Virtual Token Descriptor for eXtensible Markup Language (VTD-XML) refers to a collection of efficient XML processing technologies centered around a non-extractive XML parsing technique called Virtual Token Descriptor (VTD). Depending on the perspective, VTD-XML can be viewed as either an XML parser, a native XML indexer or a file format that uses binary data to enhance the text XML, an incremental XML content modifier, an XML slicer/splitter/assembler, or an XML editor/eraser.
Emergent is a neural network simulator with a built-in scripting language which allows for the creation and analysis of complex, sophisticated models of the brain in the world. Networks and all of their state variables are visually inspected in 3D, allowing quick "visual regression" of network dynamics and robot behavior. Emergent is a direct descendant of the PDP and PDP++ neural network packages.
VULCAN (Viscous Upwind aLgorithm for Complex flow ANalysis) offers computational fluid dynamics for subsonic speed through hypersonic turbulent reacting and non-reacting flows on a variety of serial and parallel computational platforms. The computational cost of propulsion flow analysis is reduced through the use of special turbulent wall treatments, multi-grid methods for elliptic and space marching schemes, and conditioning of the governing equations to reduce numerical stiffness. Physical modeling capabilities are improved through the inclusion of models for compressibility, Reynolds stress anisotropies, turbulent diffusivity, finite rate chemistry, and turbulence/chemistry interaction effects. VULCAN can simulate two-dimensional, three-dimensional, or axi-symmetric multi-block problems.
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.
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.
REMITT Electronic Medical Information Translation and Transmission is a standalone electronic medical billing solution. It works independent of any specific electronic medical record (EMR) or practice management (PM) system, and can interface with any EMR or PM system that implements its API. The first system to do so is FreeMED.
FreeMED is a Web-based medical records (EMR) and patient management system with a printing system, patient scheduling, an HL7 interface, a billing system, XML-RPC Web services, and many other features. It has an extensible modular architecture, allowing it to be customized based on individual practices without having to rewrite core components of the system. It is HIPAA compliant.
CGAL, the Computational Geometry Algorithms Library, is a large C++ library of geometric data structures and algorithms such as Delaunay triangulations, mesh generation, Boolean operations on polygons, and various geometry processing algorithms. CGAL is used in various areas: computer graphics, scientific visualization, computer aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning, and numerical methods.
BLAST is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. It uses a heuristic algorithm which seeks local as opposed to global alignments, and is therefore able to detect relationships among sequences which share only isolated regions of similarity. It can be run locally as a full executable, and can be used to run BLAST searches against private, local databases, or downloaded copies of the NCBI databases. It runs on Mac OS, Win32, LINUX, Solaris, IBM AIX, SGI, Compaq OSF, and HP- UX systems.