BALLView is an extensible viewer for bio-molecular structures. It provides all standard models and offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER, CHARMM, and MMFF94 force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, secondary structure calculation, molecular editing and docking. Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code. In addition, it provides a Python interface with Integrated Development Environment features to allow interactive rapid prototyping.
Brook for GPUs is a compiler and runtime implementation of the Brook stream programming language for modern graphics hardware. The goals for this project are to demonstrate general purpose programing on GPUs, to provide a useful tool for developers who want to run applications on GPUs, and to research the stream language programming model, streaming applications, and system implementations.
CellProfiler is a system for analyzing cell images. It is designed for biologists without training in computer vision or programming to make quantitative measurements of cells in thousands of images automatically. It is implemented using Matlab, but compiled standalone versions are available.
Engauge Digitizer is digitizing software that converts an image showing a graph or map into numbers. The image file can come from a scanner, digital camera, or screenshot. The numbers can be read on the screen, and written or copied to a spreadsheet. Highlights for beginners include an intuitive interface and extensive context-sensitive documentation. Highlights for experts include compensation for image distortion, cartesian and polar coordinates, linear and logarithmic coordinates, automatic scanning, graphical previews, and browser help.
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.