:: DESCRIPTION
OSCAR (Open Source Cluster Application Resources) is a snapshot of the best known practices for building, programming and using a cluster. The toolkit is geared towards a modest sized cluster (50+ nodes) and features a wizard-based GUI for cluster installation.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The SPADE provides community tools for development and deployment of essential structure and sequence equipment. Includes a chemical probing suite to support experimental verification of predicted structural models.
:: SCREENSHOTS
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Deacon J. Sweeney, Gerald M. Alter, and Michael L. Raymer
Introducing SPADE, the Structural Proteomics Application Development Environment.
Ohio Collaborative Conference on Bioinformatics (OCCBIO), 2-4 June 2008, University of Toledo.
:: DESCRIPTION
Molecules is an application for the iPhone, iPod touch, and now iPad that allows you to view three-dimensional renderings of molecules and manipulate them using your fingers. You can rotate the molecules by moving your finger across the display, zoom in or out by using two-finger pinch gestures, or pan the molecule by moving two fingers across the screen at once.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The Maxit Program Suite was developed by the PDB (Protein Data Bank) and NDB (Nucleic Acid Database) to assist in the processing and curation of macromolecular structure data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
CellExplorer is a package of computer programs to process and analyze 3D confocal image stacks of the model animal C. elegans, and can be applied to several other model systems such as fruit fly embryo/larvae as well. Some other applications include 3D cell/nuclei segmentation, quantification, gene expression analysis, automatic cell naming/annotation, cell targeting, etc.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart Kim, and Eugene Myers,
“A 3D digital atlas of C. elegans and its application to single-cell analyses,”
Nature Methods, doi:10.1038/nmeth.1366, 2009.
:: DESCRIPTION
OpenMM Zephyr is a molecular simulation application for studying molecular dynamics of proteins, RNA, and other molecules. Zephyr guides the user through a work flow for setting up and running a specialized version of the molecular dynamics application gromacs. This version of gromacs uses the OpenMM API for GPU-accelerated molecular simulations.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande.
“Accelerating Molecular Dynamic Simulation on Graphics Processing Units.”
J. Comp. Chem., 30(6):864-872 (2009)
:: DESCRIPTION
iMol is a free molecular visualization application for Mac OS X operating system. The program is an indispensable tool for chemists and molecular biologists. iMol supports several file formats. It can easily handle small and large molecules, loads multiple molecules, can move and rotate them independently, or displays a molecular dynamics trajectory.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
If you are using iMol in your research, please cite:
Piotr Rotkiewicz, “iMol Molecular Visualization Program,” (2007) http://www.pirx.com/iMol
