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AeroCalc is a python package that performs various aeronautical engineering calculations. Currently, it contains the following main modules:
  • airspeed
  • default_units
  • ssec
  • std_atm
  • unit_conversion
In short, Aletheia is software for getting science published and into the hands of everyone, for free. It's a decentralised and distributed database used as a publishing platform for scientific research. So, Aletheia is software. But software without people is nothing. To comprehensively answer the question what is Aletheia, Aletheia is software surrounded by a community of people who want to change the world through open access to scientific knowledge. For a more in depth explanation, Aletheia is an Ethereum Blockchain application utilising IPFS for decentralised storage that anyone can upload documents to, download documents from, that also handles the academic peer review process. The application runs on individual PCs, all forming part of the IPFS database. This gives us an open source platform that cannot be bought out by the large publishers (and any derivitive works must also be open source) that should also be hard to take down due to the database being spread across the globe in multiple legal jurisdictions. Aletheia is designed to be a resilient platform run transparently by the community, not some black box corporation or editorial board, meaning all users can see the decisions Aletheia is making and have a stake in that decision making process if they so desire. By this nature, Aletheia is decentralised, it has no key person risk. Should the core group who invented Aletheia dissapear Aletheia won't cease to exist, it will continue to be run by the community. The community moderates content through various mechanisms (peer review, reputation scores etc.,) to ensure quality of content.
Arvados enables you to quickly begin using cloud computing resources in your data science work. It allows you to track your methods and datasets, share them securely, and easily re-run analyses.
'Asymptote' is a script-based vector graphics language for technical drawing, inspired by MetaPost but with an improved C++-like syntax. It provides for figures the same high-quality level of typesetting that LaTeX does for scientific text. It is a programming language, not just a graphics program, so it can use the best features of both scripts and GUIs. High-level graphics commands are implemented in the language itself, so they can be tailored to specific applications. Labels and equations are typeset with LaTeX for high-quality PostScript output.
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
  • International: Translations into Chinese, French, German, Italian, Russian, Spanish, and others, with more languages to come.
  • Intuitive: Built to work easily for students and advanced researchers both.
  • Fast: Supports multi-threaded rendering and computation.
  • Extensible: Plugin architecture for developers, including rendering, interactive tools, commands, and Python scripts.
  • Flexible: Features include Open Babel import of chemical files, input generation for multiple computational chemistry packages, crystallography, and biomolecules.
BKchem is a chemical drawing program written in Python. It is platform independent.
BRL-CAD includes an interactive geometry editor, parallel ray-tracing support for rendering and geometric analysis, path-tracing for realistic image synthesis, network distributed framebuffer support, image-processing and signal-processing tools.
besssugo is a free computational tool specifically designed to aid a cognizant expert—i.e. you, whether an engineer, scientist, technician, geek, etc—to build videos showing the result of a certain scientific calculation or whatever data can be computed or storied in a digital computer. Technically speaking, it is a plugin for the computational tool wasora, which provides means to parse and understand a high-level plain-text input file containing algebraic expressions, data for function interpolation, differential equations and output instructions amongst other facilities. Therefore, any mathematical computation which can be done by wasora—i.e. solving systems of differential-algebraic equations, multidimensional interpolation of scattered data, numerical integration and differentiation, etc.—can be combined with the facilities that besssugo provides to create visual representations in the form of animations.
Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs.
The BlockCanvas project provides a visual environment for creating simulation experiments, where function and data are separated. Thus, you can define your simulation algorithm by visually connecting function blocks into a data flow network, and then run it with various data sets (known as "contexts"); likewise, you can use the same context in a different functional simulation. The project provides support for plotting, function searching and inspection, and optimization. It includes a stand-alone application that demonstrates the block-canvas environment, but the same functionality can be incorporated into other applications. The BlockCanvas project relies on included libraries that allow multiple data sets using Numeric arrays to be incorporated in a Traits-based model in a way that is simple, fast, efficient, and consistent.
Bmrblib is a Python API abstracting the Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB) NMR-STAR format ( 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.
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: <>. Adrienne Gaye Thompson is the sole author of GNU C-Graph and looks forward to sharing further development with the Free software community.
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 (
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 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 is a program which enables you to plot ERSL atmospheric gas data from the US National Oceanic and Atmospheric Administration (NOAA) web site.
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 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' 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' is a graphical use interface for the coalescence process simulator CoaSIm.
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 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 "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 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 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 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 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' 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 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' 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 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 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 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' 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' 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' 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' 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.
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' 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.
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' 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' 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.
visualization and exploration software for all kinds of graphs and networks
'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' 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 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.
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 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.
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 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' is a computational holography program that generates diffraction patterns for 2-D images.
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.
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] 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:
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.
ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine.
Infovore is designed to merge large data sets such as Freebase and DBpedia, producing 100% valid RDF output at high speed because it uses the Hadoop Framework
Integrating Modelling Toolkit
A comprehensive and extensible set of abstractions allowing definition and use of interoperable model componenents. Modellers create and IMT "world" made of IMT "agents" that will each perform a particular phase of a modelling task. The core set of agents can describe modular, distributed components either native to the IMT or from existing toolkits specialized for various modelling, analysis and simulation tasks. IMT agents are designed to easily 'glue' together in higher-level simulations while integrating different modelling paradigms and toolkits. Programming experience is not needed to start developing models with IMT; an agent or collection of agents is fully described by an XML document and can be read from and written to a URL, just like a Web page.
JPIV: Java Particle Image Velocimetry
JPIV is a platform independent, graphical stand-alone application for Particle Image Velocimetry (PIV). PIV is an optical technique for measuring fluid flow velocities. JPIV can be used for multi-pass PIV evaluation, sum of correlation ensemble evaluation, single pixel ensemble evaluation, vector field filtering, calculation of vorticity and other derivatives, third velocity component reconstruction, image and vector field display, vector field statistics and batch processing.
Jmol is a molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. It can read a variety of file types and print and export images. It can animate the results of simulations.
KNIME [naim] is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualisation and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network.
Kpl is a program for two- and three-dimensional graphical presentation of data sets and functions. It performs multidimensional nonlinear parameter fits of functions to data sets using the Levenberg-Marquardt algorithm; general linear least square parameter fits are also possible. Other applications and scripts can control Kpl through a D-BUS interface. All presentation settings may be saved in plot files. Both plot and data files may be chosen by command line parameters, through the File menu, or by drag and drop. The program supports automatic scaling and normalization as well as automatic parameter fits. Presentation settings can be changed using the Edit menu. Additional data sets and functions can be displayed in the either the same or a different data window.
'L2P' creates PNG images from LaTeX math expressions. It can work with either a fragment of LaTeX code (such as $\frac{x^2+1}{3-x}$) or with a full LaTeX document. It is designed to be fast, robust, and to offer the user a high degree of flexibility and control. It includes complete documentation.
'libTAP' (The Architectural Playground) is a prototyping system for virtual reality and augmented reality applications. It runs on a variety of platforms. RAP (rapid application prototyping) is done through the Lua interface, which mirrors the C++ namespace as closely as possible. libTAP has a small but distinctive feature set, focused on prototyping of realtime 3D simulations.
  • Also known as 'Tacitpixel'.
'libgeotiff' is a library (normally built on top of libtiff) for reading and writing coordinate system information from/to GeoTIFF files. It includes CSV files for expanding projected coordinate system codes into full projections, and definitions and examples of transforming the definitions into a form that can be used with the PROJ.4 projections library. It also includes the sample applications listgeo (for dumping GeoTIFF information in readable form) and geotifcp (for applying geotiff tags to an existing TIFF or GeoTIFF file).
librsb is a library for sparse matrix computations featuring the Recursive Sparse Blocks (RSB) matrix format. This format allows cache efficient and multi-threaded (that is, shared memory parallel) operations on large sparse matrices. The most common operations necessary to iterative solvers are available, e.g.: matrix-vector multiplication, triangular solution, rows/columns scaling, diagonal extraction / setting, blocks extraction, norm computation, formats conversion. The RSB format is especially well suited for symmetric and transposed multiplication variants. On these variants, librsb has been found to be faster than Intel MKL's implementation for CSR. Most numerical kernels code is auto generated, and the supported numerical types can be chosen by the user at build time. librsb implements the Sparse BLAS standard, as specified in the BLAS Forum documents.
LimeSurvey basically contains everything you need for doing nearly every survey with grace.
LimeSurvey currently offers:
  • Unlimited number of surveys at the same time
  • Creation of a printable survey version
  • Unlimited number of question groups in a survey
  • Unlimited numbers of questions in a group/survey
  • 20 different question types with more to come
  • Multinlingual Surveys
  • Ability to set conditions for questions depending on earlier answers (branching the survey)
  • Re-usable editable answer sets
  • Ready-made importable questions
  • Assessment surveys
  • Unlimited number of participants to a survey
  • Anonymous or open surveys as well as closed surveys
  • Optional public registration for surveys
  • Sending of invitations, reminders and tokens by email
  • Option for participants to buffer answers to continue survey at a later time
  • Cookie or session based surveys
  • Template editor for creating your own page layout
  • Extended and user-friendly administration interface
  • Back-office data entry possibility
  • Survey start & end-dates for automation
  • Enhanced import and export functions to text, CSV and MS Excel format
  • Basic statistical and graphical analysis with export facility
linSmith is a Smith charting program mainly designed for educational use. As such, there is an emphasis on capabilities that improve the 'showing the effect of'-style of operation. Users can enter either discrete components or transmission lines, then see the results on screen or generate Postscript output. Component values can be changed numerically or using scrollbars. Problems can be solved on-screen, and high-quality Postscript can be output for publication. Its features include
  • Definition of multiple load impedances (at different frequencies)
  • Addition of discrete (L, C and transformer) and line components (open and closed stubs)
  • Connection in series and parallel
  • A 'virtual' component switches from impedance to admittance to help understand parallel components
  • Charts that work in real impedances (not normalized ones)
  • Generates a 'log' file with textual results at each intermediate step
  • Stores load and circuit configuration separately, permitting several solutions without re-defining the other.
A simple implementation of Lindenmayer systems (also called L-systems, substitution systems) is provided. In basic form, a Lindenmayer system consists of a starting string of symbols from an alphabet, and has repeated transitions applied to it, specified by a list of transition search-and-replace rules. In addition to the standard formulation, two alternative implementations are included: sequential systems, in which at most one rule is applied; and tag systems, in which the transition only takes place at the beginning and end of the string.
MESH (Measuring Error between Surfaces using the Hausdorff distance) is a tool that measures distortion between two discrete surfaces (triangular meshes). It uses the Hausdorff distance to compute a maximum, mean, and root-mean-square errors between two given surfaces. Besides providing figures, MESH can also display the error values on the surface itself through a GUI.
This is a candidate for deletion: 1. No files/source found 'MIND' is a cross platform, DICOM query/retrieve tool written in C++. It can query a DICOM server on any of the four specified DICOM query levels (patient, study, series and image) and can transfer data off the server to a storage server with a simple GUI interface.
Marble offers different kind of beautiful and useful map views of the Earth including OpenStreetMap. It can also search for place names and suggest routes.
McStas lets you model very precisely a neutron instrument described as a series of various components. A source component shoots each neutron randomly (Monte-Carlo), and the particle is then propagated through the different instrument components. These later act on the neutron characteristics (position, speed, direction, spin, etc.). Usually, one installs some detectors along the neutron path to monitor its characteristics and flux.
'MCL' (Markov Cluster Algorithm) is a fast and scalable cluster algorithm for graphs based on stochastic flow. The flow process that the algorithm uses is mathematically sound and intrinsically tied to cluster structure in graphs, which is revealed as the imprint left by the process. The threaded implementation has handled graphs of up to one million nodes within hours, and is widely used in the field of protein family analysis. It comes with sibling utilities for handling and analyzing graphs, matrices, and clusterings.
'Metro' evaluates the difference between two triangular meshes. It adopts an approximated approach based on surface sampling and point-to-surface distance computation, and has been widely used in the surface simplification research community (more than 140 citations according to google). It implements three different surface sampling methods:
* Montecarlo sampling (pick k random samples in the interior of each face) * Subdivision sampling (recursively subdivide each face along the longest edge and choose the sample in the center of each cell) * Similar Triangles sampling (subdivide each face F in k polygons similar to F and sample the face in correspondence with the vertices of these polygons, internal to F)
'Munin' gathers and graphs various types of information. You can install a node on the machines in your network, as well as on a central server. The nodes will know how to extract various kinds of information, such as load average and bandwith usage, and will wait for the server to request these values. The output is in HTML. You can be optionally notified if values move outside a specified range.
Nano-archimedes Heckert gnu.tiny.png
nano-archimedes is for the simulation of quantum systems. It is based on the Wigner equation, a formulation of quantum mechanics in terms of a phase-space which is mathematically equivalent to the Schroedinger equation. GNU nano-archimedes implements the Wigner Monte Carlo method. The code can be easily extended to density functional theory (DFT) and time-dependent ab-initio simulations.
NeuroScope is an advanced viewer for electrophysiological and behavioral data (with limited editing capabilities): it can display local field potentials (EEG), neuronal spikes, behavioral events, and the position of the animal in the environment.
NodPlot was developed to facilitate visualization of rapidly changing properties in 3D structured meshes for Computational Fluid Dynamics (CFD) research. The mesh must be 3D or more explicitly: 3 dimensions in space or 2 in space and 1 in time. 2D meshes can be visualized simply by repeating twice the 2D data in the input file. The visualization is performed on a node basis, rather than a spatial and/or temporal basis, which makes it easier to visualize complex spatial geometries in 3D.
The 'number' script prints the English name of a number. You can print names of extremely large numbers (e.g. 1e1234567). 'Number' can be run on the command line, or as a CGI script when run as 'number.cgi'. It prints names in both the American and European naming system, and can print the decimal expansion of a number in either naming system.
OGDF is a self-contained C++ class library for the automatic layout of diagrams. OGDF offers sophisticated algorithms and data structures to use within your own applications or scientific projects. The library is available under the GNU General Public License.
OpenChrom is data analysis a tool for gas chromatography and mass spectrometry. Its functionality and algorithms can be extended using a flexible plugin approach. File formats from various vendors are supported.
Calculate the life cycle impacts of a product or a service. Compatible with several life cycle inventory (LCI) databases and life cycle impact analysis methods (LCIA).
OpenVRML is a VRML/X3D browser and C++ runtime library. +The library includes parsers for VRML97 and VRML-encoded X3D as well as a +full runtime system for playing VRML/X3D content. An XEmbed control is +included along with frontends for use both as a stand-alone player and as a +Mozilla Gecko Web browser plug-in
Pathomx is a workflow-based tool for the analysis and visualisation of experimental data. Initially created as a tool for metabolomic data analysis is has been extended and can now be used for any scientific and non-scientific data analysis. The software functions as a hybrid of workflow and script-based approaches to analysis. Using workflows it is possible to construct rapid, reproducible analysis constructs for experimental data. By combining this with custom inline scripting it is possible to perform any analysis imaginable. Workflows can be dynamically re-arranged to test different approaches and saved to track the development of your approach. Saved workflows can also be shared with other users or groups, allowing instant reproduction of results and methods. Tools can export images as publication-ready high resolution images in common formats.
Plotutils Heckert gnu.tiny.png
Plotutils is a package for plotting and working with 2D graphics. It includes a library, "libplot", for C and C++ for exporting 2D vector graphics in many file formats. It also has support for 2D vector graphics animations. The package also contains command-line programs for plotting scientific data.
PLplot is a software package for creating scientific plots whose plot symbols and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer. The package includes a core C library, separate language bindings for that library, and separate dynamically loaded device drivers which control how the plots are presented in non interactive and interactive plotting contexts. The PLplot core library can be used to create standard x-y plots, semi-log plots, log-log plots, contour plots, 3D surface plots, mesh plots, bar charts and pie charts. Multiple graphs (of the same or different sizes) may be placed on a single page, and multiple pages are allowed for those device formats that support them. PLplot bindings exist for many compiled and interpreted languages, including C, C++, Lisp, Lua, OCaml, Octave, Perl or Python.
Processing.js implements the Processing API in JavaScript and also converts Processing programs to JavaScript, thus allowing someone to program an HTML 5/JavaScript program by just learning the Processing programming language. Processing was originally developed to be easy for artists to program, but it is functional enough to be used for doing any visual programming including game making. Processing itself is also free software, but it depends on non-free parts of Java; therefore Processing.js is a good replacement.
PuffinPlot is a user-friendly, cross-platform program which analyses and plots palaeomagnetic data. It provides several plot types and analysis functions commonly used in palaeomagnetism, user-configurable graph layout, CSV data export, and SVG and PDF graph export. It has facilities for both interactive and bulk analysis, and can also be controlled and extended using any JVM-based scripting language (including Python). PuffinPlot is written in Java.
PyMOL is a molecular visualization system created by Warren Lyford DeLano and commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. PyMOL is one of a few free visualization tools available for use in structural biology. The Py portion of the software's name refers to the fact that it extends, and is extensible by the Python programming language. PyMOL uses OpenGL Extension Wrangler Library (GLEW) and Freeglut, and can solve Poisson–Boltzmann equations using the Adaptive Poisson Boltzmann Solver.
'PyQwt' is a set of Python bindings for the Qwt class library which contains widgets for scientific and engineering applications. It allows you to integrate PyQt, Qt, Qwt, the Numerical Python extensions, and optionally SciPy in a GUI Python application or in an interactive Python session.
PyX is a Python package for the creation of encapsulated PostScript figures. It provides both an abstraction of PostScript and a TeX/LaTeX interface. Complex tasks like 2D and 3D plots in publication-ready quality are built out of these primitives.
CAGE is a fairly generic and complete cellular automaton simulation engine. 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. It 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) and a unique implementation of a finite state machine. CAGE is intended primarily as an education toolkit, rather than an industrial-strength CA simulator.
Pyrels is a tool for exploring and visualizing relationships between Python objects. It does so by analysing and converting Python namespaces into GraphViz files in the DOT format. That means it displays relationships like references between Python names and the objects they point to, as well as containment between Python container objects (lists, tuples and dictionaries) and the respective objects they contain. At the moment pyrels is best used on Python data structures, but it is intended to develop it further so that it can also display other types of relationships like inheritance, module imports, etc. One target group for pyrels are article and/or book authors who wish to illustrate Python data structures graphically without spending a lot of time for creating these illustrations manually. Pyrels can help you automate this process.
'Pyslice' provides utility functions for parametric modeling. It creates data sets based on a configuration file and a series of template files, then runs a model against each data set. It tracks each model's progress, keeping the total number of concurrent model runs under a limit established by the user. It is useful for running many model runs on a Beowulf cluster, or for control of the model runs on single processor machines. It can also monitor the model runs through an internal queue, or place the modeling jobs into a queue managed by other software.
Qastrocam is a capture program that can work with any video4linux device (see the home page for a complete list). Its main purpose is to do astrophotography. It can control a telescope to do guiding with the images received from the video device. It can also control the extended features of a webcam modified to do long exposure (several seconds) captures. Images can be saved in a variety of formats including, BMP, PNG, and JPEG.
QtiPlot is a clone of Origin and does scientific plotting, data analysis and curve fitting. It supports making 2D, statistical and 3D plots as well as 2D and 3D function graphing. QtiPlot can export to many different formats, including vector-based files.
SImg is a software for astronomical image processing. It contains a tool for visualization of highly dynamic images. The package consists of a library and applications which use it. Some of the features are deconvolution (various methods), Video4Linux support, PSF computation, approximation by linear combination of images and polynoms, various color transforms, automatic shifting of image sets (for addition and color composition), and more.
SciDAVis is a user-friendly data analysis and visualization program primarily aimed at high-quality plotting of scientific data. It strives to combine an intuitive, easy-to-use graphical user interface with powerful features such as Python scriptability.
Seismic Toolkit
'Seismic Toolkit' processes and displays seismic signal data in a GUI. It reads seismic signals in SAC format, and provides user operations such as zooming, filtering, spectral analysis, polarisation analysis, time-frequency representation, Hilbert transform, and singular value decomposition.
SimPy is a discrete event, object-oriented, simulation package for Python 2.2 and later. It uses generators which support efficient implementation of coroutines. It allows easy interfacing to GUIs and graphing packages for analysis. Tutorial and examples are included.
SimThyr is a continuous simulation program for pituitary-thyroid feedback control. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients. SimThyr is based on a physiologically-grounded nonlinear mathematical theory of thyroid homeostasis. The application supports simulation in time domain and various methods of sensitivity analysis. Source code is provided for Lazarus and Free Pascal. The program is compatible with most desktop Linux distributions, Mac OS X and Windows.
The 'Snack' sound extension adds commands for sound play/record and sound visualization, e.g. waveforms and spectrograms. It supports in-memory sound objects, file based audio, streaming audio, WAV, AU, AIFF, and MP3 file formats, synchronous and asynchronous playback. The visualization canvas item types update in real-time and can output PostScript. New commands and file formats can be added using the Snack C-API. 'Snack' was developered primarily for handling digital recordings of speech, but is just as useful for general audio. It has also successfully been applied to other one-dimensional signals.
'SpecTcl' is a framework for data analysis of nuclear physics event data. It is delivered both as a canned program and as a C++ class framework. It is run-time extensible via the Tcl/Tk scripting language. The class framework allows the program to be easily extended, and class wrappers for Tcl/Tk make it trivial to add to the SpecTcl command set as well as to expose Tcl/Tk variables to user code.
Sphere Filler
Recreate the sphere-filling algorithm described by Jean-Francois Ferellec in the following publication: Ferellec, J. & McDowell, G. (2010). Geotechnique 60, No. 3, 227–232 [doi: 10.1680/geot.9.T.015] Application to graphics and Discrete Element Method (DEM) calculations.
'Split-Dist' calculates the number of splits (edges) that differs for two trees. When you construct phylogenetic trees using slightly different methods, or from slightly different input data, the trees will not completely agree on the topology. When they differ, it is interesting to know where they differ (which edges can be found in both trees and which cannot).
'stl2pov' reads an STL (Standard Triangulation Language) file and outputs a POVray mesh. It creates either triangles by default, but can generate smooth_trianges; can read binary STL files, and has an option to smooth the generated mesh.
Tempest consists of separate implementations in multiple programming languages (such as Perl, PHP, Python, et cetera) all conforming to a unified API specification. Each implementation can alternatively support any number of different image manipulation libraries (such as GD, ImageMagick, PIL).
'' visualizes structures and dependencies between words in a text document via graphviz-tools (
Umbrello UML Modeller
Umbrello UML Modeller is a Unified Modelling Language diagram tool for KDE. It is able to produce Class diagrams, Sequence diagrams, Collaboration diagrams, Use Case diagrams, Activity diagrams, and State diagrams. It uses an XMI-based file format. It is now part of KDE and will be released with KDE 3.2
VStar is a multi-platform, easy-to-use variable star data visualization and analysis tool that was originally developed as part of the AAVSO's Citizen Sky project. Data for a star can be read from the AAVSO International Variable Star Photometric database or from a text file of your own creation.
VTK Designer is an object oriented, plugin based software written using VTK and Qt that provides a visual and interactive method to designing VTK visualization pipelines easier. The package includes the vdf2cpp command line utility to convert pipelines to C++ code from stored VDF files. With VTKDesigner, users can:
* Create VTK pipelines visually * Edit properties and check their impact on the fly * Add their own VTK classes to VTK Designer via wrappers and plugins * Generate C++ code of the pipeline * Save and retrieve piplines into VDF files * Create large pipelines using pipeline parts
Veusz is a GUI scientific plotting and graphing package. It is designed to produce publication-ready Postscript, PDF or SVG output. In Veusz plots are created by building up plotting widgets with a powerful and consistent object-based interface. The program also provides a command line and scripting interface (based on Python) to its plotting facilities. It can also act as a Python plotting module. Data can be read from text, CSV or FITS files, and data can be manipulated or examined from within the application.
Vis5D+ includes enhancements to and additional development for the Vis5d scientific visualization tool, a program to display volumetric datasets in 3+ dimensions.
'VisLib' is a Gtk application for visualizing, editing and searching hierarchically organized couples of visual and textual information. It can handle everything from personal material like family or holiday photographs, desktop backgrounds, digital comics, to scientific data or images like material samples or bacterial cultures photographs.
Vision Egg
The Vision Egg is a programming library (with demo applications) that uses standard, inexpensive computer graphics cards to produce visual stimuli for vision research experiments. Potentially difficult tasks, such as initializing graphics, getting precise timing information, controlling stimulus parameters in real-time, and synchronizing with data acquisition are greatly eased by routines within the Vision Egg.
Vision Egg 2
The Vision Egg is a programming library (with demo applications) that uses standard, inexpensive computer graphics cards to produce visual stimuli for vision research experiments. Potentially difficult tasks, such as initializing graphics, getting precise timing information, controlling stimulus parameters in real-time, and synchronizing with data acquisition are greatly eased by routines within the Vision Egg.
WORLD is a high-quality speech analysis/synthesis system on the basis of Vocoder. It is free software under the modified BSD license, and it is not encumbered by software patents.
White dune
'white_dune' is a graphical editor, a simple NURBS/Superformula/Subdivision 3D modeller, and a animation tool for the VRML97(Virtual Reality Modelling Language)/X3D, which is the ISO standard for displaying 3D data over the web via browser plugins (or webgl via X3DOM or X_ITE javascript) . It supports animation, realtime interaction and multimedia (image, movie, sound). Dune reads VRML97/X3D files, displays, and let the user change scenegraphs/fields. 'white_dune' can also translate a VRML97/X3D file to C, C++ or java. The resulting file can be rendered with OpenGL/jogl. Under GNU/Linux white_dune is a immersive VRML editor. It has support for stereoscopic view via "quadbuffer" capable stereo visuals and support for various 3D input devices supported by the X11 XInput or Linux joystick interface.
X_ITE is a new WebGL X3D Browser engine entirely written in JavaScript and uses WebGL for 3D rendering. Authors can publish X3D source online within an HTML5 page with X_ITE that works with Web browsers without prior plugin installation. This gives X3D authors the ability to displays content in 3D, using WebGL 3D graphics technology to display X3D content in several different browsers across several different operating systems. Since X3D is backwardly compatible, X_ITE can also be used as a VRML viewer.
Integrate 3D content seamlessly into your webpage - the scene is directly written into the HTML markup. No Plugins needed.
'XCore' processes, visualizes, and analyzes scientific cores. It includes rectifying core photographs, a simple core logger, and an OpenInventor based visualization system. It also includes many special features for paleomagnetic data from cores.
'xd3d' is a simple scientific visualization tool designed to be easy to learn. It can plot 2D and 3D meshes, with shadowing, contour plots, vector fields, iso-contour (3D), as well as 3D surfaces z=f(x,y) defined by an algebraic expression or a cloud of points. It generates high-quality vector PostScript files for scientific publications and still or animated bitmap images. The distribution includes the graph plotter 'xgraphic'.
Xeukleides 2
Xeukleides is a frontend for editing and viewing figures described by the language Eukleides (which provides simple and powerful commands for creating elementary Euclidean geometry figures).
PeerLibrary is an free software project developing a collaborative online community where scholars and researchers can discover, read, and discuss scholarly literature all within one site. This project focuses on expediting access to publications, enabling public recordings of analysis and insights on said publications, and encouraging collaboration and openness in the development of science.

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