The Gnome Chemistry Utils includes the following programs: a 2D chemical editor (GChemPaint), a chemical calculator (computes raw formule, molar weight, mass composition, and isotopic pattern), a 3D molecule viewer using OpenGL to display molecular models, a crystal structure viewer and editor, a spectrum viewer, and a periodic table of the elements.
The Noble Ape Simulation is a collection of a number of autonomous simulation components including a landscape simulation, biological simulation, weather simulation, sentient creature (Noble Ape) simulation, and a simple intelligent-agent scripting language (ApeScript). Noble Ape also contains a social simulation where the Noble Apes can be tracked in terms of social groups and also over many generations to explain social phenomenon to users looking to study this kind of interaction. It has been in development for more than a fifteen years.
Open Tool Kit (Otk) is a portable widget library for making graphical user interfaces for C programs. It emphasizes simplicity for the application programmer without eliminating capability. Based on OpenGL, Otk supports Linux, Unix, and other OSs neutrally and efficiently. It is simple and compact, and it strives for easy compilation and linking to other applications. In seeking to address several issues associated with earlier graphics APIs, Otk explores some interesting methods, such as window-relative layout instead of pixel-based layout.
SHOGUN is a machine learning toolbox whose focus is on large scale kernel methods and especially on Support Vector Machines (SVM). It provides a generic SVM object interfacing to several different SVM implementations, all making use of the same underlying, efficient kernel implementations. Apart from SVMs and regression, SHOGUN also features a number of linear methods like Linear Discriminant Analysis (LDA), Linear Programming Machine (LPM), (Kernel) Perceptrons, and algorithms to train hidden Markov models. SHOGUN can be used from within C++, Matlab, R, Octave, and Python.
gipfel is a tool to find the names of mountains or points of interest on a picture. It uses a database containing names and GPS data. With the given viewpoint (the point from which the picture was taken) and two known mountains on the picture, it can compute all parameters needed to compute the positions of other mountains on the picture. gipfel can also generate (stitch) panorama images.
Veusz is a scientific plotting package, designed to create publication-ready Postscript, PDF, or SVG output. It features an easy to use graphical interface as well as a command line interface and can be scripted or embedded in Python scripts. Graphs are constructed in a modular fashion from separate components. Datasets can be interactively modified or created from within the program.
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.
cclib is a Python library for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, GAMESS (US), GAMESS-UK, Gaussian, Jaguar, and PC GAMESS. Among other data, cclib extracts coordinates, atomic orbital information, molecular orbital information, information on vibrational modes, and the results of a TD-DFT calculation. cclib also provides some calculation methods for interpreting some electronic properties of molecules using analyses such as Mulliken population analysis, overlap population analysis, and calculation of Mayer's bond orders.
Gmsh is an automatic 3D finite element grid generator with built-in CAD and post-processing facilities. Its design goal is to provide a simple meshing tool with parametric input and advanced visualization capabilities. It is built around four modules: geometry, mesh, solver, and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface (based on FLTK and OpenGL) or in ASCII text files using Gmsh's own scripting language.