Utilities

SBGrid supports 23 utilities software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title Description Linux 32-bit Linux 64-bit OS X Intel Links

a2ps

- an Any-to-PostScript filter. It processes plain text files, but also pretty prints quite a few popular languages.

 yes yes yes

  • an Any-to-PostScript filter. It processes plain text files, but also pretty prints quite a few popular languages.

Categories

Utilities

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid a2ps page.

BioPerl

- a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.

 yes yes yes

  • a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.

Categories

Utilities

Versions

Citations

Stajich et al. The Bioperl Toolkit: Perl modules for the life sciences. Genome Research. 2002. 12(10):1611-8.

License Type

This software is distributed under an Open license.


Static link to the SBGrid BioPerl page.

BioPython

- a set of tools for biological computation written in Python by an international team of developers.

 yes yes yes

  • a set of tools for biological computation written in Python by an international team of developers.

Categories

Utilities

Versions

Citations

Cock et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009. 25(11):1422-3.

License Type

This software is distributed under an Open license.


Static link to the SBGrid BioPython page.

EMBOSS

- integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

 yes yes yes

  • integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

Developers

Alan Bleasby

Peter Rice

Categories

Bioinformatics

Utilities

Versions

Citations

Olson. EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite. Briefings in bioinformatics (2002) vol. 3 (1) pp. 87-91

License Type

This software is distributed under an Open license.


Static link to the SBGrid EMBOSS page.

Ghostscript

- an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be ...

 yes yes yes

  • an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.

Categories

Utilities

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid Ghostscript page.

Gnuplot

- a portable command-line driven graphing utility originally created to allow scientists and students to visualize mathematical functions ...

 yes yes yes

  • a portable command-line driven graphing utility originally created to allow scientists and students to visualize mathematical functions and data interactively. It 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 CCP4.

Categories

Utilities

Versions

Citations

Williams and Kelley. Gnuplot 4.5: an interactive plotting program. 2011. URL http://gnuplot.info. (Last accessed: YEAR MONTH DAY)

License Type

This software is distributed under an Open license.


Static link to the SBGrid Gnuplot page.

Grace

- a general plotting, curve fitting and data trasformation program.

 yes yes

  • a general plotting, curve fitting and data trasformation program.

Categories

Utilities

Versions

Citations

No reference, please just refer website when citing: http://plasma-gate.weizmann.ac.il/Grace/

Technical Notes

Requires X11 on Mac OS X.

License Type

This software is distributed under an Open license.


Static link to the SBGrid Grace page.

Graphviz

- an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php

 yes yes yes

  • an open-source graph visualization software program. A gallery of images is available on the developer's website: http://www.graphviz.org/Gallery.php

Developers

Yifan Hu

Stephen North

John Ellson

Emden Gansner

Arif Bilgin

Graphviz

Categories

Utilities

Versions

Citations

Ellson et al. Graphviz and Dynagraph -- Static and Dynamic Graph Drawing Tools. in: Graph Drawing Software. 2004. eds:M. Junger and P. Mutzel. Springer-Verlag. 127-148.

License Type

This software is distributed under an Open license.


Static link to the SBGrid Graphviz page.

ImageJ

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It can ...

 yes yes yes

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

This installation includes the LOCI BioFormats plugin for reading and editing EM image stacks.

Categories

Electron Microscopy

Utilities

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid ImageJ page.

ImageMagick

- a software suite to create, edit, compose, or convert bitmap images.

 yes yes yes

  • a software suite to create, edit, compose, or convert bitmap images.

Categories

Utilities

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid ImageMagick page.

MGLTools

- a software package comprised of AutoDockTools (adt), Python Molecule Viewer (pmv) and a python programming environment called ...

 yes yes yes

  • a software package comprised of AutoDockTools (adt), Python Molecule Viewer (pmv) and a python programming environment called Vision. Developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures.

    AutoDockTools is graphical front-end for setting up and running AutoDock - an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

    PMV is a powerful molecular viewer that has a number of customizable features and comes with many pluggable commands ranging from displaying molecular surfaces to advanced volume rendering.

    Vision is a visual-programming environment in which a user can interactively build networks describing novel combinations of computational methods, and yielding new visualizations of their data without actually writing code.

Developers

Michael Sanner

Arthur Olson

Categories

Structure Visualization

Utilities

Versions

Citations

ADT: Sanner. Python: A Programming Language for Software Integration and Development. J. Mol. Graphics Mod. 1999. 17:57-61.

isocontour: Bajaj et al. Fast IsoContouring for Improved Interactivity, Proceedings of ACM Siggraph/IEEE Symposium on Volume Visualization, ACM Press, 1996, pages 39 - 46, San Francisco, CA

msms: Sanner et al. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 1996. 38(3):305-320.

PCVolRen: Bajaj et al. A Parallel Multi-PC Volume Rendering System, ICES and CS Technical Report, University of Texas, 2002.

Pmv: Sanner. Python: A Programming Language for Software Integration and Development. J. Mol. Graphics Mod. 1999. 17:57-61.

vision: Sanner et al. ViPEr a Visual Programming Environment for Python. 10th International Python Conference, February 2002.

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid MGLTools page.

NEdit

- a multi-purpose text editor for the X Window System, which combines a standard, easy to use, graphical ...

 yes yes yes

  • a multi-purpose text editor for the X Window System, which combines a standard, easy to use, graphical user interface with thorough functionality and stability.

Developers

NEdit Developers

Mark Edel

Joachim Lous

Categories

Utilities

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid NEdit page.

OpenBabel

- a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project ...

 yes yes yes

  • a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

Categories

Utilities

Versions

Citations

Guha et al. The Blue Obelisk -- Interoperability in Chemical Informatics. J. Chem. Inf. Model. 2006. 46(3) 991-998.

The Open Babel Package, version (xxx) http://openbabel.sourceforge.net/ (accessed Month Year)

License Type

This software is distributed under an Open license.


Static link to the SBGrid OpenBabel page.

PDB Validation Suite

- a set of tools used by the PDB for processing and checking structure data.

 yes yes

  • a set of tools used by the PDB for processing and checking structure data.

Developers

RCSB

Categories

2D Crystallography

Utilities

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid PDB Validation Suite page.

PHYLIP

- a free package of software programs for inferring phylogenies.

 yes yes yes

  • a free package of software programs for inferring phylogenies.

Developers

Joseph Felsenstein

Categories

Bioinformatics

Utilities

Versions

Citations

Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle. or Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.

Technical Notes

How to cite:

Felsenstein, J. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

or if the editor for whom you are writing insists that the citation must be to a printed publication, you could cite a notice for version 3.2 published in Cladistics:

Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166

License Type

This software is distributed under a Non-Profit license.


Static link to the SBGrid PHYLIP page.

pipe2xeasy

- performs conversions of spectra from NMRPipe to XEASY format. pipe2xeasy can read the ASCII file with header ...

 yes yes yes

  • performs conversions of spectra from NMRPipe to XEASY format. pipe2xeasy can read the ASCII file with header information, which is produced with "showhdr -verb filename".

Developers

Ralf Glaser

Categories

Utilities

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid pipe2xeasy page.

POVRAY

- (Persistence of Vision Raytracer) is a high-quality, totally free tool for creating stunning three-dimensional graphics. It is ...

 yes yes yes

  • (Persistence of Vision Raytracer) is a high-quality, totally free tool for creating stunning three-dimensional graphics. It is available in official versions for Windows, Mac OS/Mac OS X and i86 Linux. The source code is available for those wanting to do their own ports. POVRAY was originally written by David Kirk Buck and Aaron A. Collins.

Categories

Utilities

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid POVRAY page.

Probe

- an application to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms ...

 yes yes yes

  • an application to evaluate atomic packing, either within or between molecules. It generates “contact dots” where atoms are in close contact. Probe reads atomic coordinates from protein databank (PDB) format files and writes dot-lists for inclusion in a kinemage file.

Developers

Jane Richardson

David Richardson

Categories

Structure Analysis

Utilities

Versions

Citations

Word et al. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. Journal of molecular biology (1999) vol. 285 (4) pp. 1711-33

License Type

This software is distributed under an Open license.


Static link to the SBGrid Probe page.

Python

- a programming language that lets you work more quickly and integrate your systems more effectively. You can ...

 yes yes yes

  • a programming language that lets you work more quickly and integrate your systems more effectively. You can learn to use Python and see almost immediate gains in productivity and lower maintenance costs. Several versions are included to support various applications.

Categories

Utilities

Versions

Citations

First publication, but quite outdated according to website: van Rossum and de Boer. Interactively Testing Remote Servers Using the Python Programming Language. CWI Quarterly. 1991. 4 (4):283-303.

License Type

This software is distributed under an Open license.


Static link to the SBGrid Python page.

R

- a free software environment for statistical computing and graphics.

 yes yes yes

  • a free software environment for statistical computing and graphics.

Categories

Utilities

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid R page.

ULTRASCAN2

- a software package offering comprehensive analysis of hydrodynamic data from analytical ultracentrifugation experiments.

 yes yes yes

  • a software package offering comprehensive analysis of hydrodynamic data from analytical ultracentrifugation experiments.

Developers

Borries Demeler

Categories

Utilities

Versions

Citations

Demeler et al. Characterization of reversible associations by sedimentation velocity with UltraScan. Macromol Biosci. 2010. 10(7):775-82.

Demeler et al. Analysis of heterogeneity in molecular weight and shape by analytical ultracentrifugation using parallel distributed computing. Methods Enzymol. 2009. 454:87-113.

Technical Notes

Each user has to register separately and then place the license file in their home directory. Ultrascan License Request

License Type

This software is distributed under an Open license.


Static link to the SBGrid ULTRASCAN2 page.

ULTRASCAN3

- the latest multi-platform version of UltraScan, which is has now replaced the UltraScan II distribution. All users ...

 yes yes

  • the latest multi-platform version of UltraScan, which is has now replaced the UltraScan II distribution. All users are encouraged to switch to UltraScan III for any new installations, since this software will be actively maintained, while UltraScan II development has stopped, although UltraScan II will continue to be available. Please note that if you want to view legacy data from UltraScan II, you will still need to install UltraScan II, since UltraScan III is not backward compatible with UltraScan II.

Developers

Borries Demeler

Categories

Utilities

Versions

Citations

Demeler et al. Characterization of reversible associations by sedimentation velocity with UltraScan. Macromol Biosci. 2010. 10(7):775-82.

Demeler et al. Analysis of heterogeneity in molecular weight and shape by analytical ultracentrifugation using parallel distributed computing. Methods Enzymol. 2009. 454:87-113.

License Type

This software is distributed under an Open license.


Static link to the SBGrid ULTRASCAN3 page.

XDrawChem

- a two-dimensional molecule drawing program for Unix operating systems that can read and write MDL Molfiles, and ...

 yes yes

  • a two-dimensional molecule drawing program for Unix operating systems that can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.

Developers

Brian Herger

Categories

Utilities

Versions

License Type

This software is distributed under an Open license.


Static link to the SBGrid XDrawChem page.