HEALPix is a set of scientific tools implementing the Hierarchical Equal Area isoLatitude Pixelation of the sphere. As suggested in the name, this pixelation produces a subdivision of a spherical surface in which every single pixel covers the same surface area. HEALPix provides various programs and libraries in C, C++, Fortran, GDL/IDL, Java, and Python which facilitate discretization, simulation, processing, analysis, and visualization of data on the sphere up to very high resolution. It is the state-of-the-art program used in astronomy and cosmology to deal with massive full-sky data sets.
TAU (Tuning and Analysis Utilities) is a set of tools for analyzing the performance of C, C++, Fortran and Java programs. It collects much more information than is available through prof or gprof, the standard Unix utilities, including per-process, per-thread, and per-host information, inclusive and exclusive function times, profiling groups that allow you to organize data collection, access to hardware counters on some systems, per-class and per-instance information, the ability to separate data for each template instantiation, start/stop timers for profiling arbitrary sections of code, and support for collection of statistics on user-defined events.
ffnet is a fast and easy-to-use feed-forward neural network training solution for Python. You can use it to train, test, save, load, and use an artificial neural network with sigmoid activation functions. Any network connectivity without cycles is allowed (not only layered). Training can be performed with several optimization schemes, including genetic alorithm based optimization. There is access to exact partial derivatives of network outputs versus its inputs. Normalization of data is handled automatically by ffnet.
The TIGL Geometry Library can be used for easy processing of geometric data stored inside CPACS data sets. TIGL offers query functions for the geometry structure. These functions can be used, for example, to detect how many segments are attached to a certain segment, which indices these segments have, or how many wings and fuselages the current airplane configuration contains. This functionality is necessary because TIGL targets not only the modeling of simple wings or fuselages but also the description of quite complicated structures with branches or flaps. The library uses the OpenCASCADE software to represent the airplane geometry by B-spline surfaces in order to compute surface points and also to export the geometry in the IGES/VTK format. The library provides external interfaces for C, C++, Python, Java, and FORTRAN.
PLplot is a library of C functions that are useful for making scientific plots from programs written in a wide variety of languages. It can be used to create standard x-y plots, semi-log plots, log-log plots, contour plots, 3D plots, shade (gray-scale and color) plots, mesh plots, bar charts, and pie charts. Multiple graphs may be placed on a single page with multiple lines in each graph. Different line styles, widths, and colors are supported. A virtually infinite number of distinct area fill patterns may be used. A variety of output devices and file formats are supported.
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.
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.