ScalaBLAST is a high-performance multiprocessor implementation of the NCBI BLAST library. It supports all 5 primary program types (blastn, blastp, tblastn, tblastx, and blastx) and several output formats (pairwise, tabular, and XML). It will run on most multiprocessor systems which have MPI installed, and can run over a wide variety of interconnects, including infiniband, quadrics, and ethernet. It is designed to run a large number of queries against either large or small databases. It parallelizes the BLAST calculations by dynamically scheduling them across processors using a fault-resilient scheme.
View3D is a program to calculate radiation view factors, as used in radiant heat transfer problems in mechanical engineering, building design, furnace design, etc. Data input is via text file. There are 3D and 2D viewers for checking your input. View factors are output to another file for use with other calculation tools. View factors are also sometimes called "shape factors", "configuration factors", and "form factors".
The NCBI C++ Toolkit provides portable libraries and applications for assisting genetic science. These include libraries for networking, SQL and BerkeleyDB access, CGI and HTML handling, ASN.1 and XML handling, sequence alignment engines, sequence retrieval engines, BLAST database engines, FLTK and OpenGL graphics toolkits, and basic system utilities.
jHepWork (jWork) is an environment for scientific computation, data analysis, and data visualization for scientists, engineers, and students. The program is fully multi-platform (written in Java). Programs can be written in the Java, Jython/Python, and BeanShell scripting languages. Matlab/Octave is supported for symbolic calculations. The program can be used to display data and functions in D and 3D. It comes with a friendly IDE and a code assist.
Parallel Three-Dimensional Fast Fourier Transforms, dubbed P3DFFT, is a library for computing 3D FFTs using 2D (pencil) decomposition. It is written using Fortran with MPI, and is tuned to work on multiple single-CPU systems (up to 32768 of them). It is built to leverage high-performance serial 1D FFT libraries, such as FFTW or ESSL.
PHAML is a parallel program for the solution of 2D elliptic partial differential equations using low or high order finite elements, adaptive mesh refinement based on newest node bisection of triangles, and multigrid. All aspects of the method are based on the hierarchical basis functions.