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'contrib/science' section (2/1)


Astrometry.net 2MASS index files downloader (22'-30')

The astrometry engine will take any image and return the astrometry world coordinate system (WCS), a standards-based description of the transformation between image coordinates and sky coordinates. . This package downloads the 4207 index files from the 2MASS survey containing skymarks of sizes 22 arcminutes to 30 arcminutes from data.astrometry.net. The installation requires a working internet connection.


Astrometry.net 2MASS index files downloader (30'-2000')

The astrometry engine will take any image and return the astrometry world coordinate system (WCS), a standards-based description of the transformation between image coordinates and sky coordinates. . This package downloads the 4208-4219 index files from the 2MASS survey containing skymarks of sizes 30 arcminutes to 2000 arcminutes from data.astrometry.net. The installation requires a working internet connection.


Astrometry.net 2MASS index files downloader (2.8'-4')

The astrometry engine will take any image and return the astrometry world coordinate system (WCS), a standards-based description of the transformation between image coordinates and sky coordinates. . This package downloads the 4201 index files from the 2MASS survey containing skymarks of sizes 2.8 arcminutes to 4 arcminutes from data.astrometry.net. The installation requires a working internet connection.


Astrometry.net 2MASS index files downloader

The astrometry engine will take any image and return the astrometry world coordinate system (WCS), a standards-based description of the transformation between image coordinates and sky coordinates. . This package downloads all index files built from the 2MASS survey. The installation requires a working internet connection.


Astrometry.net 2MASS index files downloader (8'-11')

The astrometry engine will take any image and return the astrometry world coordinate system (WCS), a standards-based description of the transformation between image coordinates and sky coordinates. . This package downloads the 4204 index files from the 2MASS survey containing skymarks of sizes 8 arcminutes to 11 arcminutes from data.astrometry.net. The installation requires a working internet connection.


Astrometry.net 2MASS index files downloader (2'-2.8')

The astrometry engine will take any image and return the astrometry world coordinate system (WCS), a standards-based description of the transformation between image coordinates and sky coordinates. . This package downloads the 4200 index files from the 2MASS survey containing skymarks of sizes 2 arcminutes to 2.8 arcminutes from data.astrometry.net. The installation requires a working internet connection.


Astrometry.net 2MASS index files downloader (11'-16')

The astrometry engine will take any image and return the astrometry world coordinate system (WCS), a standards-based description of the transformation between image coordinates and sky coordinates. . This package downloads the 4205 index files from the 2MASS survey containing skymarks of sizes 11 arcminutes to 16 arcminutes from data.astrometry.net. The installation requires a working internet connection.


Astrometry.net 2MASS index files downloader (16'-22')

The astrometry engine will take any image and return the astrometry world coordinate system (WCS), a standards-based description of the transformation between image coordinates and sky coordinates. . This package downloads the 4206 index files from the 2MASS survey containing skymarks of sizes 16 arcminutes to 22 arcminutes from data.astrometry.net. The installation requires a working internet connection.


Astrometry.net 2MASS index files downloader (4'-5.6')

The astrometry engine will take any image and return the astrometry world coordinate system (WCS), a standards-based description of the transformation between image coordinates and sky coordinates. . This package downloads the 4202 index files from the 2MASS survey containing skymarks of sizes 4 arcminutes to 5.6 arcminutes from data.astrometry.net. The installation requires a working internet connection.


Astrometry.net 2MASS index files downloader (5.6'-8')

The astrometry engine will take any image and return the astrometry world coordinate system (WCS), a standards-based description of the transformation between image coordinates and sky coordinates. . This package downloads the 4203 index files from the 2MASS survey containing skymarks of sizes 5.6 arcminutes to 8 arcminutes from data.astrometry.net. The installation requires a working internet connection.

/contrib/bart-cuda/bart-cuda

tools for computational magnetic resonance imaging

The Berkeley Advanced Reconstruction Toolbox (BART) is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging. It consists of a programming library and a toolbox of command-line programs. The library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms. The command-line tools provide direct access to basic operations on multi-dimensional arrays as well as efficient implementations of many calibration and reconstruction algorithms for parallel imaging and compressed sensing. . This package provides BART with CUDA support.

/contrib/bcbio/bcbio

toolkit for analysing high-throughput sequencing data

This package installs the command line tools of the bcbio-nextgen toolkit implementing best-practice pipelines for fully automated high throughput sequencing analysis. . A high-level configuration file specifies inputs and analysis parameters to drive a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The project contributes a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology. . This package builds and having it in Debian unstable helps the Debian developers to synchronize their efforts. But unless a series of external dependencies are not installed manually, the functionality of bcbio in Debian is only a shadow of itself. Please use the official distribution of bcbio for the time being, which means "use conda". The TODO file in the Debian directory should give an overview on progress for Debian packaging.


Bayesian MCMC phylogenetic inference

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Included is a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.


biological data-bank updater - web interface

BioMAJ downloads remote data banks, checks their status and applies transformation workflows, with consistent state, to provide ready-to-use data for biologists and bioinformaticians. For example, it can transform original FASTA files into BLAST indexes. It is very flexible and its post-processing facilities can be extended very easily. . BioMAJ watcher provides a management interface for the BioMAJ tool. It runs in a web container (Tomcat) and is accessible under the URL http://hostname:portnumber/BmajWatcher . The web interface can give anonymous users an overview of available data. Administrators can also use it to manage data-banks, schedule updates via cron, view error logs, or use the integrated data-bank properties editor.


Tools for fast, open framework for Deep Learning (CUDA)

Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors. . It contains caffe executables, configured with CUDA.


ESO data reduction pipeline calibration data downloader for AMBER

This package downloads calibration data of the data reduction pipeline for the AMBER instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO).


ESO data reduction pipeline calibration data downloader for FORS2

This package downloads calibration and other static data of the data reduction pipeline for the FORS2 instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO).


ESO data reduction pipeline calibration data downloader for GIRAFFE

This package downloads calibration data of the data reduction pipeline for the GIRAFFE instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO).


ESO data reduction pipeline calibration data downloader for HAWK-I

This package downloads calibration data of the data reduction pipeline for the HAWK-I instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO).


ESO data reduction pipeline calibration data downloader for KMOS

This package downloads calibration and other static data of the data reduction pipeline for the KMOS instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO). . The K-band Multi Object Spectrograph (KMOS) is a second-generation instrument designed for operation on the VLT. The key feature of KMOS is its ability to perform Integral Field Spectroscopy in the near-infrared bands for 24 targets simultaneously.


ESO data reduction pipeline calibration data downloader for MUSE

This package downloads calibration and other static data of the data reduction pipeline for the Muse instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO). . MUSE, the Multi-Unit Spectroscopic Explorer, is an Integral Field Spectrograph located at the Nasmyth B focus of Yepun, the VLT UT4 telescope. It has a modular structure composed of 24 identical IFU modules that together sample, in Wide Field Mode (WFM), a near-contiguous 1 squared arcmin field of view. Spectrally the instrument samples almost the full optical domain with a mean resolution of 3000. Spatially, the instrument samples the sky with 0.2 arcseconds spatial pixels in the currently offered Wide Field Mode with natural seeing (WFM-noAO).


ESO data reduction pipeline NaCo calibration data downloader

This package downloads calibration and other static data of the data reduction pipeline for the NaCo instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO). . NaCo is short for NAOS-CONICA. It was installed at the Nasmyth B focus of UT4 from 2001 through 2013. In 2014 it was reinstalled on UT1 at the Nasmyth A. It provides adaptive optics assisted imaging, imaging polarimetry, coronography and spectroscopy, in the 1-5 micron range.


ESO data reduction pipeline calibration data downloader for SINFONI

This package downloads calibration data of the data reduction pipeline for the SINFONI instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO).


ESO data reduction pipeline calibration data downloader for UVES

This package downloads calibration and other static data of the data reduction pipeline for the UVES instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO).


ESO data reduction pipeline calibration data downloader for VIMOS

This package downloads calibration and other static data of the data reduction pipeline for the VIMOS instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO).


ESO data reduction pipeline calibration data downloader for VISIR

This package downloads calibration and other static data of the data reduction pipeline for the Visir instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO). . The VLT spectrometer and imager for the mid-infrared (VISIR) was built by CEA/DAPNIA/SAP and NFRA/ASTRON, and is located at the Cassegrain focus of UT3. It provides diffraction-limited imaging at high sensitivity in the two mid infrared (MIR) atmospheric windows: the N band between 8 to 13μm and the Q band between 16.5 and 24.5μm, respectively. In addition, it features a long-slitspectrometer with a range of spectral resolutions between 150 and 30000.


ESO data reduction pipeline calibration data downloader for XSHOOTER

This package downloads calibration and other static data of the data reduction pipeline for the XSHOOTER instrument of the Very Large Telescope (VLT) from the European Southern Observatory (ESO).

/contrib/doris/doris

Delft object-oriented radar interferometric software

DORIS is an Interferometric Synthetic Aperture Radar (InSAR) processor developed by the Delft Institute of Earth Observation and Space Systems of Delft University of Technology. . Interferometric products and endproducts such as Digital Elevation Models and displacement maps can be generated with this software from Single Look Complex data. Data from the satellites ERS, ENVISAT (first ENVISAT interferogram, DEM, and perspective view, JERS (first JERS interferogram), and RADARSAT (first RADARSAT interferogram) can be processed with the Doris software.

/contrib/horae/horae

interactive graphical processing and analysis of EXAFS data

ATHENA is an interactive graphical utility for processing EXAFS data. It handles most of the common data handling chores of interest, including deglitching, aligning, merging, background removal, and Fourier transforms. . ARTEMIS is an interactive graphical utility for fitting EXAFS data using theoretical standards from FEFF and sophisticated data modelling along with flexible data visualization and statistical analysis. . HEPHAESTUS is a souped up periodic table for the x-ray absorption spectroscopist. It provides a number of utilities involving tables of absorption coefficients and other chemical data.

/contrib/ifeffit/ifeffit

Interactive XAFS analysis program

IFEFFIT is an interactive program for XAFS analysis. It combines the high-quality analysis algorithms of AUTOBK and FEFFIT with graphical display of XAFS data and general data manipulation. . IFEFFIT comes as a command-line program, but the underlying functionality is available as a programming library. The IFEFFIT library can be used from C, Fortran, Tcl, Perl, and Python. This allows a variety of user interfaces (both graphical and non-graphical) to be written around IFEFFIT. Currently, three graphical user interfaces: G.I.FEFFIT, ATHENA/ARTEMIS, and SIXPACK are built on the underlying IFEFFIT library. IFEFFIT and all three GUIs are under active development, but are fairly well tested and ready for use.