gfit analyzes data using models. gfit lets the user create a model for virtually any type of system using a minimal amount of computer code. It is particularly useful for studying various systems in biophysics, biochemistry, and cell biology. The interface for gfit models specifies relationships between input and output variables in a rule-based fashion. It provides flexibility and allows the user to reuse same models for many related problems.
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.
Penacho is a simulation software that calculates and draws the gas dispersion of a smokestack in the atmosphere. It consists of a GUI to enter air conditions, an atmospheric dispersion modeling solver, and an interactive 3D graphics engine. Penacho draws the plume evolution, the particles' deposition and the pollutant concentration distribution, as an isosurface and a grid plane for each coordinate axis. Penacho exports its simulation results as a text file, VTK structured points, or CSV (suitable for spreadsheets).
GaussianBeam is a Gaussian optics simulator. It features table-top display of the optical setup. It computes the beam parameters. You can move optics with the mouse. Available optics: lenses, flat and curved interfaces, mirrors, dielectric slab, and generic ABCD. Magic waist function: given a target waist, GaussianBeam finds the suitable arrangement of lenses. Fit waist function: measure the beam radius or diameter to define the input beam. The ability to save and load configurations.
Evolving Games for Unnatural Intelligence is a Java package for unsupervised machine learning based on Evolutionary Game Theory on directed graphs. It is able to segment data without any previuos information on the number of segments. It has no GUI, but implements generalizations of the original method proposed by Li, Chen, He and Jiang in the arxiv paper "A Novel Clustering Algorithm Based Upon Games on Evolving Network", published on 30 Dec 2008.
Fimex is a the File Interpolation, Manipulation, and EXtraction library for gridded geospatial data. It converts between different, extensible data formats (currently netcdf, NcML, grib1/2, metgm, wdb, and felt). It enables you to change the projection and interpolation of scalar and vector grids. It makes it possible to subset the gridded data and to extract only parts of the files. For simple usage, Fimex also comes with the command line program fimex.