microwave Anisotropy Dataset Computational softWare
MAPPINGS III: Modelling And Prediction in PhotoIonized Nebulae and Gasdynamical Shocks
Pico: Parameters for the Impatient Cosmologist
PROM4: 1D isothermal and isobaric modeler for solar prominences
PROS: Multi-mission X-ray analysis software system

SAC: Sheffield Advanced Code
STF: Structure Finder
Tapir: A web interface for transit/eclipse observability
VHD: Viscous pseudo-Newtonian accretion
Yaxx: Yet another X-ray extractor

ZEUS-2D: Simulation of fluid dynamical flows

Preserving.exe: Toward a National Strategy for Preserving Software

Photo credit: Peter Teuben

On May 20 and 21, the Library of Congress’s Digital Preservation program held Preserving.exe: Toward a National Strategy for Preserving Software, which focused on preserving software as digital artifacts of life in the late 20th-early 21st century. Robert Hanisch, Peter Teuben, and Alice Allen attended, and Peter, chair of our Advisory Committee, presented a talk on the ASCL. The slides from Peter’s talk are now available online.

May 2013 additions to the ASCL

Fifteen codes were added to the ASCL in May:

AdaptaHOP: Subclump finder
ESTER: Evolution STEllaire en Rotation
FITDisk: Cataclysmic Variable Accretion Disk Demonstration Tool
GaussFit: Solving least squares and robust estimation problems
GILDAS: Grenoble Image and Line Data Analysis Software

MapCUMBA: Multi-grid map-making algorithm for CMB experiments
Merger Trees: Formation history of dark matter haloes
Non-Gaussian Realisations
PINOCCHIO: PINpointing Orbit-Crossing Collapsed HIerarchical Objects
PkdGRAV2: Parallel fast-multipole cosmological code

Pressure-Entropy SPH: Pressure-entropy smooth-particle hydrodynamics
pynbody: N-Body/SPH analysis for python
TAU: 1D radiative transfer code for transmission spectroscopy of extrasolar planet atmospheres
TPM: Tree-Particle-Mesh code
YNOGK: Calculating null geodesics in the Kerr spacetime

We also added ExoVis to our web resources and tools page.

Interesting web resource, interesting paper

ExoVis, the winner of the 2013 Open Exoplanet Catalogue visualization contest, is an exosystem visualizer programmed by Tom Hands, a PdD student at the University of Leicester. It’s quite elegant. ExoVis has been added to our list of Web Resources and Tools.

Streams Going Notts: The tidal debris finder comparison project popped up on arXiv recently. This paper, which has been added to our thread for papers of possible interest, discusses testing four codes, S-Tracker, VELOCIraptor (formerly known as the STructure Finder, STF), ROCKSTAR, and HOT6D, to determine how well they find tidal debris in a fully cosmological Milky Way type simulation. The paper compares the algorithms used by the codes and quantifies the findings.

April 2013 additions to the ASCL

Twenty-one codes were added to the ASCL in April:

Astropy: Community Python library for astronomy
Copter: Cosmological perturbation theory
CosmicEmuLog: Cosmological Power Spectra Emulator
CosmoRec: Cosmological Recombination code
DESPOTIC: Derive the Energetics and SPectra of Optically Thick Interstellar Clouds

Diffusion.f: Diffusion of elements in stars
GALSVM: Automated Morphology Classification
IFrIT: Ionization FRont Interactive Tool
MPgrafic: A parallel MPI version of Grafic-1
ORIGAMI: Structure-finding routine in N-body simulation

PEC: Period Error Calculator
pyCloudy: Tools to manage astronomical Cloudy photoionization code
PyNeb: Analysis of emission lines
Qhull: Quickhull algorithm for computing the convex hull
Sérsic: Exact deprojection of Sérsic surface brightness profiles

SFH: Star Formation History
SZpack: Computation of Sunyaev-Zeldovich (SZ) signals
TPZ: Trees for Photo-Z
TVD: Total Variation Diminishing code
VOBOZ/ZOBOV: Halo-finding and Void-finding algorithms

Wqed: Lightcurve Analysis Suite