The CUPID package allows the identification and analysis of clumps of emission within 1, 2 or 3 dimensional data arrays. Whilst targeted primarily at sub-mm cubes, it can be used on any regularly gridded 1, 2 or 3D data. A variety of clump finding algorithms are implemented within CUPID, including the established ClumpFind (ascl:1107.014) and GAUSSCLUMPS (ascl:1406.018) algorithms. In addition, two new algorithms called FellWalker and Reinhold are also provided. CUPID allows easy inter-comparison between the results of different algorithms; the catalogues produced by each algorithm contains a standard set of columns containing clump peak position, clump centroid position, the integrated data value within the clump, clump volume, and the dimensions of the clump. In addition, pixel masks are produced identifying which input pixels contribute to each clump. CUPID is distributed as part of the Starlink (ascl:1110.012) software collection.

Written in c, the Customizable User Pipeline for IRS Data (CUPID) allows users to run the Spitzer IRS Pipelines to re-create Basic Calibrated Data and extract calibrated spectra from the archived raw files. CUPID provides full access to all the parameters of the BCD, COADD, BKSUB, BKSUBX, and COADDX pipelines, as well as the opportunity for users to provide their own calibration files (e.g., flats or darks). CUPID is available for Mac, Linux, and Solaris operating systems.

CosmoTherm allows precise computation of CMB spectral distortions caused by energy release in the early Universe. Different energy-release scenarios (e.g., decaying or annihilating particles) are implemented using the Green's function of the cosmological thermalization problem, allowing fast computation of the distortion signal. The full thermalization problem can be solved on a case-by-case basis for a wide range of energy-release scenarios using the full PDE solver of CosmoTherm. A simple Monte-Carlo toolkit is included for parameter estimation and forecasts using the Green's function method.

ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. The package is designed to compute a few eigenvalues and corresponding eigenvectors of a general n by n matrix A. It is most appropriate for large sparse or structured matrices A where structured means that a matrix-vector product w <- Av requires order n rather than the usual order n2 floating point operations. This software is based upon an algorithmic variant of the Arnoldi process called the Implicitly Restarted Arnoldi Method (IRAM). When the matrix A is symmetric it reduces to a variant of the Lanczos process called the Implicitly Restarted Lanczos Method (IRLM). These variants may be viewed as a synthesis of the Arnoldi/Lanczos process with the Implicitly Shifted QR technique that is suitable for large scale problems. For many standard problems, a matrix factorization is not required; only the action of the matrix on a vector is needed. ARPACK is capable of solving large scale symmetric, nonsymmetric, and generalized eigenproblems from significant application areas.

A common community-maintained repository for this software, ARPACK-NG (ascl:2306.049), is available.

MUSIC generates multi-scale initial conditions with multiple levels of refinements for cosmological ‘zoom-in’ simulations. The code uses an adaptive convolution of Gaussian white noise with a real-space transfer function kernel together with an adaptive multi-grid Poisson solver to generate displacements and velocities following first- (1LPT) or second-order Lagrangian perturbation theory (2LPT). MUSIC achieves rms relative errors of the order of 10−4 for displacements and velocities in the refinement region and thus improves in terms of errors by about two orders of magnitude over previous approaches. In addition, errors are localized at coarse-fine boundaries and do not suffer from Fourier space-induced interference ringing.

Written for the Wide-Field Infrared Survey Telescope (WFIRST) high-latitude survey, the exposure time calculator (ETC) works in both imaging and spectroscopic modes. In addition to the standard ETC functions (e.g. background and S/N determination), the calculator integrates over the galaxy population and forecasts the density and redshift distribution of galaxy shapes usable for weak lensing (in imaging mode) and the detected emission lines (in spectroscopic mode). The program may be useful outside of WFIRST but no warranties are made regarding its suitability for general purposes. The software is available for download; IPAC maintains a web interface for those who wish to run a small number of cases without having to download the package.

ORAC-DR is a generic data reduction pipeline infrastructure; it includes specific data processing recipes for a number of instruments. It is used at the James Clerk Maxwell Telescope, United Kingdom Infrared Telescope, AAT, and LCOGT. This pipeline runs at the JCMT Science Archive hosted by CADC to generate near-publication quality data products; the code has been in use since 1998.

PyMSES provides a python solution for getting data out of RAMSES (ascl:1011.007) astrophysical fluid dynamics simulations. It permits transparent manipulation of large simulations and interfaces with common Python libraries and existing code, and can serve as a post-processing toolbox for data analysis. It also does three-dimensional volume rendering with a specific algorithm optimized to work on RAMSES distributed data (Guillet et al. 2011 and Jones et a. 2011).

AIDA is an implementation and extension of the MISTRAL myopic deconvolution method developed by Mugnier et al. (2004) (see J. Opt. Soc. Am. A 21:1841-1854). The MISTRAL approach has been shown to yield object reconstructions with excellent edge preservation and photometric precision when used to process astronomical images. AIDA improves upon the original MISTRAL implementation. AIDA, written in Python, can deconvolve multiple frame data and three-dimensional image stacks encountered in adaptive optics and light microscopic imaging.

AIRY simulates optical and near-infrared interferometric observations; it can also perform subsequent image restoration or deconvolution. It is based on the CAOS (ascl:1106.017) Problem Solving Environment. Written in IDL, it consists of a set of specific modules, each handling a particular task.

ASPRO 2 (Astronomical Software to PRepare Observations) is an observation preparation tool for interferometric observations with the VLTI or other interferometers such as CHARA and SUSI. It is a Java standalone program that provides a dynamic graphical interface to simulate the projected baseline evolution during observations (super-synthesis) and derive visibilities for targets (i.e., single star, binaries, user defined FITS image). It offers other useful functions such as the ability to load and save your observation settings and generate Observing Blocks.

AIPSLite is an extension for ParselTongue (ascl:1208.020) that allows machines without an AIPS (ascl:9911.003) distribution to bootstrap themselves with a minimal AIPS environment. This allows deployment of AIPS routines on distributed systems, which is useful when data can be easily be split into smaller chunks and handled independently.

SMURF reduces submillimeter single-dish continuum and heterodyne data. It is mainly targeted at data produced by the James Clerk Maxwell Telescope but data from other telescopes have been reduced using the package. SMURF is released as part of the bundle that comprises Starlink (ascl:1110.012) and most of the packages that use it. The two key commands are MAKEMAP for the creation of maps from sub millimeter continuum data and MAKECUBE for the creation of data cubes from heterodyne array instruments. The software can also convert data from legacy JCMT file formats to the modern form to allow it to be processed by MAKECUBE. SMURF is a core component of the ORAC-DR (ascl:1310.001) data reduction pipeline for JCMT.

SPECX is a general purpose line data reduction system. It can read and write FITS data cubes but has specialist support for the GSD format data from the James Clerk Maxwell Telescope. It includes commands to store and retrieve intermediate spectra in storage registers and perform the fitting and removal of polynomial, harmonic and Gaussian baselines.

SPECX can filter and edit spectra and list and display spectra on a graphics terminal. It is able to perform Fourier transform and power spectrum calculations, process up to eight spectra (quadrants) simultaneously with either the same or different center, and assemble a number of reduced individual spectra into a map file and contour or greyscale any plane or planes of the resulting cube.

Two versions of SPECX are distributed. Version 6.x is the VMS and Unix version and is distributed as part of the Starlink software collection. Version 7.x is a complete rewrite of SPECX distributed for Windows.

AstroImageJ is generic ImageJ (ascl:1206.013) with customizations to the base code and a packaged set of astronomy specific plugins. It reads and writes FITS images with standard headers, displays astronomical coordinates for images with WCS, supports photometry for developing color-magnitude data, offers flat field, scaled dark, and non-linearity processing, and includes tools for precision photometry that can be used during real-time data acquisition.

VAPHOT is an aperture photometry package for precise time−series photometry of uncrowded fields, geared towards the extraction of target lightcurves of eclipsing or transiting systems. Its photometric main routine works within the IRAF (ascl:9911.002) environment and is built upon the standard aperture photometry task 'phot' from IRAF, using optimized aperture sizes. The associated analysis program 'VANALIZ' works in the IDL environment. It performs differential photometry with graphical and numerical output. VANALIZ produces plots indicative of photometric stability and permits the interactive evaluation and weighting of comparison stars. Also possible is the automatic or manual suppression of data-points and the output of statistical analyses. Several methods for the calculation of the reference brightness are offered. Specific routines for the analysis of transit 'on'-'off' photometry, comparing the target brightness inside against outside a transit are also available.

LOSP is a FORTRAN77 numerical package that computes the orbital parameters of spectroscopic binaries. The package deals with SB1 and SB2 systems and is able to adjust either circular or eccentric orbits through a weighted fit.

The Spherical Library provides an efficient and accurate mathematical representation of shapes on the celestial sphere, such as sky coverage and footprints. Shapes of arbitrary complexity and size can be dynamically created from simple building blocks, whose exact area is also analytically computed. This methodology is also perfectly suited for censoring problematic parts of datasets, e.g., bad seeing, satellite trails or diffraction spikes of bright stars.

SATMC is a general purpose, MCMC-based SED fitting code written for IDL and Python. Following Bayesian statistics and Monte Carlo Markov Chain algorithms, SATMC derives the best fit parameter values and returns the sampling of parameter space used to construct confidence intervals and parameter-parameter confidence contours. The fitting may cover any range of wavelengths. The code is designed to incorporate any models (and potential priors) of the user's choice. The user guide lists all the relevant details for including observations, models and usage under both IDL and Python.

VOPlot is a tool for visualizing astronomical data. It was developed in Java and acts on data available in VOTABLE, ASCII and FITS formats. VOPlot is available as a stand alone version, which is to be installed on the user's machine, or as a web-based version fully integrated with the VizieR database.

VOMegaPlot, a Java based tool, has been developed for visualizing astronomical data that is available in VOTable format. It has been specifically optimized for handling large number of points (in the range of millions). It has the same look and feel as VOPlot (ascl:1309.006) and both these tools have certain common functionality.

VOStat allows astronomers to use both simple and sophisticated statistical routines on large datasets. This tool uses the large public-domain statistical computing package R. Datasets can be uploaded in either ASCII or VOTABLE (preferred) format. The statistical computations are performed by the VOStat and results are returned to the user.

SMILE is interactive software for studying a variety of 2D and 3D models, including arbitrary potentials represented by a basis-set expansion, a spherical-harmonic expansion with coefficients being smooth functions of radius (splines), or a set of fixed point masses. Its main features include:

• orbit integration in various 2d and 3d potentials (including N-body and basis-set representations of an arbitrary potential);
• methods for analysis of orbital class, fundamental frequencies, regular or chaotic nature of an orbit, computation of Lyapunov exponents;
• Poincaré sections (in 2d) and frequency maps (in 3d) for analyzing orbital structure of potential;
• construction of self-consistent Schwarzschild models; and
• convenient visualization and integrated GUI environment, and a console scriptable version.

LOSSCONE computes the rates of capture of stars by supermassive black holes. It uses a stationary and time-dependent solutions for the Fokker-Planck equation describing the evolution of the distribution function of stars due to two-body relaxation, and works for arbitrary spherical and axisymmetric galactic models that are provided by the user in the form of M(r), the cumulative mass as a function of radius.

MapCurvature, written in IDL, can create map projections with Goldberg-Gott indicatrices. These indicatrices measure the flexion and skewness of a map, and are useful for determining whether features are faithfully reproduced on a particular projection.

LensEnt2 is a maximum entropy reconstructor of weak lensing mass maps. The method takes each galaxy shape as an independent estimator of the reduced shear field and incorporates an intrinsic smoothness, determined by Bayesian methods, into the reconstruction. The uncertainties from both the intrinsic distribution of galaxy shapes and galaxy shape estimation are carried through to the final mass reconstruction, and the mass within arbitrarily shaped apertures are calculated with corresponding uncertainties. The input is a galaxy ellipticity catalog with each measured galaxy shape treated as a noisy tracer of the reduced shear field, which is inferred on a fine pixel grid assuming positivity, and smoothness on scales of w arcsec where w is an input parameter. The ICF width w can be chosen by computing the evidence for it.

APPSPACK is serial or parallel, derivative-free optimization software for solving nonlinear unconstrained, bound-constrained, and linearly-constrained optimization problems, with possibly noisy and expensive objective functions.

BASIN (Beowulf Analysis Symbolic INterface) is a flexible, integrated suite of tools for multiuser parallel data analysis and visualization that allows researchers to harness the power of Beowulf PC clusters and multi-processor machines without necessarily being experts in parallel programming. It also includes general tools for data distribution and parallel operations on distributed data for developing libraries for specific tasks.

SYNAPPS is a spectrum fitter embedding a highly parameterized synthetic SN spectrum calculation within a parallel asynchronous optimizer. This open-source code is aimed primarily at the problem of systematically interpreting large sets of SN spectroscopy data.

SYN++ is a standalone SN spectrum synthesis program. It is a rewrite of the original SYNOW (ascl:1010.055) code in modern C++. It offers further enhancements, a new structured input control file format, and the atomic data files have been repackaged and are more complete than those of SYNOW.

CReSyPS (Code Rennais de Synthèse de Populations Stellaires) is a stellar population synthesis code that determines core overshooting amount for Magellanic clouds main sequence stars.

GYRE is an oscillation code that solves the stellar pulsation equations (both adiabatic and non-adiabatic) using a novel Magnus Multiple Shooting numerical scheme devised to overcome certain weaknesses of the usual relaxation and shooting schemes. The code is accurate (up to 6th order in the number of grid points), robust, and makes efficient use of multiple processor cores and/or nodes.

CRUSH is an astronomical data reduction/imaging tool for certain imaging cameras, especially at the millimeter, sub-millimeter, and far-infrared wavelengths. It supports the SHARC-2, LABOCA, SABOCA, ASZCA, p-ArTeMiS, PolKa, GISMO, MAKO and SCUBA-2 instruments. The code is written entirely in Java, allowing it to run on virtually any platform. It is normally run from the command-line with several arguments.

RADLite is a raytracer that is optimized for producing infrared line spectra and images from axisymmetric density structures, originally developed to function on top of the dust radiative transfer code RADMC. RADLite can consistently deal with a wide range of velocity gradients, such as those typical for the inner regions of protoplanetary disks. The code is intended as a back-end for chemical and excitation codes, and can rapidly produce spectra of thousands of lines for grids of models for comparison with observations. It includes functionality for simulating telescopic images for optical/IR/midIR/farIR telescopes. It takes advantage of multi-threaded CPUs and includes an escape-probability non-LTE module.

THELI is an easy-to-use, end-to-end pipeline for the reduction of any optical, near-IR and mid-IR imaging data. It combines a variety of processing algorithms and third party software into a single, homogeneous tool. Over 90 optical and infrared instruments at observatories world-wide are pre-configured; more can be added by the user. The code's online appendix contains three walk-through examples using public data (optical, near-IR and mid-IR) and additional online documentation is available for training and troubleshooting.

SPEX is optimized for the analysis and interpretation of high-resolution cosmic X-ray spectra. The software is especially suited for fitting spectra obtained by current X-ray observatories like XMM-Newton, Chandra, and Suzaku. SPEX can fit multiple spectra with different model components simultaneously and handles highly complex models with many free parameters.

Ceph_code fits multi-band Cepheid light-curves using templates derived from OGLE observations. The templates include short period stars (<10 day) and overtone stars.

JHelioview is open source visualization software for solar physics data. The JHelioviewer client application enables users to browse petabyte-scale image archives; the JHelioviewer server integrates a JPIP server, metadata catalog, and an event server. JHelioview uses the JPEG 2000 image compression standard, which provides efficient access to petabyte-scale image archives; JHelioviewer also allows users to locate and manipulate specific data sets.

ChiantiPy is an object-orient Python package for calculating astrophysical spectra using the CHIANTI atomic database for astrophysical spectroscopy. It provides access to the database and the ability to calculate various physical quantities for the interpretation of astrophysical spectra.

MOOGStokes is a version of the MOOG one-dimensional local thermodynamic equilibrium radiative transfer code that incorporates a Stokes vector treatment of polarized radiation through a magnetic medium. It consists of three complementary programs that together can synthesize the disk-averaged emergent spectrum of a star with a magnetic field. The MOOGStokes package synthesizes emergent spectra of stars with magnetic fields in a familiar computational framework and produces disk-averaged spectra for all Stokes vectors ( I, Q, U, V ), normalized by the continuum.

DustEM computes the extinction and the emission of interstellar dust grains heated by photons. It is written in Fortran 95 and is jointly developed by IAS and CESR. The dust emission is calculated in the optically thin limit (no radiative transfer) and the default spectral range is 40 to 108 nm. The code is designed so dust properties can easily be changed and mixed and to allow for the inclusion of new grain physics.

Monte Python is a parameter inference code which combines the flexibility of the python language and the robustness of the cosmological code CLASS (ascl:1106.020) into a simple and easy to manipulate Monte Carlo Markov Chain code.

This version has been archived and replaced by MontePython 3 (ascl:1805.027).

K3Match is a C library with Python bindings for fast matching of points in 3D space. It uses an implementation of three dimensional binary trees to efficiently find matches between points in 3D space. Two lists of points are compared and match indices as well as distances are given. K3Match can find either the nearest neighbour or all matches within a given search distance in 3D Cartesian space or on the surface of the 2D unit sphere in standard spherical or celestial coordinates.

FieldInf is a collection of fast modern Fortran routines for computing exactly the background evolution and primordial power spectra of any single field inflationary models. It implements reheating without any assumptions through the "reheating parameter" R allowing robust inflationary parameter estimations and inference on the reheating energy scale. The underlying perturbation code actually deals with N fields minimally-coupled and/or non-minimally coupled to gravity and works for flat FLRW only.

Lensview models resolved gravitational lens systems based on LensMEM but using the Skilling & Bryan MEM algorithm. Though its primary purpose is to find statistically acceptable lens models for lensed images and to reconstruct the surface brightness profile of the source, LENSVIEW can also be used for more simple tasks such as projecting a given source through a lens model to generate a “true” image by conserving surface brightness. The user can specify complicated lens models based on one or more components, such as softened isothermal ellipsoids, point masses, exponential discs, and external shears; LENSVIEW generates a best-fitting source matching the observed data for each specific combination of model parameters.

im2shape is a Bayesian approach to the problem of accurate measurement of galaxy ellipticities for weak lensing studies, in particular cosmic shear. im2shape parameterizes galaxies as sums of Gaussians, convolved with a psf which is also a sum of Gaussians. The uncertainties in the output parameters are calculated using a Markov Chain Monte Carlo approach.

AstroTaverna is a plugin for Taverna Workbench that provides the means to build astronomy workflows using Virtual Observatory services discovery and efficient manipulation of VOTables (based on STIL tool set). It integrates SAMP-enabled software, allowing data exchange and communication among local VO tools, as well as the ability to execute Aladin scripts and macros.

Obit is a group of software packages for handling radio astronomy data, especially interferometric and single dish OTF imaging. Obit is primarily an environment in which new data processing algorithms can be developed and tested but which can also be used for production processing of a certain range of scientific problems. The package supports both prepackaged, compiled tasks and a python interface to the major class functionality to allow rapid prototyping using python scripts; it allows access to multiple disk--resident data formats, in particular access to either AIPS disk data or FITS files. Obit applications are interoperable with Classic AIPS and the ObitTalk python interface gives access to AIPS tasks as well as Obit libraries and tasks.

MAH calculates the posterior distribution of the "minimum atmospheric height" (MAH) of an exoplanet by inputting the joint posterior distribution of the mass and radius. The code collapses the two dimensions of mass and radius into a one dimensional term that most directly speaks to whether the planet has an atmosphere or not. The joint mass-radius posteriors derived from a fit of some exoplanet data (likely using MCMC) can be used by MAH to evaluate the posterior distribution of R_MAH, from which the significance of a non-zero R_MAH (i.e. an atmosphere is present) is calculated.

Cosmoxi2d is written in C and computes the theoretical two-point galaxy correlation function as a function of cosmological and galaxy nuisance parameters. It numerically evaluates the model described in detail in Reid and White 2011 (arxiv:1105.4165) and Reid et al. 2012 (arxiv:1203.6641) for the multipole moments (up to ell = 4) for the observed redshift space correlation function of biased tracers as a function of cosmological (though an input linear matter power spectrum, growth rate f, and Alcock-Paczynski geometric factors alphaperp and alphapar) as well as nuisance parameters describing the tracers (bias and small scale additive velocity dispersion, isotropicdisp1d).

This model works best for highly biased tracers where the 2nd order bias term is small. On scales larger than 100 Mpc, the code relies on 2nd order Lagrangian Perturbation theory as detailed in Matsubara 2008 (PRD 78, 083519), and uses the analytic version of Reid and White 2011 on smaller scales.