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.
Finesse is a numeric simulation for laser interferometers using the frequency domain and Hermite-Gauss modes. It is easy to use for students. For basic use, including graphical output, no commercial software is required. The implemented physics are well documented in a 180-page manual. Simple examples are provided. Finesse can be used to compute a great variety of interferometer signals for control systems, including longitudinal control, alignment control, and thermal compensation.
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.
ODE is a high performance library for simulating rigid body dynamics. It is fully featured, stable, mature, and platform independent with an easy-to-use C/C++ API. It has advanced joint types and integrated collision detection with friction. ODE is useful for simulating vehicles, objects in virtual reality environments, and virtual creatures. It is currently used in many computer games, 3D authoring tools, and simulation tools.
pyXSD maps XML and XSD (XML Schema) files into Python, checks the XML against the schema, and transforms XML documents according to user-specified Python classes. There is a framework to make these transformation classes easy to write. The program uses a simple, pythonic, non-DOM interface with the XML tree structure.