Papers of Possible Interest to Astronomical Software Users

[owlice]

Contents of this thread
Oldest --> newest addition in each section

General articles, not about specific codes
Making Access to Astronomical Software More Efficient
Astronomical Software Wants To Be Free: A Manifesto
Publish your computer code: it is good enough
Talking Amongst Ourselves - Communication in the Astronomical Software Community
Computational science: ...Error …why scientific programming does not compute

A Journal for the Astronomical Computing Community?
Where's the Real Bottleneck in Scientific Computing?
The CRAPL: An academic-strength open source license
Scientific Software Production: Incentives and Collaboration
Linking to Data - Effect on Citation Rates in Astronomy

The case for open computer programs
Astroinformatics: A 21st Century Approach to Astronomy
Publish or be damned? An alternative impact manifesto for research software
Best Practices for Scientific Computing


Articles about specific codes and resources
How well do STARLAB and NBODY4 compare? I: Simple models
Monte Carlo simulation of the electron transport through thin slabs: A comparative study of PENELOPE, GEANT3, GEANT4, EGSnrc and MCNPX
Computational AstroStatistics: Fast and Efficient Tools for Analysing Huge Astronomical Data Sources
Astrocomp: a web service for the use of high performance computers in Astrophysics
Group Identification in N-Body Simulations: SKID and DENMAX Versus Friends-of-Friends

Comparing Numerical Methods for Isothermal Magnetized Supersonic Turbulence
Haloes gone MAD: The Halo-Finder Comparison Project
GEMS: Galaxy fitting catalogues and testing parametric galaxy fitting codes
A Comparison of Cosmological Codes (TVD, ENZO, and GADGET)
Running your first SPH simulation

A Guide to Comparisons of Star Formation Simulations with Observations
Galaxies going MAD: The Galaxy-Finder Comparison Project
Streams Going Notts: The tidal debris finder comparison project

[owlice]

Making Access to Astronomical Software More Efficient

http://arxiv.org/abs/1004.4430

Abstract: Access to astronomical data through archives and VO is essential but does not solve all problems. Availability of appropriate software for analyzing the data is often equally important for the efficiency with which a researcher can publish results. A number of legacy systems (e.g. IRAF, MIDAS, Starlink, AIPS, Gipsy), as well as others now coming online are available but have very different user interfaces and may no longer be fully supported. Users may need multiple systems or stand-alone packages to complete the full analysis which introduces significant overhead. The OPTICON Network on `Future Astronomical Software Environments' and the USVAO have discussed these issues and have outlined a general architectural concept that solves many of the current problems in accessing software packages. It foresees a layered structure with clear separation of astronomical code and IT infrastructure. By relying on modern IT concepts for messaging and distributed execution, it provides full scalability from desktops to clusters of computers. A generic parameter passing mechanism and common interfaces will offer easy access to a wide range of astronomical software, including legacy packages, through a single scripting language such as Python. A prototype based upon a proposed standard architecture is being developed as a proof-of-concept. It will be followed by definition of standard interfaces as well as a reference implementation which can be evaluated by the user community. For the long-term success of such an environment, stable interface specifications and adoption by major astronomical institutions as well as a reasonable level of support for the infrastructure are mandatory. Development and maintenance of astronomical packages would follow an open-source, Internet concept.

Authors: P. Grosbol, D. Tody

[owlice]

Astronomical Software Wants To Be Free: A Manifesto

http://arxiv.org/abs/0903.3971

Abstract: Astronomical software is now a fact of daily life for all hands-on members of our community. Purpose-built software for data reduction and modeling tasks becomes ever more critical as we handle larger amounts of data and simulations. However, the writing of astronomical software is unglamorous, the rewards are not always clear, and there are structural disincentives to releasing software publicly and to embedding it in the scientific literature, which can lead to significant duplication of effort and an incomplete scientific record. We identify some of these structural disincentives and suggest a variety of approaches to address them, with the goals of raising the quality of astronomical software, improving the lot of scientist-authors, and providing benefits to the entire community, analogous to the benefits provided by open access to large survey and simulation datasets. Our aim is to open a conversation on how to move forward. We advocate that: (1) the astronomical community consider software as an integral and fundable part of facility construction and science programs; (2) that software release be considered as integral to the open and reproducible scientific process as are publication and data release; (3) that we adopt technologies and repositories for releasing and collaboration on software that have worked for open-source software; (4) that we seek structural incentives to make the release of software and related publications easier for scientist-authors; (5) that we consider new ways of funding the development of grass-roots software; (6) and that we rethink our values to acknowledge that astronomical software development is not just a technical endeavor, but a fundamental part of our scientific practice.

Credit: Benjamin J. Weiner, Michael R. Blanton, Alison L. Coil, Michael C. Cooper, Romeel Davé, David W. Hogg, Bradford P. Holden, Patrik Jonsson, Susan A. Kassin, Jennifer M. Lotz, John Moustakas, Jeffrey A. Newman, J.X. Prochaska, Peter J. Teuben, Christy A. Tremonti, Christopher N.A. Willmer

[RJN]

Publish your computer code: it is good enough

by Nick Barnes

http://www.nature.com/news/2010/101013/ ... 7753a.html

... openness improved both the code used by the scientists and the ability of the public to engage with their work. This is to be expected. Other scientific methods improve through peer review. The open-source movement has led to rapid improvements within the software industry. But science source code, not exposed to scrutiny, cannot benefit in this way.

[owlice]

How well do STARLAB and NBODY4 compare? I: Simple models

http://arxiv.org/abs/0902.4636

Abstract: N-body simulations are widely used to simulate the dynamical evolution of a variety of systems, among them star clusters. Much of our understanding of their evolution rests on the results of such direct N-body simulations. They provide insight in the structural evolution of star clusters, as well as into the occurrence of stellar exotica. Although the major pure N-body codes STARLAB/KIRA and NBODY4 are widely used for a range of applications, there is no thorough comparison study yet. Here we thoroughly compare basic quantities as derived from simulations performed either with STARLAB/KIRA or NBODY4.

We construct a large number of star cluster models for various stellar mass function settings (but without stellar/binary evolution, primordial binaries, external tidal fields etc), evolve them in parallel with STARLAB/KIRA and NBODY4, analyse them in a consistent way and compare the averaged results quantitatively. For this quantitative comparison we develop a bootstrap algorithm for functional dependencies.

We find an overall excellent agreement between the codes, both for the clusters' structural and energy parameters as well as for the properties of the dynamically created binaries. However, we identify small differences, like in the energy conservation before core collapse and the energies of escaping stars, which deserve further studies. Our results reassure the comparability and the possibility to combine results from these two major N-body codes, at least for the purely dynamical models (i.e. without stellar/binary evolution) we performed. (abridged)

Credit: P. Anders, H. Baumgardt, N. Bissantz, S. Portegies Zwart

[owlice]

Monte Carlo simulation of the electron transport through thin slabs: A comparative study of PENELOPE, GEANT3, GEANT4, EGSnrc and MCNPX

http://arxiv.org/abs/physics/0612044

Abstract: The Monte Carlo simulation of the electron transport through thin slabs is studied with five general purpose codes: PENELOPE, GEANT3, GEANT4, EGSnrc and MCNPX. The different material foils analyzed in the old experiments of Kulchitsky and Latyshev [Phys. Rev. 61 (1942) 254-266] and Hanson et al. [Phys. Rev. 84 (1951) 634-637] are used to perform the comparison between the Monte Carlo codes. Non-negligible differences are observed in the angular distributions of the transmitted electrons obtained with the some of the codes. The experimental data are reasonably well described by EGSnrc, PENELOPE (v. 2005) and GEANT4. A general good agreement is found for EGSnrc and GEANT4 in all the cases analyzed.

Credit: M. Vilches, S. Garcia-Pareja, R. Guerrero, M. Anguiano, A.M. Lallena

[owlice]

Computational AstroStatistics: Fast and Efficient Tools for Analysing Huge Astronomical Data Sources

http://arxiv.org/abs/astro-ph/0110230

Abstract: I present here a review of past and present multi-disciplinary research of the Pittsburgh Computational AstroStatistics (PiCA) group. This group is dedicated to developing fast and efficient statistical algorithms for analysing huge astronomical data sources. I begin with a short review of multi-resolutional kd-trees which are the building blocks for many of our algorithms. For example, quick range queries and fast n-point correlation functions. I will present new results from the use of Mixture Models (Connolly et al. 2000) in density estimation of multi-color data from the Sloan Digital Sky Survey (SDSS). Specifically, the selection of quasars and the automated identification of X-ray sources. I will also present a brief overview of the False Discovery Rate (FDR) procedure (Miller et al. 2001a) and show how it has been used in the detection of ``Baryon Wiggles'' in the local galaxy power spectrum and source identification in radio data. Finally, I will look forward to new research on an automated Bayes Network anomaly detector and the possible use of the Locally Linear Embedding algorithm (LLE; Roweis & Saul 2000) for spectral classification of SDSS spectra.

Credit: R. C. Nichol, S. Chong, A. J. Connolly, S. Davies, C. Genovese, A. M. Hopkins, C. J. Miller, A. W. Moore, D. Pelleg, G. T. Richards, J. Schneider, I. Szapudi, L. Wasserman

[owlice]

Talking Amongst Ourselves - Communication
in the Astronomical Software Community

http://arxiv.org/abs/0902.0255

Abstract: Meetings such as ADASS demonstrate that there is an enthusiasm for communication within the astronomical software community. However, the amount of information and experience that can flow around in the course of one, relatively short, meeting is really quite limited. Ideally, these meetings should be just a part of a much greater, continuous exchange of knowledge. In practice, with some notable - but often short-lived - exceptions, we generally fall short of that ideal. Keeping track of what is being used, where, and how successfully, can be a challenge. A variety of new technologies such as those roughly classed as 'Web 2.0' are now available, and getting information to flow ought to be getting simpler, but somehow it seems harder to find the time to keep that information current. This paper looks at some of the ways we communicate, used to communicate, have failed to communicate, no longer communicate, and perhaps could communicate better. It is presented in the hope of stimulating additional discussion - and possibly even a little action - aimed at improving the current situation.

Credit: Keith Shortridge

[owlice]

Astrocomp: a web service for the use of high performance computers in Astrophysics

http://arxiv.org/abs/astro-ph/0407550

Abstract: Astrocomp is a joint project, developed by the INAF-Astrophysical Observatory of Catania, University of Roma La Sapienza and Enea. The project has the goal of providing the scientific community of a web-based user-friendly interface which allows running parallel codes on a set of high-performance computing (HPC) resources, without any need for specific knowledge about parallel programming and Operating Systems commands. Astrocomp provides, also, computing time on a set of parallel computing systems, available to the authorized user. At present, the portal makes a few codes available, among which: FLY, a cosmological code for studying three-dimensional collisionless self-gravitating systems with periodic boundary conditions; ATD, a parallel tree-code for the simulation of the dynamics of boundary-free collisional and collisionless self-gravitating systems and MARA, a code for stellar light curves analysis. Other codes are going to be added to the portal.

Credit: U. Becciani, R. Capuzzo Dolcetta, A. Costa, P. Di Matteo, P. Miocchi, V. Rosato

[owlice]

Group Identification in N-Body Simulations: SKID and DENMAX Versus Friends-of-Friends

http://arxiv.org/abs/astro-ph/9811393

Abstract: Three popular algorithms (FOF, DENMAX, and SKID) to identify halos in cosmological N-body simulations are compared with each other and with the predicted mass function from Press-Schechter theory. It is shown that the resulting distribution of halo masses strongly depends upon the choice of free parameters in the three algorithms, and therefore much care in their choice is needed. For many parameter values, DENMAX and SKID have the tendency to include in the halos particles at large distances from the halo center with low peculiar velocities. FOF does not suffer from this problem, and its mass distribution furthermore is reproduced well by the prediction from Press-Schechter theory.

Credit: M. Goetz, J. P. Huchra, R. H. Brandenberger

[owlice]

Computational science: ...Error
…why scientific programming does not compute

by Zeeya Merali

http://www.nature.com/news/2010/101013/ ... tml?ref=nf

A quarter of a century ago, most of the computing work done by scientists was relatively straightforward. But as computers and programming tools have grown more complex, scientists have hit a "steep learning curve", says James Hack, director of the US National Center for Computational Sciences at Oak Ridge National Laboratory in Tennessee. "The level of effort and skills needed to keep up aren't in the wheelhouse of the average scientist."

As a general rule, researchers do not test or document their programs rigorously, and they rarely release their codes, making it almost impossible to reproduce and verify published results generated by scientific software, say computer scientists. At best, poorly written programs cause researchers such as Harry to waste valuable time and energy. But the coding problems can sometimes cause substantial harm, and have forced some scientists to retract papers.

As recognition of these issues has grown, software experts and scientists have started exploring ways to improve the codes used in science.

[owlice]

A Journal for the Astronomical Computing Community?

http://arxiv.org/abs/1103.1982

Abstract: One of the Birds of a Feather (BoF) discussion sessions at ADASS XX considered whether a new journal is needed to serve the astronomical computing community. In this paper we discuss the nature and requirements of that community, outline the analysis that led us to propose this as a topic for a BoF, and review the discussion from the BoF session itself. We also present the results from a survey designed to assess the suitability of astronomical computing papers of different kinds for publication in a range of existing astronomical and scientific computing journals. The discussion in the BoF session was somewhat inconclusive, and it seems likely that this topic will be debated again at a future ADASS or in a similar forum.

Credit: Norman Gray, Robert G Mann

[owlice]

Comparing Numerical Methods for Isothermal Magnetized Supersonic Turbulence

http://arxiv.org/abs/1103.5525

Abstract: We employ simulations of supersonic super-Alfv\'enic turbulence decay as a benchmark test problem to assess and compare the performance of nine astrophysical MHD methods actively used to model star formation. The set of nine codes includes: ENZO, FLASH, KT-MHD, LL-MHD, PLUTO, PPML, RAMSES, STAGGER, and ZEUS. We present a comprehensive set of statistical measures designed to quantify the effects of numerical dissipation in these MHD solvers. We compare power spectra for basic fields to determine the effective spectral bandwidth of the methods and rank them based on their relative effective Reynolds numbers. We also compare numerical dissipation for solenoidal and dilatational velocity components to check for possible impacts of the numerics on small-scale density statistics. Finally, we discuss convergence of various characteristics for the turbulence decay test and impacts of various components of numerical schemes on the accuracy of solutions. We show that the best performing codes employ a consistently high order of accuracy for spatial reconstruction of the evolved fields, transverse gradient interpolation, conservation law update step, and Lorentz force computation. The best results are achieved with divergence-free evolution of the magnetic field using the constrained transport method, and using little to no explicit artificial viscosity. Codes which fall short in one or more of these areas are still useful, but they must compensate higher numerical dissipation with higher numerical resolution. This paper is the largest, most comprehensive MHD code comparison on an application-like test problem to date. We hope this work will help developers improve their numerical algorithms while helping users to make informed choices in picking optimal applications for their specific astrophysical problems.

Credit: Alexei G. Kritsuk, Aake Nordlund, David Collins, Paolo Padoan, Michael L. Norman, Tom Abel, Robi Banerjee, Christoph Federrath, Mario Flock, Dongwook Lee, Pak Shing Li, Wolf-Christian Mueller, Romain Teyssier, Sergey D. Ustyugov, Christian Vogel, Hao Xu

[owlice]

Haloes gone MAD: The Halo-Finder Comparison Project

http://arxiv.org/abs/1104.0949

Abstract: We present a detailed comparison of fundamental dark matter halo properties retrieved by a substantial number of different halo finders. These codes span a wide range of techniques including friends-of-friends (FOF), spherical-overdensity (SO) and phase-space based algorithms. We further introduce a robust (and publicly available) suite of test scenarios that allows halo finder developers to compare the performance of their codes against those presented here. This set includes mock haloes containing various levels and distributions of substructure at a range of resolutions as well as a cosmological simulation of the large-scale structure of the universe. All the halo finding codes tested could successfully recover the spatial location of our mock haloes. They further returned lists of particles (potentially) belonging to the object that led to coinciding values for the maximum of the circular velocity profile and the radius where it is reached. All the finders based in configuration space struggled to recover substructure that was located close to the centre of the host halo and the radial dependence of the mass recovered varies from finder to finder. Those finders based in phase space could resolve central substructure although they found difficulties in accurately recovering its properties. Via a resolution study we found that most of the finders could not reliably recover substructure containing fewer than 30-40 particles. However, also here the phase space finders excelled by resolving substructure down to 10-20 particles. By comparing the halo finders using a high resolution cosmological volume we found that they agree remarkably well on fundamental properties of astrophysical significance (e.g. mass, position, velocity, and peak of the rotation curve).

Credit: Alexander Knebe, Steffen R. Knollmann, Stuart I. Muldrew, Frazer R. Pearce, Miguel Angel Aragon-Calvo, Yago Ascasibar, Peter S. Behroozi, Daniel Ceverino, Stephane Colombi, Juerg Diemand, Klaus Dolag, Bridget L. Falck, Patricia Fasel, Jeff Gardner, Stefan Gottloeber, Chung-Hsing Hsu, Francesca Iannuzzi, Anatoly Klypin, Zarija Lukic, Michal Maciejewski, Cameron McBride, Mark C. Neyrinck, Susana Planelles, Doug Potter, Vicent Quilis, Yann Rasera, Justin I. Read, Paul M. Ricker, Fabrice Roy, Volker Springel, Joachim Stadel, Greg Stinson, P. M. Sutter, Victor Turchaninov, Dylan Tweed, Gustavo Yepes, Marcel Zemp

Comments: 27 interesting pages, 20 beautiful figures, and 4 informative tables accepted for publication in MNRAS. The high-resolution version of the paper as well as all the test cases and analysis can be found at this web site.

[owlice]

GEMS: Galaxy fitting catalogues and testing parametric galaxy fitting codes

http://arxiv.org/abs/0704.2601

Abstract: In the context of measuring structure and morphology of intermediate redshift galaxies with recent HST/ACS surveys, we tune, test, and compare two widely used fitting codes (GALFIT and GIM2D) for fitting single-component Sersic models to the light profiles of both simulated and real galaxy data. We find that fitting accuracy depends sensitively on galaxy profile shape. Exponential disks are well fit with Sersic models and have small measurement errors, whereas fits to de Vaucouleurs profiles show larger uncertainties owing to the large amount of light at large radii. We find that both codes provide reliable fits and little systematic error, when the effective surface brightness is above that of the sky. Moreover, both codes return errors that significantly underestimate the true fitting uncertainties, which are best estimated with simulations. We find that GIM2D suffers significant systematic errors for spheroids with close companions owing to the difficulty of effectively masking out neighboring galaxy light; there appears to be no work around to this important systematic in GIM2D's current implementation. While this crowding error affects only a small fraction of galaxies in GEMS, it must be accounted for in the analysis of deeper cosmological images or of more crowded fields with GIM2D. In contrast, GALFIT results are robust to the presence of neighbors because it can simultaneously fit the profiles of multiple companions thereby deblending their effect on the fit to the galaxy of interest. We find GALFIT's robustness to nearby companions and factor of >~20 faster runtime speed are important advantages over GIM2D for analyzing large HST/ACS datasets. Finally we include our final catalog of fit results for all 41,495 objects detected in GEMS.

Credit: Boris Häußler, Daniel H. McIntosh, Marco Barden, Eric F. Bell, Hans-Walter Rix, Andrea Borch, Steven V. W. Beckwith, John A. R. Caldwell, Catherine Heymans, Knud Jahnke, Shardha Jogee, Sergey E. Koposov, Klaus Meisenheimer, Sebastian F. Sánchez, Rachel S. Somerville, Lutz Wisotzki, Christian Wolf

[owlice]

Where's the Real Bottleneck in Scientific Computing?
Scientists would do well to pick up some tools widely used in the software industry

By Greg Wilson

http://www.americanscientist.org/issues ... -computing

Most scientists had simply never been shown how to program efficiently. After a generic freshman programming course in C or Java, and possibly a course on statistics or numerical methods in their junior or senior year, they were expected to discover or reinvent everything else themselves, which is about as reasonable as showing someone how to differentiate polynomials and then telling them to go and do some tensor calculus.

Yes, the relevant information was all on the Web, but it was, and is, scattered across hundreds of different sites. More important, people would have to invest months or years acquiring background knowledge before they could make sense of it all. As another physicist (somewhat older and more cynical than my friend) said to me when I suggested that he take a couple of weeks and learn some Perl, "Sure, just as soon as you take a couple of weeks and learn some quantum chromodynamics so that you can do my job."

[owlice]

The CRAPL: An academic-strength open source license

By Matt Might

http://www.matt.might.net/articles/crapl/

Academics rarely release code, but I hope a license can encourage them.

Generally, academic software is stapled together on a tight deadline; an expert user has to coerce it into running; and it's not pretty code. Academic code is about "proof of concept." These rough edges make academics reluctant to release their software. But, that doesn't mean they shouldn't.

Most open source licenses (1) require source and modifications to be shared with binaries, and (2) absolve authors of legal liability.

An open source license for academics has additional needs: (1) it should require that source and modifications used to validate scientific claims be released with those claims; and (2) more importantly, it should absolve authors of shame, embarrassment and ridicule for ugly code.

Openness should also hinge on publication: once a paper is accepted, the license should force the release of modifications. During peer review, the license should enable the confidential disclosure of modifications to peer reviewers. If the paper is rejected, the modifications should remain closed to protect the authors' right to priority.

Toward these ends, I've drafted the CRAPL--the Community Research and Academic Programming License. The CRAPL is an open source "license" for academics that encourages code-sharing, regardless of how much how much Red Bull and coffee went into its production. (The text of the CRAPL is in the article body.)

[owlice]

Scientific Software Production: Incentives and Collaboration

http://james.howison.name/pubs/HowisonHerbsleb2011SciSoftIncentives.pdf, CSCW 2011

Abstract: Software plays an increasingly critical role in science, including data analysis, simulations, and managing workflows. Unlike other technologies supporting science, software can be copied and distributed at essentially no cost, potentially opening the door to unprecedented levels of sharing and collaborative innovation. Yet we do not have a clear picture of how software development for science fits into the day-to-day practice of science, or how well the methods and incentives of its production facilitate realization of this potential. We report the results of a multiple-case study of software development in three fields: high energy physics, structural biology, and microbiology. In each case, we identify a typical publication, and use qualitative methods to explore the production of the software used in the science represented by the publication. We identify several different production systems, characterized primarily by differences in incentive structures. We identify ways in which incentives are matched and mismatched with the needs of the science fields, especially with respect to collaboration.

Credit: James Howison and Jim Herbsleb

[owlice]

A Comparison of Cosmological Codes: Properties of Thermal Gas and Shock Waves in Large Scale Structures

http://arxiv.org/abs/1106.2159

Abstract: We present results for the statistics of thermal gas and the shock wave properties for a large volume simulated with three different cosmological numerical codes: the Eulerian total variations diminishing code TVD, the Eulerian piecewise parabolic method-based code ENZO, and the Lagrangian smoothed-particle hydrodynamics code GADGET. Starting from a shared set of initial conditions, we present convergence tests for a cosmological volume of side-length 100 Mpc/h, studying in detail the morphological and statistical properties of the thermal gas as a function of mass and spatial resolution in all codes. By applying shock finding methods to each code, we measure the statistics of shock waves and the related cosmic ray acceleration efficiencies, within the sample of simulations and for the results of the different approaches. We discuss the regimes of uncertainties and disagreement among codes, with a particular focus on the results at the scale of galaxy clusters. We report that, even if the bulk of thermal and shock properties are reasonably in agreement among the three codes, yet some differences exist (especially between Eulerian methods and smoothed particle hydrodynamics) and are mostly associated with a different reconstruction of shock heating and entropy production in the accretion regions at the outskirts of galaxy clusters.

Credit: F. Vazza, K. Dolag, D. Ryu, G. Brunetti, C. Gheller, H. Kang, C. Pfrommer

[owlice]

Running your first SPH simulation

By Nathan Goldbaum

http://astrobites.com/2011/06/11/runnin ... imulation/

Today’s astrobite will be a sequel to a post I wrote a few months ago on using the smoothed particle hydrodynamics (SPH) code Gadget-2. In the first post, I went over how to install Gadget and showed how to run one of the test cases included in the Gadget distribution. Today, I’d like to show how to set up, run, and analyze a simple hydrodynamics test problem of your own.

[owlice]

A Guide to Comparisons of Star Formation Simulations with Observations

http://arxiv.org/abs/1107.2827

Abstract: We review an approach to observation-theory comparisons we call "Taste-Testing." In this approach, synthetic observations are made of numerical simulations, and then both real and synthetic observations are "tasted" (compared) using a variety of statistical tests. We first lay out arguments for bringing theory to observational space rather than observations to theory space. Next, we explain that generating synthetic observations is only a step along the way to the quantitative, statistical, taste tests that offer the most insight. We offer a set of examples focused on polarimetry, scattering and emission by dust, and spectral-line mapping in starforming regions. We conclude with a discussion of the connection between statistical tests used to date and the physics we seek to understand. In particular, we suggest that the "lognormal" nature of molecular clouds can be created by the interaction of many random processes, as can the lognormal nature of the IMF, so that the fact that both the "Clump Mass Function" (CMF) and IMF appear lognormal does not necessarily imply a direct relationship between them.

Credit: Alyssa A. Goodman

[owlice]

Linking to Data - Effect on Citation Rates in Astronomy

http://arxiv.org/abs/1111.3618

Abstract: Is there a difference in citation rates between articles that were published with links to data and articles that were not? Besides being interesting from a purely academic point of view, this question is also highly relevant for the process of furthering science. Data sharing not only helps the process of verification of claims, but also the discovery of new findings in archival data. However, linking to data still is a far cry away from being a "practice", especially where it comes to authors providing these links during the writing and submission process. You need to have both a willingness and a publication mechanism in order to create such a practice. Showing that articles with links to data get higher citation rates might increase the willingness of scientists to take the extra steps of linking data sources to their publications. In this presentation we will show this is indeed the case: articles with links to data result in higher citation rates than articles without such links. The ADS is funded by NASA Grant NNX09AB39G.

Credit: Edwin A. Henneken, Alberto Accomazzi

[owlice]

The case for open computer programs

by Darrel C. Ince, Leslie Hatton & John Graham-Cumming

http://www.nature.com/nature/journal/v4 ... 10836.html

We examine the problem of reproducibility (for an early attempt at solving it, see ref. 1) in the context of openly available computer programs, or code. Our view is that we have reached the point that, with some exceptions, anything less than release of actual source code is an indefensible approach for any scientific results that depend on computation, because not releasing such code raises needless, and needlessly confusing, roadblocks to reproducibility.

[owlice]

Astroinformatics: A 21st Century Approach to Astronomy

http://arxiv.org/abs/0909.3892

Abstract: Data volumes from multiple sky surveys have grown from gigabytes into terabytes during the past decade, and will grow from terabytes into tens (or hundreds) of petabytes in the next decade. This exponential growth of new data both enables and challenges effective astronomical research, requiring new approaches. Thus far, astronomy has tended to address these challenges in an informal and ad hoc manner, with the necessary special expertise being assigned to e-Science or survey science. However, we see an even wider scope and therefore promote a broader vision of this data-driven revolution in astronomical research. For astronomy to effectively cope with and reap the maximum scientific return from existing and future large sky surveys, facilities, and data-producing projects, we need our own information science specialists. We therefore recommend the formal creation, recognition, and support of a major new discipline, which we call Astroinformatics. Astroinformatics includes a set of naturally-related specialties including data organization, data description, astronomical classification taxonomies, astronomical concept ontologies, data mining, machine learning, visualization, and astrostatistics. By virtue of its new stature, we propose that astronomy now needs to integrate Astroinformatics as a formal sub-discipline within agency funding plans, university departments, research programs, graduate training, and undergraduate education. Now is the time for the recognition of Astroinformatics as an essential methodology of astronomical research. The future of astronomy depends on it.

Credit: Kirk D. Borne

[owlice]

Publish or be damned? An alternative impact manifesto for research software

By Neil Chue Hong

http://software.ac.uk/blog/2011-05-02-p ... h-software

The Research Software Impact Manifesto

... we subscribe to the following principles:

• Communality: software is considered as the collective creation of all who have contributed
• Openness: the ability of others to reuse, extend and repurpose our software should be rewarded
• One of Many: we recognise that software is an intrinsic part of research, and should not be divorced from other research outputs
• Pride: we shouldn't be embarassed by publishing code which is imperfect, nor should other people embarass us
• Explanation: we will provide sufficient associated data and metadata to allow the significant characteristics of the software to be defined
• Recognition: if we use a piece of software for our research we will acknowledge its use and let its authors know
• Availability: when a version of software is "released" we commit to making it available for an extended length of time
• Tools: the methods of identification and description of software objects must lend themselves to the simple use of multiple tools for tracking impact
• Equality: credit is due to both the producer and consumer in equal measure, and due to all who have contributed, whether they are academics or not