AGM Build is a molecular builder and conformational editor. It can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. It features geometry editing, lattice building, building of chain molecules (e.g. proteins), chains with predetermined conformations, and charges and atom types according to selected Force Field.
APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.
The Artificial SEM Image Generator (artimagen) library generates artificial scanning electron microscope (SEM) and helium-ion microscope images of various samples, including gold-on-carbon resolution samples and some semiconductor structures. Numerous effects that appear in real SEMs are simulated (noise, drift-distortion, edge-effect, etc.), which enables assessment of imaging, metrology, and other techniques that work with SEM micrographs. Unlike the real SEM images, the artificial images exhibit defined types and amounts of these effects, which is their key advantage.
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.
CONSIDEO MODELER allows you to mindmap a complex problem, analyse it qualitatively to discover levers and bottlenecks, and even to simulate it by automatically building a system dynamics model. One can integrate any external data and setup a customized management cockpit for playing out scenarios. It is useful for organizational problems, project management, financial analysis, production processes, score cards, and much more.
Cadabra is a computer algebra system designed specifically for the solution of problems encountered in field theory. It has extensive functionality for tensor polynomial simplification including multi-term symmetries, fermions and anti-commuting variables, Clifford algebras and Fierz transformations, implicit coordinate dependence, multiple index types, and many more. The input format is a subset of TeX. Both a command-line and a graphical interface are available.
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.
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.