- Drug Discovery and Development
- Health Care
- Physiological modelling
- Product Safety
- mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems.
- MPI-HMMER is an open source MPI implementation of the HMMER protein sequence analysis suite. The main search algorithms, hmmpfam and hmmsearch, have been ported to MPI in order to provide high throughput HMMER searches
HPC Domains and their Applications
Sequential Applications (Farm)
These applications run on a single core. While they may not be parallel (use multiple cores) the end user may run many copies of the same program with different input parameters. This type of computing is often called parametric processing. These types of programs can be written in any type of computer language.
Threaded Applications (SMP-Server)
These applications use multiple cores, but only on one SMP node. Most of these programs are written using C/C++ or Fortran and use pthreads or OpenMP - As core counts increase many HPC users are taking advantage of this approach.
Parallel Applications (Cluster)
These applications are written to use multiple cores across many nodes. They are mostly written in Fortran or C/C++ and use MPI as way to send messages between nodes.
While these may not be "parallel applications", they assist in visualizing results from some of the applications mentioned.
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.
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
OpenDX (Open Data eXplorer) gives you new control over your data and new insights into their meaning. Yet OpenDX is easy to use because it lets you visualize data in ways you've never dreamed of -- without getting bogged down in the technology. If you need visualization for anything from examining simple data sets to analyzing complex, time-dependent data from disparate sources, OpenDX has what you need: features and functions that let you easily gain meaningful insight into your data.