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Bmrblib
Bmrblib is a Python API abstracting the Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) NMR-STAR format (http://www.bmrb.wisc.edu/). It allows the writing of NMR-STAR files for BMRB data deposition and the reading and easy extraction of data from files residing in the BMRB data bank, all without knowledge of the Self-Defining Text Archive and Retrieval (STAR) format.
Brightway2
Life cycle assessment, Monte Carlo uncertainty analysis, visualization of results
C-graph Heckert gnu.tiny.png
GNU C-Graph is a tool for visualizing the mathematical operation of convolution underlying natural phenomena susceptible to analysis in terms of engineering signals and systems theory. "C-Graph" is an abbreviation for "Convolution Graph". The package is derived from the BSc. Honours dissertation in Electrical Engineering "Interactive Computer Package Demonstrating: Sampling Convolution and the FFT", Adrienne Gaye Thompson, University of Aberdeen (1983). The package computes the linear convolution of two signals in the time domain then compares their circular convolution by demonstrating the convolution theorem. Each signal is modelled by a register of discrete values simulating samples of a signal, and the discrete Fourier transform (DFT) computed by means of the Fast Fourier Transform (FFT). GNU C-Graph is interactive, prompting the user to enter character or numerical values from the keyboard, dispensing with the learning curve for writing code. The software will be useful to students of signals and systems theory. C-Graph is written in contemporary Fortran. You can find pre-GNU development versions at: <http://codeartnow.com/code/download/c-graph-1/c-graph-version-2-preview>. Adrienne Gaye Thompson is the sole author of GNU C-Graph and looks forward to sharing further development with the Free software community.
CAGE
A generic and fairly complete cellular automata simulation engine. CAGE is a fairy generic and complete cellular automaton simulation engine in Python. It supports both 1D and 2D automata, a variety of prepackaged rules, and the concept of "agents" which can move about independently on the map for implementing agent behavior. CAGE comes with numerous examples of fully-functional CA systems, including Conway's Game of Life, Langton's self-reproducing automaton, Langton's "vants," and 1D automata rule explorers. It also comes with simple displayers (including a curses interface for 2D automata). Also included is a unique implementation of a finite state machine (ant.py).
CCVisu
The tool CCVisu is a light-weight tool for force-directed graph layout. The tool reads the input graph from a file in RSF (Rigi Standard Format), which is a standard text format for relations. The layout of the graph is computed using standard techniques from force-directed layout. The tool supports several energy models, which can be selected by setting command line parameters. The weighted edge-repulsion LinLog energy model (default) is good for producing layouts that fulfill certain clustering criteria. The Fruchterman Reingold energy model is good for producing layouts that fulfill certain esthetic criteria like uniform edge length. CCVisu stores the resulting layout in certain text file formats such as VRML or SVG, or it displays the layout on the screen.
CERTI
CERTI is an HLA RTI. HLA (High-Level Architecture) is a general purpose architecture for distributed computer simulation systems. In HLA systems, the RTI (RunTime Infrastructure) manages data exchange between simulations. CERTI focuses on HLA 1.3 specification and its C++ API (IEEE 1516 will be supported too).
Ccg
ccg is a program which enables you to plot ERSL atmospheric gas data from the US National Oceanic and Atmospheric Administration (NOAA) web site.
Chaco
Chaco is a software for partitioning graphs mainly intended for parallel computing and scientific simulations. It implements a set of algorithms for this task ranging from a generalization of KL/FM with weighted graphs support to the premiere multilevel algorithms which combine high quality partitioning schemes and low computational costs.
Cl-ana
cl-ana is a library of modular utilities for reasonably high performance data analysis & visualization using Common Lisp. (Reasonably means I have to be able to use it for analyzing particle accelerator data). The library is made of various sublibraries and is designed in a very bottom-up way so that if you don't care about some feature you don't have to load it. The functionality support so far are
  • Tabular data analysis: Read-write of large datasets stored in HDF5 files are supported, along with ntuple datasets, CSVs, and in-memory data tables. Users can add their own table types by defining 4 methods and extending the table CLOS type.
  • Histograms: Binned data analysis is supported with both contiguous and sparse histogram types; functional interface is provided via map (which allows reduce/fold) and filter.
  • Plotting: Uses gnuplot for plotting dataset samples, plain-old lisp functions, histograms, strings-as-formulae, and anything else the user wishes to add via methods on a couple of generics.
  • Fitting: Uses GSL for non-linear least squares fitting. Uses plain-old lisp functions as the fit functions and can fit against dataset samples, histograms, and whatever the user adds.
  • Generic mathematics: CL doesn't provide extendable math functions, so cl-ana provides these as well as a convenient mechanism (a single function) for using these functions instead of the non-extendable versions. Already included are error propogation and quantities (values with units, e.g. 5 meters) as well as a GNU Octave-style handling of sequences (e.g. (+ (1 2) (3 4)) --> (4 6)).
CoaSim
'CoaSim' is a tool for simulating the coalescent process with recombination and gene conversion under the assumption of exponential population growth. It constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP and micro-satellite haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.
CoaSim-gui
'CoaSim-gui' is a graphical use interface for the coalescence process simulator CoaSIm.
Coin
Coin is a platform-independent retained-mode 3D graphics library that uses scene-graph data structures to render real-time graphics+suitable for mostly all kinds of scientific and engineering visualization applications. It is fully compatible with Open Inventor 2.1. Coin is built on the OpenGL immediate-mode rendering library, adds abstractions for higher-level primitives, provides 3D interactivity, increases programmer convenience and productivity, and contains optimization features for fast +rendering that are transparent for the application programmer.
Ctioga2
ctioga2 is a plotting program in the spirit of gnuplot. It can be used either directly on command-line or writing command files (or a mix of both). It produces publication-quality PDF files. It is based on the Tioga plotting library.
CubicSDR
CubicSDR "allows you to navigate the radio spectrum and demodulate any signals you might discover" utilizing a modular 'piping' architecture that simplifies real-time analysis of discovered signals. CubicSDR creates live "waterfall" visual graphs representing a spectrum bandwidth and associated signal intensity.
Drishti
Drishti stands for vision or insight in Sanskrit, an Indian language. Drishti has been developed keeping in mind the end-use : visualizing tomography data, electron-microscopy data, etc. Understanding the data set is important and conveying that understanding to the research community or a lay person is equally important. Drishti is aiming for both. The central idea about Drishti is that the scientists should be able to use it for exploring volumetric datasets as well as use it in presentations.
EMAN
EMAN is a scientific image processing suite designed mainly to perform single-particle reconstructions of individual molecules. In this method, a transmission electron microscope is used to collect images of thousands of individual molecules. A complex series of algorithms then turns the individual 2D images into a high-resolution 3D structure of the molecule. The core of EMAN is a C++ based scientific image processing library.
Earth3D
Earth3D visualizes the earth in realtime in a 3D view. You can rotate and zoom the view until countries, cities and even single houses become visible (in areas where the necessary map resolution is available), and fly around. You can also embed external data like current earthquake positions or cloud data. Additional data layers can be added to the view, e.g. country flags and names. The package uses data from NASA, USGS, the CIA, and the city of Osnabrück. The data is loaded on demand over the Internet.
Electric Fields Visualization Python
This is educational software that demonstrates the field and fluxlines for electric charge particles.
Elfelli Flux Line Simulator
Elfelli is a tool to simulate and visualize electric flux lines around arbitrarily positioned, electrically charged bodies. It is able to export PNG files of the current canvas. It is written in C++ and uses gtkmm.
Elmer
Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics and heat transfer. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM). Elmer comprises of several different parts: The geometry, boundary conditions and physical models are defined in ElmerFront. The resulting problem definition is solved by ElmerSolver. Finally the results are visualized by ElmerPost. Additionally a utility ElmerGrid may be used for simple mesh manipulation. The different parts of Elmer software may also be used independently. The strongest of the components is ElmerSolver which includes many sophisticated features. For pre- and postprosessing the users may find also other alternatives. The software runs on unix and windows platforms and can be compiled on a large variety of compilers. The solver can also be used in parallel mode on platforms that support MPI.<\p>
Engauge
'Engauge' converts an image file showing a graph or map into numbers. The image file can come from a scanner, digital camera or screenshot. The numbers can be read on the screen, and written or copied to a spreadsheet. The process starts with an image file containing a graph or map; The final result is digitized data that can be used by other tools such as Gnumeric. Its features include automatic grid line removal, point matching, and curve tracing; the ability to handle cartesian, polar, linear and logarithmic graphs; image processing that highlights data by removing grid lines and backgrounds; context sensitive help; and preview windows that give immediate feedback while modifying various settings.
Eonums
Eonums is a simple module providing conversion between normal integer numbers and the corresponding textual expression in the Esperano language. It was mainly developped in order to explore the regularity of Esperanto expressions for big integer numbers. Names for 10**k (k = 6, 9, 12, ...) like "miliono" (10**6) or "miliardo" (10**9) are chosen from the so-called "Longa Skalo" as described on this page about big numbers (in Esperanto). The integer numbers eonums can convert to or from such Esperanto expressions can be arbitrarily large, but are limited in practice by the largest number for which there is a name in Esperanto (on the "Longa Skalo")", which is, on the previous page, 10**63 (dekiliardo). Hence, the largest integer you can handle with this module is 10**66 - 1. (This module makes no attempt to extend the Esperanto naming rules by introducing names like "undekiliono", "undekiliardo", "dudekiliono" etc.) This module can be fully translated automatically to Python 3.0 using its migration tool named 2to3. Features
  • convert Python integers to Esperanto integer strings (Unicode)
  • convert Esperanto integer strings (Unicode) to Python integers
  • validate Esperanto integer strings (Unicode)
  • handle integers from 0 to 10**66 - 1
  • provide conversion functions and command-line scripts
  • provide a Unittest test suite
  • can be automatically migrated to Python 3.0 using 2to3
Eqe
'eqe' is a clone of the LaTeX equation editor found on Mac OS X. There's a zone to type LaTeX input, which generates an image to represent it (color, font, and size are customisable). You can drag the image to other applications (like OpenOffice Impress, Mozilla, the Gimp). It also exports to any image format ImageMagick supports. 'eqe'is composed of two parts: eqedit, which is a command line tool that generates images from LaTeX input, and eqe which wraps eqedit into a graphical user interface.
Eukleides
Eukleides is a Euclidean geometry drawing language. The package includes eukleides, a compiler which lets you typeset geometry figures within a (La)TeX document. This program is also useful to convert such figures in EPS format or in various other vector graphic formats. It also includes xeukleides, an X-Window front-end which makes possible to create interactive geometry figures. This program is also useful to edit and tune some Eukleides code.
Extrema
Extrema is a powerful visualization and data analysis tool that enables researchers to quickly distill their large, complex data sets into meaningful information. Its flexibility, sophistication, and power allow you to easily develop your own commands and create highly customized graphs.
Fbi IMproved
FIM is a lightweight universal image viewer, mostly for Linux (but not only). FIM aims to be a highly customizable and scriptable image viewer for users who are comfortable with software like the VIM text editor or the Mutt mail user agent. It has been developed with Linux in mind, but can be built to run on several Unix systems or even on MS-Windows.
Fityk
Fityk is nonlinear curve-fitting and data analysis software. It supports data visualization, separation of overlapping peaks, and least squares fitting using standard Levenberg-Marquardt algorithm, a genetic algorithm, or Nelder-Mead simplex method. It knows common bell-shaped functions (Gaussian, Lorentzian, Pearson 7, Voigt, Pseudo-Voigt) and polynomials, but more sophisticated formulae can be added if needed. It also enables background substracting, data calibration and task automation with a simple script language. It is being developed to analyze powder diffraction patterns, but can be used to fit analytical functions to any kind of data.
Flounder
'Flounder' visualizes 4D data (x,y,z,t). It can produce isosurfaces, 3D surface and solid renderings, as well as 2D slices. Several data sets can be viewed simultaneously. Temporal data at a spatial location can be examined with output in several formats including PNG and GIF animations.
FreeMat
'Freemat' is an interpreted, matrix-oriented development environment for engineering and scientific applications. It includes several novel features such as a codeless interface to external C/C++/FORTRAN code, parallel/distributed algorithm development (via MPI), and plotting, visualization and image manipulation capabilities as well as parallel programming.
Fung-Calc
'Fung-Calc' is an advanced yet easy to use graphing calculator written using the Qt libraries. It supports various graphing modes in both 2D and 3D. It combines all the features of a full-blown mathematical analysis package with ease of use.
GDIS
"GDIS' is a GTK/OpenGL based program for displaying isolated molecules, periodic systems, and crystalline habits. It also acts as a GUI to packages such as GAMESS, GULP, and POVRay to provide energy minimizations and publication quality rendering.
GDL
The Gnu Data Language (GDL) is a free alternative to the data visualization and analysis tool, called IDL (Interactive Data Language), frequently used by scientists. GDL and its library routines are designed as a tool for numerical data analysis and visualisation. GDL is dynamically typed, vectorized and has object-oriented programming capabilities. The library routines handle numerical calculations, data visualisation, signal/image processing, file input/output (incl. graphical and scientific data formats such as TIFF, PNG, netCDF, HDF etc) and interaction with host OS. Despite its name, GDL is not a GNU package.
GLE
'GLE' is a package of C functions that draw extruded surfaces, including surfaces of revolution, sweeps, tubes, polycones, polycylinders and helicoids. The extruded surface is specified with a 2D polyline that is extruded along a 3D path. A local coordinate system allows for additional flexibility in the primitives drawn. Extrusions may be texture mapped in a variety of ways. The GLE library generates 3D triangle coordinates, lighting normal vectors and texture coordinates as output. It uses the GL or OpenGL API's to perform the actual rendering.
GNOME Water Temperature Applet
The GNOME Water Temperature Applet displays water temperatures of rivers, lakes and oceans in your GNOME panel.
GTO
The GTO format's primary usage is storage of static geometric data. The types of data you might find in a GTO file are things like polygonal meshes, various types of subdivision surfaces, NURBS or UBS surfaces, coordinate systems, hierarchies of objects, material bindings, and even images. "GTO' is used at Tweak Films to streamline the modeling, animation, rendering, and 3-D paint processes. It includes source code for a Maya plug-in, various command line tools, a Wavefront .obj parser, and a Python module for reading and writing GTO files. There is also an emacs mode gto-mode.el for editing GTO text files.
Gabedit
'Gabedit' is a graphical interface to the Molpro and Gaussian computational chemistry packages, running locally or on a remote server. It includes a 3D molecule editor and viewer. Most major molecular file formats are supported, and graphics can be exported in many formats.
Gdpc
'gdpc' is a tool for visualising the output files of a molecular dynamic simulation. It can be customized to read almost any input file format, animate it, and output images of each frame.
Gephi
visualization and exploration software for all kinds of graphs and networks
Gmsh
'Gmsh' is an automatic 3D finite element mesh generator with build-in CAD and post-processing facilities. Its design goal is to provide a simple meshing tool for academic test cases with parametric input and up to date visualization capabilities. It can respect a characteristic length field for the generation of adapted meshes on lines, surfaces and volumes, and mix these meshes with simple structured grids. Gmsh 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 or in ASCII text files using Gmsh's own scripting language.
Gnucap Heckert gnu.tiny.png
GNUcap is a modern analog and mixed signal circuit simulator. The primary component is a general purpose circuit simulator. It performs nonlinear dc and transient analyses, fourier analysis, and ac analysis. It is fully interactive and command driven. It can also be run in batch mode or as a server.
Gpiv
'Gpiv' is a graphic user interface for analyzing images obtained from a fluid flow that has been seeded with tracer particles by the so-called Particle Image Velocimetry technique (PIV). It is meant to have a quick overview of the parameters of all piv processes, easily changing them, running the processes and visualizing their results interactively.
Graph-tool
graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms of graph-tool are implemented in C++, making extensive use of metaprogramming, based heavily on the Boost Graph Library. This confers a level of performance which is comparable (both in memory usage and computation time) to that of a pure C++ library.
Graphviz
The Graphviz layout program takes descriptions of graphs in a simple text language, and makes diagrams in various formats such as images and SVG for web pages, Postscript for inclusion in PDF or other documents, or for display in an interactive graph browser. Graphviz also supports GXL, an XML dialect. Its features include options for colors, fonts, tabular node layouts, line styles, hyperlinks, and custom shapes. Graphs are usually generated from an external data sources, but they can also be created and edited manually, either as raw text files or within a graphical editor.
Gri
Gri is an extensible plotting language designed for scientists. It can draw x-y plots, contour plots, and image plots, and has rudimentary programming capabilities. It is not mouse driven, nor gui-based; rather, it is an interpreted scriping language. Users regard it as an analogue to the latex document formatting language: users gain considerable power, at the price of a moderate learning curve.
GtkDatabox
The GtkDatabox widget (for use with the GTK+ widget set) is used to display large amounts of numerical data in graphical representation. Several sets of data may be shown at one time. You may zoom in and out and navigate via scrollbars. The display of data is rather fast, so you can use the widget for quickly changing data (i.e. an oscilloscope for example) as well. The widget has already been adapted to several scientific projects around the world.
H5utils
h5utils is a set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format. Programs included are:
  • h5totxt and h5fromtxt: convert HDF5 datasets to/from ASCII text (e.g. comma- or tab-delimited).
  • h5topng: convert 2d slices of HDF5 datasets to PNG images, with a variety of color tables and other options.
  • h5tov5d: convert HDF5 datasets to the format used by the free 3d+ visualization tool Vis5d.
  • h5tovtk: convert HDF5 datasets to VTK format for use by the free Visualization ToolKit (along with supporting programs like MayaVi).
  • h5read.oct: a plug-in for GNU Octave (a Matlab-like program) to read 2d slices of HDF5 datasets. (The latest versions of Octave also include native support for HDF5.)
  • h5fromh4: convert HDF (version 4) datasets to HDF5; mostly superseded by the h4toh5 program included with recent versions of HDF5.
  • Please note that the programs to convert to/from PNG, Vis5d, GNU Octave, and HDF(4) will only be built if the corresponding libraries/programs are installed.
Holocrunchies
'Holocrunchies' is a computational holography program that generates diffraction patterns for 2-D images.
HuffmanView
This is a candidate for deletion: Links broken. Email to maintainer broken. Poppy-one (talk) 17:54, 2 August 2018 (EDT) 'HuffmanView' is a small application to visualize the Huffman tree algorithm. It may be useful for educational purposes. Huffman coding is a graph algorithm used for lossless variable length encoding resulting in a prefix-free code.
INFOTOPO
Programs for Information Topology Data Analysis Information Topology is a program written in Python (compatible with Python 3.4.x), with a graphic interface built using TKinter [1], plots drawn using Matplotlib [2], calculations made using NumPy [3], and scaffold representations drawn using NetworkX [4]. It computes all the results on information presented in the study [5], that is all the usual information functions: entropy, joint entropy between k random variables (Hk), mutual informations between k random variables (Ik), conditional entropies and mutual informations and provides their cohomological (and homotopy) visualisation in the form of information landscapes and information paths together with an approximation of the minimum information energy complex [5]. It is applicable on any set of empirical data that is data with several trials-repetitions-essays (parameter m), and also allows to compute the undersampling regime, the degree k above which the sample size m is to small to provide good estimations of the information functions [5]. The computational exploration is restricted to the simplicial sublattice of random variable (all the subsets of k=n random variables) and has hence a complexity in O(2^n). In this simplicial setting we can exhaustively estimate information functions on the simplicial information structure, that is joint-entropy Hk and mutual-informations Ik at all degrees k=<n and for every k-tuple, with a standard commercial personal computer (a laptop with processor Intel Core i7-4910MQ CPU @ 2.90GHz * 8) up to k=n=21 in reasonable time (about 3 hours). Using the expression of joint-entropy and the probability obtained using equation and marginalization [5], it is possible to compute the joint-entropy and marginal entropy of all the variables. The alternated expression of n-mutual information given by equation then allows a direct evaluation of all of these quantities. The definitions, formulas and theorems are sufficient to obtain the algorithm [5]. We will further develop a refined interface (help welcome) but for the moment it works like this, and requires minimum Python use knowledge. Please contact pierre.baudot [at] gmail.com for questions, request, developments (etc.): [1] J.W. Shipman. Tkinter reference: a gui for python. . New Mexico Tech Computer Center, Socorro, New Mexico, 2010. [2] J.D. Hunter. Matplotlib: a 2d graphics environment. Comput. Sci. Eng., 9:22–30, 2007. [3] S. Van Der Walt, C. Colbert, and G. Varoquaux. The numpy array: a structure for efficient numerical computation. Comput. Sci. Eng., 13:22– 30, 2011. [4] A.A. Hagberg, D.A. Schult, and P.J. Swart. Exploring network structure, dynamics, and function using networkx. Proceedings of the 7th Python in Science Conference (SciPy2008). Gel Varoquaux, Travis Vaught, and Jarrod Millman (Eds), (Pasadena, CA USA), pages 11–15, 2008. [5] M. Tapia, P. Baudot, M. Dufour, C. Formisano-Tréziny, S. Temporal, M. Lasserre, J. Gabert, K. Kobayashi, JM. Goaillard . Information topology of gene expression profile in dopaminergic neurons doi: https://doi.org/10.1101/168740 http://www.biorxiv.org/content/early/2017/07/26/168740
ImLib3D
ImLib3D is a C++ library and visualization system for 3D (volumetric) image processing. It provides a library for developing image processing software in C++, an executable, for using image processors from the command line, and an executable, which is an interactive GUI for 3D volumetric visualization.


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