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Applications glossary for Condor

  • Applications on Condor

  • Compilers on Condor

  • Libraries on Condor

  • Tools on Condor

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     Applications on Condor

     Arlequin: a software for population genetics data analysis

    Arlequin is an exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data). 

    A variety of population genetics methods has been implemented either at the intra-population or at the inter-population level, and they can be conveniently selected and parameterized through a graphical interface. Arlequin has no equivalent in this field and will be extremely useful to analyze the large data sets which are now available by the use of the latest molecular engineering techniques.

    Version: 3.5.1.2

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA for BIOSI > Arlequin

     


     Figtree 1.3.1: a graphical viewer of phylogenetic trees

     Figtree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of Andrew Rambaut's programs, it was written for his own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.

    Version: 1.3.1

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA for BIOSI > Figtree

     

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     IMa2: Generating posterior probabilities for complex demographic models

     The program implements a method for generating posterior probabilities for complex demographic population genetic models. IMa2 works similarly to the older IMa program, with some important additions. IMa2 can handle data and implement a model for multiple populations (for numbers of sampled populations between one and ten) – not just two populations (as was the case with the original IM and IMa programs). The method for multiple populations is described in two papers (Hey 2010b, a).

     Version: 6.3.10

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA for BIOSI > IMa2

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  •  Microsoft Visual Studio: integrated development environment

    Visual Studio is a comprehensive, high productivity professional development environment (for developers working alone or in small teams) for building high performance, multi-tier applications for Windows, the Web, and mobile devices.

    Version: 2005

    Version: 2008

    License: Microsoft Select Agreement

    Application: Start > Networked Applications > Departmental Software > ARCCA > Microsoft

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  •  MinSpNet: computes a minimum spanning network among a set of OTUs

    Version: 1993

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA for BIOSI > MinSpNet

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  •  NewHybrids

     This implements a Gibbs sampler to estimate the posterior probability that genetically sampled individuals fall into each of a set of user-defined hybrid categories. The method is described in Anderson, E.C. and Thompson, E.A. (2002). A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160: 1217-1229.

    Version: 1.1b3

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA for BIOSI > NewHybrids

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  •  ParaView: a turnkey visualization system

     ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.

    Version: 3.8.0

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > Paraview

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  •  PuTTY: A client program for the SSH protocol

     The SSH protocol is used to run a remote session on a computer, over a network. PuTTY implements the client end of that session: the end at which the session is displayed, rather than the end at which it runs. In really simple terms: you run PuTTY on a Windows machine, and tell it to connect to (for example) a Unix machine. PuTTY opens a window. Then, anything you type into that window is sent straight to the Unix machine, and everything the Unix machine sends back is displayed in the window. So you can work on the Unix machine as if you were sitting at its console, while actually sitting somewhere else.

    Version: 0.60

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > Putty

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  •  PyMOL: a molecular visualization system

     PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is well suited to producing high quality 3D images of small molecules and biological macromolecules such as proteins. According to the author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL. PyMOL is one of few open source visualization tools available for use in structural biology. The 'Py' portion of the software's name refers to the fact that it extends, and is extensible by the Python programming language.

    Version: 0.99rc6

    License: Free for 0.99rc6, Commercial for later versions

    Application: Start > Networked Applications > Departmental Software > ARCCA > Pymol

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  •  R: statistical computing and graphics

    R is an integrated suite of software facilities for data manipulation, calculation and graphical display. Among other things it has an effective data handling and storage facility; a suite of operators for calculations on arrays, in particular matrices; a large, coherent, integrated collection of intermediate tools for data analysis; graphical facilities for data analysis and display either directly at the computer or on hardcopy; and a well developed, simple and effective programming language (called 'S') which includes conditionals, loops, user defined recursive functions and input and output facilities. (Indeed most of the system supplied functions are themselves written in the S language.)

    Version: 2.11.1

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > R

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  •  VisIt: a turnkey visualization system

    VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes. VisIt was designed to handle very large data set sizes in the terascale range and yet can also handle small data sets in the kilobyte range.

    Version: 2.0.1

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > Visit

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  •  VMD (Visual Molecular Dynamics): a turnkey visualization system

    VMD is designed for modeling, 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 coloring 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 analyze 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.

    Version: 1.8.7

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > VMD

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  •  WinSCP: a file transfer program for the SSH protocol

    WinSCP is an open source free SFTP client and FTP client for Windows. Legacy SCP protocol is also supported. Its main function is safe copying of files between a local and a remote computer.  The first interface  is based on Norton Commander and similar file managers. The interface displays a local folder in the left panel and a remote folder in the right panel. Most of the time, you’ll transfer files between these folders, though you can also transfer files to a different folder. The second interface is similar to Windows Explorer, and you only see the remote folder.

    Version: 4.2.8

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > Winscp

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  •  Xming: an X11 client for Microsoft Windows

     Xming is the leading X Window Server for Microsoft XP/Vista/Windows7. It is fully featured, lean, fast, current, simple to install and because it is standalone native Microsoft Windows®, easily transported portable as a pocket X server.

     Xming is totally secure when used with SSH and optionally includes an enhanced PuTTY Link SSH client and a portable PuTTY replacement package. Xming can work completely independent of the Window's registry when used with Xming-portablePuTTY. 

    Version: 6.9.0.31

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > Xming

     

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     Zeiss Image Browser: a browser for images from Zeiss Laser Scanning Microscopes

     The Zeiss LSM Image Browser can be used for

    •  Viewing, comparing, sorting and printing LSM 5 images
    •  Presenting LSM 5 images in the gallery, form or table mode in the LSM 5 database
    •  Changing image contrast and brightness
    •  Displaying LSM 5 images in superimposed and split image mode
    •  Displaying up to 8 channels simultaneously
    •  Assigning each channel a predefined color
    •  Set zoom (automatic fit, resize and zoom factors in power-of-two steps)
    •  Presenting stack animations at variable frame rates and with variable start and end image
    •  Displaying individual slices of a stack by the slice function
    •  Presenting a stack in gallery mode with Z section information
    •  Exporting and importing images to/from multiple file formats

    Version: 4.2.0.121

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > Zeiss

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  •  Compilers on Condor

     ActivePerl: a Perl implementation for Windows

    ActivePerl is the industry-standard, commercial-grade Perl distribution used by millions of developers around the world for easy Perl installation and quality-assured code. ActivePerl comes pre-compiled for out-of-the-box installation and includes core Perl binaries, popular modules, the Perl Package Manager (PPM) and complete documentation. Whether you're using Perl for mission-critical applications or open source projects, ActivePerl offers significant time savings over open source Perl for installing, removing, upgrading, and managing common Perl modules.

    Version: 5.10.1.1007

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > Activestate

     

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     ActivePython: a python implementation for Windows

     ActivePython is the industry-standard, commercial-grade Python distribution used by millions of developers around the world for easy Python installation and quality-assured code. ActivePython comes precompiled for out-of-the-box installation and includes core python binaries, popular modules, the Python Package Manager (PyPM) and complete documentation. Whether you're using Python for mission-critical applications or open source projects, ActivePython offers significant time savings over open source Python for installing, removing, upgrading, and managing common Python modules. ActivePython comes in different editions to satisfy the spectrum of users - from large enterprises running Python on distributed or critical applications to community developers building open source applications.

    Version: 2.6.5.14

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > Activestate

     

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     Gnu Compiler Collection: a suite of compilers, a profiler, and a debugger for Windows

     Equation Solution provides builds of Fortran, C and C++ compilers for Windows for download. Equation Solution build the compilers from GCC. gFortran, gcc and g++ are high performance compilers, and absolutely free under General Public License. Binaries distributed by Equation Solution are a variant of GCC. Distributions of Equation Solution have independent settings. The major change is the library to support parallel processing has been replaced. The compilers support OpenMP, for multiple-core and multiple-processor computers. Distribution v4.3 supports OpenMP v2.5, and distribution v4.4 or latest version supports OpenMP v3.0. 

    Version: 4.5.0

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > Gcc

     

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     Intel C++ and Fortran Compilers: commercial C++ and Fortran compilers for Windows

     Intel® Professional Edition Compilers include advanced optimization features, multithreading capabilities, and support for Intel® processors and compatible processors. They also provide highly optimized performance libraries for creating multi-threaded applications. Each compiler delivers advanced capabilities for development of application parallelism and winning performance for the full range of Intel® processor-based platforms. Each includes advanced optimization and multi-threading features as well as automatic processor dispatch, vectorization, and loop unrolling.

    Version: 10.1

    Version: 11.1

    License: Commercial

    Application: Start > Networked Applications > Departmental Software > ARCCA > Intel

     

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     Portland C++ and Fortran Compilers: commercial C++ and Fortran compilers for Windows

     The suite includes The Portland Group's native parallelizing/optimizing FORTRAN 77, Fortran 90/95/03 and HPF compilers for 64-bit x64 and 32-bit x86 processor-based Linux, Apple Mac OS X and Microsoft Windows workstations. PGI Fortran Workstation provides the features, quality, and reliability necessary for developing and maintaining advanced scientific and technical applications. The suite also includes The Portland Group's native parallelizing/optimizing OpenMP C++ and ANSI C compilers. The C++ compiler closely tracks the proposed ANSI standard and is compatible with cfront versions 2 and 3. All C++ functions are compatible with Fortran and C functions, so you can compose programs from components written in all three languages.

    Version: 8.06

    Version: 10.1

    Version: 10.6

    License: Commercial

    Application: Start > Networked Applications > Departmental Software > ARCCA > Portland

     

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     Libraries on Condor

      Intel Math Kernel Library: commercial math libraries for Windows

     Intel® Math Kernel Library (Intel® MKL) is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Offering performance optimizations for current and next-generation Intel® processors, it includes improved integration with Microsoft Visual Studio*, Eclipse*, and XCode*. Intel MKL allows for full integration of the Intel Compatibility OpenMP* run-time library for greater Windows*/Linux* cross-platform compatibility.

    Version: 10.0

    Version: 10.2

    License: Commercial

    Application: Start > Networked Applications > Departmental Software > ARCCA > Intel

     

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     Tools on Condor

     Sysinternals: a suite of diagnostic applications

    Depends allows you to check an executable file for DLL dependencies. Diskmon allows you to monitor all disk activity on a system. Filemon also allows you to monitor disk activity but it also tells you which files are read from and written to and by which process. Procmon tells you which processes are running, and Regmon tells you which processes are reading from and writing to the system registry.

    License: Free

    Application: Start > Networked Applications > Departmental Software > ARCCA > Sysinternals