BioMAJ (BIOlogie Mises A Jour) is a workflow engine dedicated to data synchronization and processing. It automates the update cycle and the supervision of the locally mirrored data repository. The application is generalist, but was applied in the bioinformatics field for biological data bank management. The packaging includes workflow and indexing post-processing scripts for most used biological data banks. Developed in Java and Ant, the application is compatible with various Unix-based systems.
Cain performs stochastic and deterministic simulations of chemical reactions. It can spawn multiple simulation processes to utilize multi-core computers. It stores models, simulation parameters, and simulation results (populations and reaction counts) in an XML format. In addition, SBML models can be imported and exported. The models and simulation parameters can be read from input files or edited within the program. Solvers are implemented as command line executables, which makes it easy to launch batch jobs and simplifies the process of adding new solvers. Solvers include Gillespie's direct method, Gillespie's first reaction method, Gibson and Bruck's next reaction method, Tau-leaping, and Hybrid direct/tau-leaping.
Chaos Visualization is a program for quickly calculating the amount of predictability in a very simple system: a spring with one side connected to the origin and the other to a weight under gravity. This amount is chaos is visualized in TIFF images, which can be put in a sequence to show the evolution of chaotic behaviour in this system.
Code_Aster offers a full range of multi-physical analysis and modelling methods that go well beyond the standard functions of software for computational thermomechanics: static and dynamic mechanics, linear or not, modal analysis, harmonic and random response, seismic analysis, acoustics, thermics, fracture, damage and fatigue, multiphysics, drying and hydratation, metallurgy analysis ,soil-structure, fluid-structure interactions, geometric and material non linearities, and contact and friction. It has a wide range of material properties (95 constitutive laws): porous media, geomaterials, damage, elastoplasticity, elastoviscoplasticity, etc., a wide range of finite elements (395), and a wide range of loadings.
Quaternions are numbers with 4 parts: one for time and three for space. Command Line Quaternions is a set of command line functions that generate thousands of points of quaternions, which are fed into animation software. This forms the foundations of analytic animations, a logical extension of analytic geometry.
Dataguzzler is a laboratory data acquisition platform for high performance waveform and image acquisition. It uses a reconfigurable modular architecture and is controllable from a command console, graphical interface, and by remote over TCP/IP. A variety of prebuilt modules, for hardware from function generators to waveform capture cards to framegrabbers, are included. As distributed, Dataguzzler comes pre-configured for two applications: A software oscilloscope, based on the Measurement Computing PCI-DAS4020/12 card, and a CameraLink imager, based on the EDT PCI-DV/CLink card.
Debyer takes a file with atom positions as input and can output X-ray and neutron diffraction patterns, the total scattering structure function, the pair distribution function (PDF), and related functions (RDF, reduced PDF). It can be used for comparison of molecular dynamics simulations or other models of atomistic structure of the material with X-ray and neutron powder diffraction experiments. The parallel version uses the MPI library.
ESMF is software for building and coupling weather, climate, and related models. The premise is that complicated applications should be broken up into smaller pieces, or components. A component is a unit of software composition that has a coherent function, and a standard calling interface and behavior. Components can be assembled to create multiple applications, and different implementations of a component may be available.