ACCORD is a C library for composition of SEM or scanning helium-ion microscope images with correction of drift. It is able to compose (average) large sets of extremely noisy images that were acquired by scanning charged-particle microscopes at the highest possible speeds (lowest pixel-dwell times). If the images are composed using traditional techniques, they usually become extensively blurry. The technique that is implemented in this software corrects these derogations by pre-shifting the composed frames.
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.
Bullet is a 3D game multiphysics library that provides state of the art collision detection and soft body and rigid body dynamics. Bullet is integrated into Cinema 4D, Lightwave, and Blender. A Houdini and Maya Plugin is available. It has a modular extendible C++ design with hot-swap of most components. The back-ends were optimized for pthreads/Win32 Threads multi-threading and PS3 Cell SPU. Other features include discrete and continuous collision detection (CCD), swept collision queries, ray casting with custom collision filtering, generic convex support (using GJK), capsule, cylinder, cone, sphere, box, and non-convex triangle meshes. Rigid body dynamics include constraint solvers, generic constraints, ragdolls, hinges, and ball-sockets. Constraint limits and motors are supported. Soft body support includes cloth, rope, and deformable objects. Import and export into COLLADA 1.4 Physics format is supported. Dynamic deformation of non-convex triangle meshes is supported by refitting the acceleration structures.
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.