2dfdr is an automatic data reduction pipeline dedicated to reducing multi-fibre spectroscopy data, with current implementations for AAOmega (fed by the 2dF, KOALA-IFU, SAMI Multi-IFU or older SPIRAL front-ends), HERMES, 2dF (spectrograph), 6dF, and FMOS. A graphical user interface is provided to control data reduction and allow inspection of the reduced spectra. It is being continually developed at the AAO in response to user feedback. You can reduce most of your data by simply pressing START AUTO REDUCTION in the Graphical User Interface.
The ADF modeling suite offers DFT to MD software with an integrated graphical interface. With a molecular and periodic DFT code (ADF, BAND), semi-empirical codes (MOPAC, DFTB), reactive MD (ReaxFF) and a COSMO-RS module, hard problems in chemistry and materials science can be tackled with an easy set up.
"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
Anaconda is a free enterprise-ready Python distribution for data analytics, processing, and scientific computing. Anaconda comes with Python 2.7 or Python 3.4 and 100+ cross-platform tested and optimized Python packages. All of the usual Python ecosystem tools work with Anaconda. Additionally, Anaconda can create custom environments that mix and match different Python versions (2.6, 2.7, 3.3 or 3.4) and other packages into isolated environments and easily switch between them using conda, our innovative multi-platform package manager for Python and other languages.
GNU Aspell is a Free and Open Source spell checker designed to eventually replace Ispell. It can either be used as a library or as an independent spell checker. Its main feature is that it does a superior job of suggesting possible replacements for a misspelled word than just about any other spell checker out there for the English language. Unlike Ispell, Aspell can also easily check documents in UTF-8 without having to use a special dictionary. Aspell will also do its best to respect the current locale setting. Other advantages over Ispell include support for using multiple dictionaries at once and intelligently handling personal dictionaries when more than one Aspell process is open at once.
If you have astronomical imaging of the sky with celestial coordinates you do not know—or do not trust—then Astrometry.net is for you. Input an image and we'll give you back astrometric calibration meta-data, plus lists of known objects falling inside the field of view.
The ATLAS (Automatically Tuned Linear Algebra Software) project is an ongoing research effort focusing on applying empirical techniques in order to provide portable performance.
AVL FIRE® is a powerful multi-purpose thermo-fluid software representing the latest generation of 3D CFD. It is being developed and continuously improved to solve the most demanding problems in respect of geometrical complexity, physics and chemistry.
Boost provides free peer-reviewed portable C++ source libraries.
bsdiff and bspatch are tools for building and applying patches to binary files. bsdiff is quite memory-hungry. It requires max(17*n,9*n+m)+O(1) bytes of memory, where n is the size of the old file and m is the size of the new file. bsdiff runs in O((n+m) log n) time.
CASA, the Common Astronomy Software Applications package, is being developed with the primary goal of supporting the data post-processing needs of the next generation of radio astronomical telescopes such as ALMA and VLA. The package can process both interferometric and single dish data, and is developed by an international consortium of scientists based at the National Radio Astronomical Observatory (NRAO), the European Southern Observatory (ESO), the National Astronomical Observatory of Japan (NAOJ), the CSIRO Australia Telescope National Facility (CSIRO/ATNF), and the Netherlands Institute for Radio Astronomy (ASTRON) under the guidance of NRAO.
The CDSClient package is a set of C and csh routines which allow to query some databases located at CDS or on mirrors over the network.
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
Charm++ is a parallel programming framework in C++ supported by an adaptive runtime system, which enhances user productivity and allows programs to run portably from small multicore computers (your laptop) to the largest supercomputers. It enables users to easily expose and express much of the parallelism in their algorithms while automating many of the requirements for high performance and scalability. It permits writing parallel programs in units that are natural to the domain, without having to deal with processors and threads.
CLAPACK is a C version of LAPACK.
CMake is an extensible, open-source system that manages the build process in an operating system and in a compiler-independent manner. Unlike many cross-platform systems, CMake is designed to be used in conjunction with the native build environment. Simple configuration files placed in each source directory (called CMakeLists.txt files) are used to generate standard build files (e.g., makefiles on Unix) which are used in the usual way. CMake can generate a native build environment that will compile source code, create libraries, generate wrappers and build executables in arbitrary combinations. CMake supports in-place and out-of-place builds, and can therefore support multiple builds from a single source tree. CMake also supports static and dynamic library builds.
You can model and simulate any physics-based system using software from COMSOL®. COMSOL Multiphysics® includes the COMSOL Desktop® graphical user interface (GUI) and a set of predefined user interfaces with associated modeling tools, referred to as physics interfaces, for modeling common applications. A suite of add-on products expands this multiphysics simulation platform for modeling specific application areas as well as interfacing with third-party software and their capabilities. COMSOL Multiphysics is required to run any of the add-on products. The physics-based modules augment the core physics interfaces of COMSOL Multiphysics and provide additional interfaces for electrical, mechanical, fluid flow, and chemical applications. Any number of modules can be seamlessly combined to handle challenging multiphysics applications.
The Common Pipeline Library (CPL) comprises a set of ISO-C libraries that provide a comprehensive, efficient and robust software toolkit. It forms a basis for the creation of automated astronomical data-reduction tasks (known as "pipelines"). The CPL was developed to standardise the way VLT instrument pipelines are built, to shorten their development cycle and to ease their maintenance. However, it may be more generally applied to any similar application, and the details of the CPL code have been engineered in a way to make the library portable and flexible, as well as minimising external dependencies.
stands for Compute Unified Device Architecture, is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers direct access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
SAOImage DS9 is an astronomical imaging and data visualization application. DS9 supports FITS images and binary tables, multiple frame buffers, region manipulation, and many scale algorithms and colormaps. It provides for easy communication with external analysis tasks and is highly configurable and extensible via XPA and SAMP.
Duchamp is a solution to this problem of three-dimensional source finding. It has the following features:
EsoRex is the ESO Recipe Execution Tool. It can list, configure and execute CPL-based recipes from the command line.
Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
f2c is a program to convert Fortran 77 to C code.
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library.
GALFIT is a data analysis algorithm that fits 2-D analytic functions to galaxies and point sources directly to digital images.
Gaussian 09 is the latest version of the Gaussian® series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian 09’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures).
GBTIDL is an interactive package for reduction and analysis of spectral line data taken with the Robert C. Byrd Green Bank Telescope (GBT).
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,...).
This Python package and extensions are a number of tools for programming and manipulating the GDAL Geospatial Data Abstraction Library. Actually, it is two libraries – GDAL for manipulating geospatial raster data and OGR for manipulating geospatial vector data.
GDB, the GNU Project debugger, allows you to see what is going on `inside' another program while it executes -- or what another program was doing at the moment it crashed. GDB can do four main kinds of things (plus other things in support of these) to help you catch bugs in the act:
GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions. GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS). As such, it aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced topology functions. Capabilities Included:
GHC, is an open source native code compiler for the functional programming language Haskell. It provides a cross-platform environment for the writing and testing of Haskell code and it supports numerous extensions, libraries, and optimizations that streamline the process of generating and executing code.
Ghostscript is an interpreter for PostScript™ and Portable Document Format (PDF) files.
GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers. There is no practical limit to the precision except the ones implied by the available memory in the machine GMP runs on. GMP has a rich set of functions, and the functions have a regular interface. The main target applications for GMP are cryptography applications and research, Internet security applications, algebra systems, computational algebra research, etc.
Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave.
Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif (recent versions of Lesstif should be fine too). Grace is a descendant of ACE/gr, also known as Xmgr.
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.
ghostview allows to view and navigate through PostScript and PDF documents on an X display by providing a user interface for the ghostscript interpreter.
The Haskell Platform is the easiest way to get started with programming Haskell. The platform consists of the Glasgow Haskell Compiler (GHC) and an extensive set of standard libraries and utilities with full documentation.
Hierarchical Data Format (HDF) is a set of file formats (HDF4, HDF5) designed to store and organize large amounts of numerical data. Originally developed at the National Center for Supercomputing Applications, it is supported by the non-profit HDF Group, whose mission is to ensure continued development of HDF5 technologies, and the continued accessibility of data stored in HDF.
A Unified Release of the FTOOLS and XANADU Software Packages.
IDL, short for Interactive Data Language, is a programming language used for data analysis. It is popular in particular areas of science, such as astronomy and medical imaging. IDL is vectorized, numerical, and interactive, and is commonly used for interactive processing of large amounts of data (including image processing). The syntax includes many constructs from Fortran and some from C.
idlutils is a collection of IDL utilities useful for astronomical applications, developed by an assortment of folks over the years. Various pipelines for the Sloan Digital Sky Survey and other projects rely on tools from this product.
inotify-tools is a C library and a set of command-line programs for Linux providing a simple interface to inotify. These programs can be used to monitor and act upon filesystem events. The general purpose of this package is to allow inotify's features to be used from within shell scripts.
Intel Parallel Studio - Composer Edition includes compilers, performance libraries, and parallel models optimized to build fast parallel code. The compilers generate optimized code for IA-32 and Intel 64 architectures, but non-optimized code on non-Intel but compatible processors, such as certain AMD processors.
IRAF (image reduction and analysis facility) is a collection of software written at the National Optical Astronomy Observatory (NOAO) geared towards the reduction of astronomical images in pixel array form. This is primarily data taken from imaging array detectors such as CCDs.
ISIS (Image Subtraction Package) is a complete package to process CCD images using the image subtraction method. ISIS contains 3 sub-packages, and allows to build light curves of variables objects from a series of CCD images.
Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. The library, largely written in Julia itself, also integrates mature, best-of-breed C and Fortran libraries for linear algebra, random number generation, signal processing, and string processing.
Karma is a toolkit for interprocess communications, authentication, encryption, graphics display, user interface and manipulating the Karma network data structure. It contains KarmaLib (the structured libraries and API) and a large number of modules (applications) to perform many standard tasks. A suite of visualisation tools is also distributed with the library.
The kdtree package can construct, modify and search kd-trees.
LAMMPS is a classical molecular dynamics code. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. The code includes the following functionalities:
LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. The associated matrix factorizations (LU, Cholesky, QR, SVD, Schur, generalized Schur) are also provided, as are related computations such as reordering of the Schur factorizations and estimating condition numbers. Dense and banded matrices are handled, but not general sparse matrices. In all areas, similar functionality is provided for real and complex matrices, in both single and double precision.
ibctl is a free Guile-based library implementing flexible control files for scientific simulations.
libhugetlbfs is a library which provides easy access to huge pages of memory. It is a wrapper for the hugetlbfs file system. Applications can use huge pages to fulfill malloc() requests without being recompiled by using LD_PRELOAD. Alternatively, applications can be linked against libhugetlbfs without source modifications to load text or BSS or BSS, data, and text segments into large pages. The library also comes with several userspace tools to help with huge page usability, environment setup, and control.
MAKEE is a data reduction package for the HIRES and ESI instruments at Keck Observatory. It is optimized for the spectral extraction of single, unresolved point sources (see ideal inputs ). MAKEE is designed to run non-interactively using a set of default parameters. Taking the raw HIRES FITS files as input, MAKEE determines the position (or trace) of each echelle order, defines the object and background extraction boundaries, optimally extracts a spectrum for each order, and computes wavelength calibrations. MAKEE does not do flux calibration. MAKEE produces FITS format "spectral images" (each row is a separate echelle order spectrum). The data values are in arbitrary (relative) flux units. The wavelength calibration is defined by a a 6th order polynomial fit to each echelle order on a heliocentric, vacuum wavelength scale (in Angstroms) which is stored in the FITS header. MAKEE will reduce data from all HIRES formats, including the single CCD format, the single CCD with Red and UV cross dispersers, and the current 3 CCD system. It can handle a variety of pixel binnings, including 1x1, 1x2, 1x4 (column x row).
Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields, based on symbolic mathematics.
MATLAB® (MAtrix LABoratory) is the high-level language and interactive environment. It lets you explore and visualize ideas and collaborate across disciplines including signal and image processing, communications, control systems, and computational finance.
MESA (Modules for Experiments in Stellar Astrophysics) is a suite of open source, robust, efficient, thread-safe libraries for a wide range of applications in computational stellar astrophysics. A one-dimensional stellar evolution module, MESAstar, combines many of the numerical and physics modules for simulations of a wide range of stellar evolution scenarios ranging from very low mass to massive stars, including advanced evolutionary phases. MESAstar solves the fully coupled structure and composition equations simultaneously. It uses adaptive mesh refinement and sophisticated timestep controls, and supports shared memory parallelism based on OpenMP
Miriad is a radio interferometry data reduction package of particular interest to users of the Australia Telescope Compact Array (ATCA). It can be used for the reduction of continuum and spectral line observations from beginning to end, starting with the loading of the data (either FITS, the ATNF RPFITS or old BIMA formats) through to image synthesis, analysis and display with publication quality graphics.
Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format. Molden reads all the required information from the GAMESS / GAUSSIAN outputfile. Molden is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets. Molden supports contour plots, 3-d grid plots with hidden lines and a combination of both.
Montage is a toolkit for assembling Flexible Image Transport System (FITS) images into custom mosaics.
The MIT Photonic-Bands (MPB) package computes the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers. This program computes definite-frequency eigenstates (harmonic modes) of Maxwell's equations in periodic dielectric structures for arbitrary wavevectors, using fully-vectorial and three-dimensional methods. It is especially designed for the study of photonic crystals (a.k.a. photonic band-gap materials), but is also applicable to many other problems in optics, such as waveguides and resonator systems.
Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal.
The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. The main goal of MPFR is to provide a library for multiple-precision floating-point computation which is both efficient and has a well-defined semantics. It copies the good ideas from the ANSI/IEEE-754 standard for double-precision floating-point arithmetic.
MPI for Python provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
A high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
Mpiexec is a replacement program for the script mpirun, which is part of the mpich package. It is used to initialize a parallel job from within a PBS batch or interactive environment. Mpiexec uses the task manager library of PBS to spawn copies of the executable on the nodes in a PBS allocation.
This is the MapReduce-MPI library from Sandia National Laboratories. It is used for implementing MapReduce part of the mr-mpi-blast.
MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions.
Data Reduction Pipeline for the MUSE instrument at the VLT.
MPI over Infiniband.
MPI over Infiniband.
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.
Ndiff compares putatively similar files, ignoring small numeric differences.
A fast, compact Motif/X11 plain text editor, for most popular Unix systems. Features significant support for programmers including syntax highlighting, macro language, and streamlined keyboard navigation.
NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data for FORTRAN language.
GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and non-linear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable.
ompP is a profiling tool for OpenMP applications. ompP's profiling report becomes available immediately after program termination in a human-readable ASCII format.
The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.
GNU Parallel is a shell tool for executing jobs in parallel using one or more computers. A job is can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU Parallel can then split the input and pipe it into commands in parallel.
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PCRE has its own native API, as well as a set of wrapper functions that correspond to the POSIX regular expression API.
Using PGI Accelerator compilers, programmers can accelerate applications on x64+GPU platforms by adding OpenMP-like compiler directives to existing high-level standard-compliant Fortran,C and C++ programs and then recompiling with appropriate compiler options.
The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. The PGPLOT library consists of two major parts: a device-independent part and a set of device-dependent ``device handler'' subroutines for output on various terminals, image displays, dot-matrix printers, laser printers, and pen plotters. Common file formats supported include PostScript and GIF. PGPLOT itself is written mostly in standard Fortran-77, with a few non-standard, system-dependent subroutines. PGPLOT subroutines can be called directly from a Fortran-77 or Fortran-90 program. A C binding library (cpgplot) and header file (cpgplot.h) are provided that allow PGPLOT to be called from a C or C++ program; the binding library handles conversion between C and Fortran argument-passing conventions.
pgpool-II is a middleware that works between PostgreSQL servers and a PostgreSQL database client. It provides the following features:
Postgres-XC is a write-scalable synchronous multi-master PostgreSQL cluster with the following features. 1) Both read and write scalability. 2) Configured with more than one server. 3) Complete global transaction and visibility management.
PLplot is a cross-platform software package for creating scientific plots whose plot symbols and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer. The PLplot core library can be used to create standard x-y plots, semi-log plots, log-log plots, contour plots, 3D surface plots, mesh plots, bar charts and pie charts. Multiple graphs (of the same or different sizes) may be placed on a single page, and multiple pages are allowed for those device formats that support them.
PnetCDF is a library providing high-performance parallel I/O while still maintaining file-format compatibility with Unidata's NetCDF, specifically the formats of CDF-1 and CDF-2. Although NetCDF supports parallel I/O starting from version 4, the files must be in HDF5 format. PnetCDF is currently the only choice for carrying out parallel I/O on files that are in classic formats (CDF-1 and 2). In addition, PnetCDF supports the CDF-5 file format, an extension of CDF-2, that supports more data types and allows users to define large dimensions, attributes, and variables (>2B elements).
PostgreSQL is a powerful, open source object-relational database system. It runs on all major operating systems, including Linux, UNIX (AIX, BSD, HP-UX, SGI IRIX, Mac OS X, Solaris, Tru64), and Windows. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others.
proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into Cartesian coordinates. For many of the projection functions the inverse conversion can also be performed.
PSFEx ("PSF Extractor"”) extracts models of the Point Spread Function (PSF) from FITS images processed with SExtractor, and measures the quality of images. The generated PSF models can be used for model-fitting photometry or morphological analyses.
pyenv lets you easily switch between multiple versions of Python. It's simple, unobtrusive, and follows the UNIX tradition of single-purpose tools that do one thing well. pyenv allows to:
PySide is the Python Qt bindings project, providing access the complete Qt 4.8 framework as well as to generator tools for rapidly generating bindings for any C++ libraries.
Python is a programming language that lets you work more quickly and integrate your systems more effectively.
QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.
Qt is a cross-platform application framework that is widely used for developing application software that can be run on various software and hardware platforms with little or no change in the underlying code-base, while having the power and speed of native applications.
R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.
The ROOT system provides a set of frameworks with all the functionality needed to handle and analyse large amounts of data in a very efficient way. Having the data defined as a set of objects, specialized storage methods are used to get direct access to the separate attributes of the selected objects, without having to touch the bulk of the data. Included are histogram methods in an arbitrary number of dimensions, curve fitting, function evaluation, minimization, graphics and visualization classes to allow the easy setup of an analysis system that can query and process the data interactively or in batch mode, as well as a general parallel processing framework, that can considerably speed up an analysis.
RPFITS is used to record synthesis visibility data obtained from the Australia Telescope Compact Array (ATCA) at Narrabri, NSW. It is also used for single-dish spectral line data obtained from Parkes and Mopra, including Parkes multibeam data. While RPFITS superficially resembles random group FITS it differs in the following important respects:
RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
A dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
RUNZ (formerly: SRUN) is a "pseudo-new" way to run (and install) software on Linux (only Debian, Ubuntu and Super OS supported at the moment, but I plan to support as many Linux distros as possible).
SCAMP reads SExtractor catalogs and computes astrometric and photometric solutions for any arbitrary sequence of FITS images in a completely automatic way.
SExtractor is a program that builds a catalogue of objects from an astronomical image. Although it is particularly oriented towards reduction of large scale galaxy-survey data, it can perform reasonably well on moderately crowded star fields.
Shiboken is a plugin (front-end) for Generator Runner. It generates bindings for C++ libraries using CPython source code.
SNANA contains a light curve fitter and simulation that can be applied to any supernova (SN) model and to any data set.
SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++.
The DEIMOS pipeline software, contained in the spec2d package, was specifically designed for the purpose of reducing DEEP2 survey data. Considerable efforts were made by the DEEP2 team at UCB to generalize the pipeline for general mask designs and instrument setups. The success of the pipeline will undoubtedly vary depending on the choice of grating, the wavelength range of the data, and the slit-mask design specifications.
SQLite is a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine.
The Starlink Software Collection includes about 20 major packages covering a wide range of astronomical data reduction and analysis techniques. At the core of most of these packages is a common software environment which provides many of the functions which applications need, and offers standardised methods of structuring and accessing data.
Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.
Sublime Text is a sophisticated text editor for code, markup and prose.
SWarp is a program that resamples and co-adds together FITS images using any arbitrary astrometric projection defined in the WCS standard.
Texinfo is the official documentation format of the GNU project. Texinfo uses a single source file to produce output in a number of formats, both online and printed (dvi, html, info, pdf, xml, etc.). This means that instead of writing different documents for online information and another for a printed manual, you need write only one document. And when the work is revised, you need revise only that one document. The Texinfo system is well-integrated with GNU Emacs.
THELI is a tool for the automated reduction of astronomical images. It comes in two flavours which are maintained independently:
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
The UVES Pipeline as a subsystem of the VLT Dataflow is intended to be used by Paranal Science Operations (PSO) to assess the quality of the ongoing observations and to monitor the instrument’s health. On Paranal the pipeline does automatic data reduction using calibration and reference frames which are updated from time to time. This allows the observer to have a quick check of the ongoing observation to verify the S/N of the extracted spectrum, to detect a degradation of the performance of the instrument, to decide whether an observation has to be repeated, or to monitor the instrument’s health.
Vala is a new programming language that aims to bring modern programming language features to GNOME developers without imposing any additional runtime requirements and without using a different ABI compared to applications and libraries written in C.
Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools. The Valgrind distribution currently includes six production-quality tools: a memory error detector, two thread error detectors, a cache and branch-prediction profiler, a call-graph generating cache and branch-prediction profiler, and a heap profiler. It also includes three experimental tools: a stack/global array overrun detector, a second heap profiler that examines how heap blocks are used, and a SimPoint basic block vector generator.
The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. VASP computes an approximate solution to the many-body Schrödinger equation, either within density functional theory (DFT), solving the Kohn-Sham equations, or within the Hartree-Fock (HF) approximation, solving the Roothaan equations. Hybrid functionals that mix the Hartree-Fock approach with density functional theory are implemented as well. Furthermore, Green's functions methods (GW quasiparticles, and ACFDT-RPA) and many-body perturbation theory (2nd-order Møller-Plesset) are available in VASP.
Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set. It's useful whether you're already using vi or using a different editor.
VMD is designed for modelling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and colouring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyse the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
VNC enables you to remotely access and control your devices wherever you are in the world, whenever you need to.
Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles.
The VPFIT program enables you to fit multiple Voigt profiles (convolved with the instrument profiles) to spectroscopic data.
The FITS "World Coordinate System" (WCS) standard defines keywords and usage that provide for the description of astronomical coordinate systems in a FITS image header.
WCSTools is a package of programs and a library of utility subroutines for setting and using the world coordinate systems (WCS) in the headers of the most common astronomical image formats, FITS and IRAF .imh, to relate image pixels to sky coordinates.
'Xaw3d' is a general-purpose replacement for the Athena toolkit which adds a 3D appearance and support for XPM images.
xdvi is a program to display TeX .dvi files under the X Window System. It runs under Unix (and look-alikes) and possibly VMS.
XEmacs is a highly customizable open source text editor and application development system.
Yorick is an interpreted programming language for scientific simulations or calculations, post-processing or steering large simulation codes, interactive scientific graphics, and reading, writing, or translating large files of numbers. Yorick includes an interactive graphics package, and a binary file package capable of translating to and from the raw numeric formats of all modern computers.