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.
The National Library of Medicine Insight Segmentation and Registration Toolkit (ITK) is a software system to support the Visible Human Project. Segmentation is the process of identifying and classifying data found in a digitally sampled representation. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be aligned with an MRI scan in order to combine the information contained in both.
Electron Gamma Shower (EGS) is a general purpose package for the Monte Carlo simulation of the coupled transport of electrons and photons in an arbitrary geometry for particles with energies from a few keV up to several TeV. Simulations can be performed in arbitrarily complex physical geometries, and a wide range of physical processes are modeled.
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.
GATE is a software package dedicated to numerical simulations in medical imaging and radiotherapy. It supports simulations of Emission Tomography (Positron Emission Tomography (PET) and Single Photon Emission Computed Tomography (SPECT)), Computed Tomography (CT), and Radiotherapy experiments. It makes it easy to use existing Monte Carlo simulation packages according to the requirements of a simulation. It allows accurate description of time-dependent phenomena such as source or detector movement and source decay kinetics. It includes well-validated physics models, geometry modeling tools accommodating complex scanner geometries, models for detector electronic response, and efficient visualization utilities. Modelling of CT scans and calculation of dose can also be performed.
Raster3D is a set of powerful tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm that is independent of any graphics hardware.
Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input, score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation. Building the local genealogy trees is based on a number of heuristics that are not guaranteed to build true trees, but have the advantage over more sophisticated methods of being extremely fast. Blossoc can therefore handle much larger data sets than more sophisticated tools, but at the cost of sacrificing some accuracy.
HapCluster++ is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. HapCluster++ is a C++ implementation of the method described in the paper "Fine Mapping of Disease Genes via Haplotype Clustering" by E.R.B. Waldron, J.C. Whitaker, and D.J. Balding. Genetic Epidemiology. 30: 170–179. (2006).