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.
ChronoJump is software and hardware to track jump, run, and reaction time and pulse. It uses a contact platform suitable for two events (in-platform, out-platform), and also a chronometer printed circuit designed ad-hoc in order to obtain precise and trustworthy measurements. Chronojump consists of free software and open hardware. It features a simulator that can be used if you don't have the hardware.
ImageJ is an image processing program inspired by NIH Image for the Macintosh. It can display, edit, analyze, process, save, and print 8-bit, 16-bit, and 32-bit images. There are modules for biology, astronomy, nuclear medicine, physics, and more. If you can take a picture of something, whether with a microscope, a telescope, an oscilloscope, an xray machine, or a scanner, then this program will let you enhance, manipulate, and measure the results.
SENTENSA Knowledge Miner is a platform independent tool for searching any text. SENTENSA uses robust methods of indexing and searching text, leveraging experience from more than 20 years of information retrieval. SENTENSA products offer advanced text retrieval solutions for large databases that will make your searches for key information fast and effective. You can index on one platform and query on another.
The Sample Inventory Program (SIP) is a laboratory inventory management system (LIMS) for Zope. Many integration tests exist for various aspects of the SIP application, ranging from command line importing of samples and project configuration to CSV Web-based importing of sample modifications.
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.
GeneRecon 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. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position.
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.