Gwyddion is a modular SPM (Scanning Probe Microsope) data visualization and analysis tool. It can be used for all most frequently used data processing operations including: leveling, false color plotting, shading, filtering, denoising, data editing, integral transforms, grain analysis, profile extraction, fractal analysis, and many more. The program is primarily focused on SPM data analysis (e.g. data obtained from AFM, STM, NSOM, and similar microscopes). However, it can also be used for analyzing SEM (scaning electron microscopy) data or any other 2D data.

MathGL is a library for making high-quality scientific graphics under Linux and Windows, fast data plotting and handling of large data arrays, working in window and console modes, and easily embedding into other programs. It has more than 40 general types of graphics for 1d, 2d, and 3d data arrays. It can export graphics to raster and vector (EPS or SVG) formats. It has an OpenGL interface and can be used from console programs. It has functions for data handling and MGL language scripting for simplification of data plotting. It has several types of transparency and smoothed lightning, vector fonts and TeX-like formula drawing, an arbitrary curvilinear coordinate system, and many other useful things.

SHTns is a high-performance Spherical Harmonic Transform library. It was designed for numerical simulation (fluid flows, mhd, etc.) in spherical geometries, but can be used for any kind of problem involving scalar or vector spherical harmonics. It is very fast, thanks to careful vectorization and runtime tuning. It supports multi-threaded transforms via OpenMP. It features scalar and vector transforms, synthesis and analysis, and flexible truncation and normalization. A Python interface is included.

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.

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.

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.