[[Science::+]]

AElhometta: Archaic attempt at autonomous non-sandboxed distributed artificial life of assembler automaton type, it features: separation of descriptive and executive data that provides branches and loops without jump instructions, publish-subscribe interaction with other instances over Tor, input/output through ordinary files associated with external sensors and actuators, and built-in shell.

AITALC: The main goal is to create numerical programs directly from Feynman rules. It is actually developed for few known models like the electroweak standard model and QED, and the limit of application is, for the moment, the 2 to 2 particles reactions involving only external fermions

Achoz: will offer search and tools to reduce your data, keep it clean, fast and easy. in alpha development stage.

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

Aletheia: 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.

Alpine3D: Alpine3D is a spatially distributed (surface), three dimensional (atmospheric) model for analyzing and predicting dynamics of snow-dominated surface processes in mountainous topography. It includes models for snow cover (SNOWPACK), vegetation and soil, snow transport, radiation transfer and runoff which can be enabled or disabled on demand.

Amide: AMIDE: (Amide's a Medical Imaging Data Examiner) AMIDE is a tool for viewing and analyzing medical image data sets such as DICOM. It's capabilities include the simultaneous handling of multiple data sets imported from a variety of file formats, image fusion, 3D region of interest drawing and analysis, volume rendering, and rigid body alignments.

Antidote: Antidote is an free software implementation of the IEEE 11073-20601 standard. It also contains the implementation of a D-Bus based 11073 manager service.

Arvados: 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.

Astro Catalog: The Astro::Catalog module is an generic, object-oriented astronomical catalogue. It provides access to the online USNO-A2 and Guide Star Catalogues provided by ESO/ST-ECF, and additionally provides read/write access to ARK CLUSTER format files.

Astroconst: Astroconst makes header files in C, Fortran, Perl, IDL, Java, and GNUplot defining many astrophysical constants useful for scientific programming. A single modifiable data file automatically generates these header files, so you can add new constants to the data file and generate new header files in all appropriate languages without fiddling with each header file individually.

Astronomical Papers Library: A C library containing theories of motion of solar system objects that have been published in various astronomical journals such as Astronomy & Astrophysics, the Astronomical Journal, and Astronimcal Papers prepared for the use of the American Ephemeris. Currently this includes such theories as Newcomb's "Tables of the Sun" and all the planets as well as the theory known as "The Improved Lunar Ephemeris".

Asymptote: '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.

Atlc: 'atlc' (Arbitrary Transmission Line Calculator) is a computer aided design (CAD) package for designing and analysing electrical transmission lines and directional couplers of totally arbitrary cross section, with an arbitrary number of different dielectrics. The analysis programs in 'atlc' lets users find the electrical properties of a transmission line or coupler whose physical dimensions are known. The design programs lets users physically realise a transmission line or coupler with certain given electrical properties. The package supports multiple CPUs, as some parts are CPU intensive. It is most likely to be useful to radio amateurs.

Avaneya: Whether you are a fan of science fiction, a space–science enthusiast, hobbyist, photographer, gamer or a patron of grass–roots libre arts and technology, you are sure to find the first successful images from the surface of Mars highly captivating. These mind blowing images were taken by NASA's Viking landers during the highly ambitious, billion–dollar mission first launched in 1975. However, many images were nearly lost to history due to magnetic tape deterioration and archaic proprietary technology. With NASA's blessing, our team developed the technology to recover many of these images. This research tool was part of the design phase of our parent project, Avaneya — our upcoming libre cerebral science fiction game for the GNU operating system set on Mars, described in the words of Richard Stallman as an exciting, pioneering project. Originally an internal research tool, overwhelming public interest compelled us to release the technology on this DVD for all. Now everyone can relive the original breathtaking experience that captured the world's attention and marked the first successful moment in history that humanity saw Mars — not as a distant, impersonal, celestial body, beheld through a telescope for centuries, but as a tangible and alien world well within its reach.

Avogadro

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.

Avsomat: 'avsomat' is a framework for automating the scheduling of variable star observations, identification and photometry of variable stars on CCD images, and the reporting, management, and verification of results. It uses electronic charts of the star fields in which variable stars appear, and maintains a view of the current results in the form of a collection of interlinked Web pages.

BRL-CAD: 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.

Bamtools: BamTools provides both a programmer's API and an end-user's toolkit for handling genome alignment files in the BAM and SAM format. A BAM file (.bam) is the binary version of a SAM file. A SAM file (.sam) is a tab-delimited text file that contains sequence alignment data.

Bcbio-nextgen: A python toolkit providing best-practice pipelines for fully automated high throughput RNA sequencing analysis. It can work with BWA, .bam or .fastq files.

Bcrypt: Password hashing Python library.

Beremiz: Beremiz is an integrated development environment for machine automation. It is Free Software, conforming to IEC-61131 among other standards. It relies on open standards to be independent of the targeted device, and let you turn any processor into a PLC. Beremiz includes tools to create HMI, and to connect your PLC programs to existing supervisions, databases, or fieldbuses.

Besssugo: 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.

BioMail: BioMail automates searching for recent scientific papers in the PubMed Medline database, and can periodically run a customized Medline search and send all recent matching articles to the user's e-mail address. You can save search patterns: no more remembering which search was good and which wasn't. It is intended for medical researchers, biologists, and anyone who wants to know the latest information about a disease or a biological phenomenon. It is also useful for users who have email address but slow or sporadic Web access; they can set up searches and have them emailed to an address instead of having to surf the Web themselves for the information.

BioRuby: BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple, stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation.

Bioinformatics Template Library: This library focuses on the data structures and algorithms used in bioinformatics and molecular modelling, following closely the approach of the Standard Template Library (STL) to implement efficient generic programming modules using compile time mechanisms. Although the BTL was designed with biomolecular applications in mind it contains classes of more general utility: for instance, the Matrix class could be used for matrix algebra in many contexts.

Bioperl: The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g., Ensembl. The recommended packages are needed to run some of the included binaries, for a detailed explanation including the specific Perl modules please see README.Debian. The suggested package enhances the manual pages.

Bioperl-run: Contains scripts from the BioPerl-Run package. This package will also install all wrappable applications packaged in Debian. The ones that are not Free are "Suggested" by this package.

Biskit: 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.

Bkchem: BKchem is a chemical drawing program written in Python. It is platform independent.

BlockCanvas: 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.

Blossoc: Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input, score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation. Building the local genealogy trees is based on a number of heuristics that are not guaranteed to build true trees, but have the advantage over more sophisticated methods of being extremely fast. Blossoc can therefore handle much larger data sets than more sophisticated tools, but at the cost of sacrificing some accuracy.

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.

Botec: BOTEC is a simple astrophysical and orbital mechanics calculator, including a database of all named Solar System objects. BOTEC is intended as a simple but useful calculator to assist with making astrophysical, orbital mechanics, and space navigation calculations. As the origin of the acronym applies, BOTEC is more of a "back-of-the-envelope calculator" rather than an industrial-strength calculator, although this may change in the future.

Brightway2: Life cycle assessment, Monte Carlo uncertainty analysis, visualization of results

C-graph: 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: Code Art Now. 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.

CLHep: 'CLHelp' is a set of HEP (High Energy Physics)-specific foundation and utility classes such as random generators, physics vectors, geometry, and linear algebra.

CT Sim: Computed Tomography is the technique of estimating the interior of objects from the measurements of radiation projected through the object. That radiation can be transmitted through the object such as in X-ray computed tomography or emitted from internal radiation sources as in nuclear medicine scans. CTSim simulates the transmission of X-rays through phantom objects. These X-ray data are called projections; CTSim reconstructs the original phantom image from the projections using a variety of algorithms. The program also has a wide array of image analysis and image processing functions.

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.

Celestia: Celestia is a real-time visual simulation of space. Choose a point within the Local Group of galaxies, and Celestia will show you an approximation of how it would appear to your eyes were you actually there. Some of what Celestia shows is necessarily hypothetical--the farther away from Earth you get, the less real data there is and the more guesswork is involved. Thus Celestia supplements observational data with good guesses based on models of stellar and planetary processes. You can also navigate at an immense range of scales. Orbit a couple kilometers above the surface of a tiny, irregular asteroid, then head off toward Jupiter, watching it grow from a bright point of light into a looming sphere filling your field of vision. Leave our solar system entirely and observe the sun as it fades from a brilliant disk to a bright star, disappearing almost entirely as you head off toward the Upsilon Andromeda system to orbit around its innermost giant planet.

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).

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.

Chadeche: This software is associated to an hardware part a modular battery charger/discharger. It allow to describe and control any kind of law of charge/discharge. Charge and discharge scenarios are described into a configuration file. During the charge/discharge process battery voltage is continuously monitored and some data are displayed and recorded for further analysis. Chyradeche has been tested on a Raspberry Pi A+ under Raspbian Lite operating system. The Rapsberry Pi needs to be connected to the Chadeche hardware.

Charlemagne: Charlemagne is a genetic programming application that includes both a commandline client and an interactive console mode. It is written in Python and Lisp, and is user extensible to some degree in both languages. It features built-in input-output mapping support and provides the ability to define complex fitness calculations in Lisp or Python.

Chemtool: Chemtool is a GTK+-based 2D chemical structure editor for X11. It draws organic molecules easily and store them as a X bitmap file. You can export drawings in XFig format for further annotation, or as Postscript files (using xfig's companion program transfig). The distribution includes a set of sample molecular structure drawings. The package also contains a helper program, cht, to calculate sum formula and (exact) molecular weight from a chemtool drawing file.

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.

CodeGen: Based on paper: Program synthesis strives to generate a computer program as a solution to a given problem specification, expressed with input-output examples or natural language descriptions. The prevalence of large language models advances the state-of-the-art for program synthesis, though limited training resources and data impede open access to such models. To democratize this, we train and release a family of large language models up to 16.1B parameters, called CODEGEN, on natural language and programming language data, and the training library JAXFORMER.

CodeGen2: Based on paper: CodeGen2 is a family of autoregressive language models for program synthesis.

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.

CvEyeTracker: 'cvEyeTracker' is a toolkit for low-cost real-time eye tracking. It is intended to provide a hardware design and a set of software tools useful for the analysis of eye movement data collection using inexpensive, off-the-shelf hardware. Available tools include algorithms to measure eye movements from digital videos, techniques to calibrate the eye tracking system, and example software to facilitate real-time eye-tracking application development.

DAMASK: At the core of DAMASK is a flexible and hierarchically structured model of material point behavior for the solution of elastoplastic boundary value problems along with damage and thermal physics. Its main purpose is the simulation of crystal plasticity within a finite-strain continuum mechanical framework.

DGPS: On a stationary GPS without a differential correction signal, you should see a 20 meter average radius "random walk" pattern. On the same receiver with DGPS corrections and a good view of the sky, the error should be reduced to approx. 2 meters average radius.

DataMelt: DataMelt (DMelt) is an environment for numeric computation, statistical analysis, data mining, and graphical data visualization on the Java platform. This Java multiplatform program is integrated with a number of scripting languages: Jython (Python), Groovy, JRuby, BeanShell. DMelt can be used to plot functions and data in 2D and 3D, perform statistical tests, data mining, numeric computations, function minimization, linear algebra, solving systems of linear and differential equations. Linear, non-linear and symbolic regression are also available. Neural networks and various data-manipulation methods are integrated using powerful Java API. Elements of symbolic computations using Octave/Matlab scripting are supported.

DataStatix: DataStatix is a free software for GNU/Linux and Windows useful to manage data of every kind (although it has been written to manage biomedical data), to create descriptive statistics and graphs and to export items easily to R environment or to other statistic softwares. In order to handle properly big amount of data and many concurrent users, DataStatix works with MySql database and it has been developed and tested with MySql community edition 5.5. Some features of the software are: users management (create, delete, modify password) within the software; different users levels of data access (administrator, default, read only); user defined templates (models) of data, to create new databases easily; importation and esportation of data in CSV format (used also by Calc and Excel); updating of existing data from a CSV file created with DataStatix; descriptive statistics from every data (some more kind of statistics to come); graphs from every data.

Datamash: Datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files. Datamash is designed to be portable and reliable, and aid researchers to easily automate analysis pipelines, without writing code or even short scripts.

Dbacl: 'dbacl' is a digramic Bayesian text classifier. Given some text, it calculates the posterior probabilities that the input resembles one of any number of previously learned document collections. It can be used to sort incoming email into arbitrary categories such as spam, work, and play, or simply to distinguish an English text from a French text. It fully supports international character sets, and uses sophisticated statistical models based on the Maximum Entropy Principle.

Deduce: 'Deduce' is an artificial intelligence program which accepts natural language sentences as input. These sentences describe properties and relationships between objects, (for example, "Spot is a dog", "A liquid will evaporate", or "Water does not flow uphill"). The user can then ask questions against that input, to which Deduce will attempt to answer using deductive reasoning techniques.

DeepSpeech: From GitHub README: DeepSpeech is an Speech-To-Text engine, using a model trained by machine learning techniques based on Baidu's Deep Speech research paper. Project DeepSpeech uses Google's TensorFlow to make the implementation easier.

Degate: Degate is a tool that aids VLSI- reverse engineering of digital logic in integrated circuits (ICs). Degate helps you to explore layered images from ICs. It matches standard cells on the imagery given by graphical templates and to some degree degate matches vias and wires and assists you in tracing circuit paths and in reconstructing the net list. Degate is not a completely automatic analyzing tool. Degate helps you with some automation in your manual chip reverse engineering process.

Dezyne: The Dezyne language has formal semantics expressed in mCRL2 developed at the department of Mathematics and Computer Science of the Eindhoven University of Technology (TUE). Dezyne requires that every model is finite, deterministic and free of deadlocks, livelocks, and contract violations. This achieved by means of the language itself as well as by builtin verification through model checking. This allows the construction of complex systems by assembling independently verified components.

Dimnum: The dimnum library contains templated C++ classes for storage and manipulation of dimensionful numbers, as encountered in physics and engineering. Since it uses templates, there is no size or speed penalty with respect to normal variables (depending on compiler optimisations).

Dinrhiw2

Primary aim of the dinrhiw is to be linear algebra library and machine learning library. For this reason dinrhiw implements PCA and neural network codes. Currently, the neural network code only supports:

hamiltonian monte carlo sampling (HMC) and simple bayesian neural network
second order L-BFGS search
gradient descent (backpropagation)

As well as mathematical routines for arbitrary precision mathematics, hermite curve interpolation and many other things.

Dionysus: Dionysus is a convenient system for quickly retrieving the values of mathematical constants used in science and engineering. Values can be searched using a simple command-line tool, choosing from three databases: universal constants, atomic numbers, and constants related to semiconductors.

Discosnp: Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS). Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed. The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP: 1) its mean read coverage 2) the (phred) quality of reads generating the polymorphism.

Discrete Event Calculus Reasoner: The Discrete Event Calculus Reasoner allows a programmer to add common-sense reasoning capabilities to programs. It supports deduction/temporal projection, abduction/planning, postdiction, and model finding. It allows default reasoning about action, change, space, and mental states. It is based on the event calculus, a comprehensive and highly usable logic-based formalism. It helps applications understand the world, make inferences, adapt to unexpected situations, and be more flexible.

DragGAN: Synthesizing visual content that meets users' needs often requires flexible and precise controllability of the pose, shape, expression, and layout of the generated objects. Existing approaches gain controllability of generative adversarial networks (GANs) via manually annotated training data or a prior 3D model, which often lack flexibility, precision, and generality. In this work, we study a powerful yet much less explored way of controlling GANs, that is, to "drag" any points of the image to precisely reach target points in a user-interactive manner, as shown in Fig.1. To achieve this, we propose DragGAN, which consists of two main components including: 1) a feature-based motion supervision that drives the handle point to move towards the target position, and 2) a new point tracking approach that leverages the discriminative GAN features to keep localizing the position of the handle points. Through DragGAN, anyone can deform an image with precise control over where pixels go, thus manipulating the pose, shape, expression, and layout of diverse categories such as animals, cars, humans, landscapes, etc. As these manipulations are performed on the learned generative image manifold of a GAN, they tend to produce realistic outputs even for challenging scenarios such as hallucinating occluded content and deforming shapes that consistently follow the object's rigidity. Both qualitative and quantitative comparisons demonstrate the advantage of DragGAN over prior approaches in the tasks of image manipulation and point tracking. We also showcase the manipulation of real images through GAN inversion.

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.

Drmaa: This is a Python implementation of the Distributed Resource Management (DRM) Application API (DRMAA). It provides all high- level functionality necessary to consign a job to a DRM system (e.g. Sun Gridengine), including common operations on jobs, such as termination or suspension.

E-CELL Simulation Environment: E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components, driven by multiple algorithms with different timescales, to coexist. The core library is written in C++ with a Python binding, and frontend software uses Python.

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.

EPICS: 'EPICS' is a software infrastructure for building distributed control systems to operate devices such as particle accelerators, large experiments and major telescopes. These systems comprise tens or hundreds of computers, networked together so they can communicate and provide control and feedback of the various parts from a control room, or remotely over the Internet. EPICS uses Client/Server and Publish/Subscribe techniques to communicate between the various computers. Most servers (called Input/Output Controllers or IOCs) perform real-world I/O and local control tasks, and publish this information to clients using the Channel Access (CA) network protocol. CA is specially designed for the kind of high bandwidth, soft real-time networking applications that EPICS is used for, and is one reason why it can be used to build a control system comprising hundreds of computers.

EWOK: An interactive graphic program for synthesizing a particular class of mechanisms called four-bar linkages to produce specific coupler motions.

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 OsnabrÃÂ¼ck. The data is loaded on demand over the Internet.

Edlib: Lightweight, super fast C/C++ library for sequence alignment using edit distance.

Electric: Electric is a CAD program for designing electrical circuits, handling custom IC layout, schematic drawing and hardware description language specifications. Several CAD operations are supported, such as rule checking and simulation. Many different types of designs can be produced and input or output in a wide variety of formats. GNU Electric offers a wide range of synthesis and analysis tools for working on the circuitry, including design rule checking, simulation, routing, layout vs. schematic, logical effort… It also has many importers and exporters for interfacing to other EDA (Electronic Design Automation) systems. It even has a constraint system for managing chip layout.

Electric Fields Visualization Python: This is educational software that demonstrates the field and fluxlines for electric charge particles.

Electrocardiognosis: Electrocardiognosis (a.k.a. Ecgnosis) is a software package designed to assist the physician in formulating diagnoses on 24h ambulatory ECG monitoring (Holter) recordings.

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>

Emacs madx-mode: This program creates a madx major for emacs that highlights the cern (Methodical Accelerator Design) MAD-X 5 syntax. This is not a GNU package.

Emgr: Empirical gramians can be computed for linear and nonlinear control systems for purposes of model order reduction, uncertainty quantification or system identification. Model reduction using empirical gramians can be applied to the state space, the parameter space of dynamical systems and control systems. The emgr framework is a compact open source toolbox for (empirical) gramian-based model reduction and compatible with OCTAVE and MATLAB.

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

Ephemeris: 'Ephemeris' reads, writes, and interpolates the JPL planetary ephemeris data that is the world standard planetary dataset. It should compile on any machine that uses gcc and supports IEEE floating point arithmetic, and has been tested under GNU/Linux. It uses an included library, gnulliver.c, that automatically handles integer and floating point Big-endian/Little-endian byte swapping to match Big-endian/network order on any computer. gnulliver.c can be used separately under the LGPL 2.1. This is a redesign of JPL's original FORTRAN code, available on JPL's FTP website (ftp://ssd.jpl.nasa.gov/pub/eph/export/), with some added flexibility (including patching some inconsistencies in the original JPL data files). 'Ephemeris' is not associated with JPL or NASA, but just uses JPL's data.

EpiR: A package for analysing epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.

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.

FANN: Fast Artificial Neural Network Library (fann) implements multi-layer feedforward networks that support both fully connected and sparsely connected networks. It supports execution in fixed point arithmetic to allow for fast execution on systems with no floating point processor. To overcome the problems of integer overflow, the library calculates a position of the decimal point after training and guarantees that integer overflow cannot occur with this decimal point. FANN is designed to be fast, versatile, and easy to use. Several benchmarks have been executed to test its performance. It is significantly faster than other libraries on systems without a floating point processor, and comparable to other highly optimized libraries on systems with a floating point processor.

Fairseq: From GitHub README: Fairseq(-py) is a sequence modeling toolkit that allows researchers and developers to train custom models for translation, summarization, language modeling and other text generation tasks. We provide reference implementations of various sequence modeling papers.

FastDNAml: 'fastDNAml' estimates maximum likelihood phylogenetic trees from nucleotide sequences. It is derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). 'fastDNAml' tries to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML program from PASCAL to C.

FastQC: FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are * Import of data from BAM, SAM or FastQ files (any variant) * Providing a quick overview to tell you in which areas there may be problems * Summary graphs and tables to quickly assess your data * Export of results to an HTML based permanent report * Offline operation to allow automated generation of reports without running the interactive application

Ffpi: The FFPI-III is an open-access questionnaire, consisting of 100 questions about how someone is as a person. For example: Is this person someone who... ... adapts easily? o o o o o no ? yes Answering the questions takes approximately 15 minutes. The responses are processed into a personality profile on the trait factors Extraversion, Mildness, Orderliness, Emotional Stability and Autonomy, and a summarizing characterization. In de report (which you can download), the profile is set alongside the average self-report of the (Dutch) adult.

Fisicalab

FísicaLab is an educational application for solving physics problems creatively. Current modules includes:

Kinematics of particles 2D
Circular kinematics of particles 2D
Static of particles 2D
Static of rigid bodies 2D
Dynamics of particles 2D
Circular dynamics of particles 2D
Calorimetry, ideal gas and expansion

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.

FlightGear

FlightGear Flight Simulator (often shortened to FlightGear or FGFS) is a free, open-source, multi-platform, flight simulator, created by volunteers. FlightGear is an atmospheric and orbital flight simulator used in aerospace research and industry. Its flight dynamics engine (JSBSim) is used in a 2015 NASA benchmark to judge new simulation code to the standards of the space industry. FlightGear 2020.3 has 700+ aircraft in launcher with 1-click install and update, that can be filtered by advancement level in flight dynamics model (FDM), systems, or art. The rest are available through 3rd party hangars or from development repositories. Broad overview of features as of 2020: 3d buildings & roads for entire planet based on OpenStreetMap (OSM) data and automatic generation, terrain-driven weather simulation, addons, multiplayer environment, orbital rendering, a flexible and open aircraft modelling system, varied networking and interfacing options, multiple display support, multiple flight dynamics engines, multiple rendering pipelines, detailed weather visualisation with ALS renderer, a powerful scripting language, and other features suited for settings in research, industry, DiY projects, and desktop simulation, combined with an open architecture. Used professionally, as well as non-professionally. Platforms: Windows, GNU/Linux, Mac, FreeBSD, others. Compiles for ARM processors, including Raspberry Pi. See:

Applications and usages
Tours
News
Info, help, and contribution: wiki, forum, mailing list
Quick aircraft recommendations - see screenshots and caption text in install aircraft page

Professional and Educational usages The FlightGear project has been used in a range of projects in research and industry, including by NASA for both Earth and Mars conditions (e.g. in ARES glider design for Mars^[1]. It has been used as a research and development platform by various agencies and universities. Other than aerospace research and development, FlightGear is used in aviation or aviation-adjacent industries in various ways. For example, teaching student pilots procedures or handling in a simulator saving expensive flight time - e.g. FlightGear is integrated into various FAA certified training simulators^[2], in contrast to use in full-motion (6-DoF) research simulators like at the University of Naples^[3] where FlightGear is utilised for physics not just used for visualisation/interface. Similarly, FlightGear has been used to teach air traffic controllers (ATC)^[4] and allows for dedicated ATC client/instructor interfaces as well as visuals using real-life ATC tools like binoculars or cameras - teachers can alter traffic, weather, re-create traffic patterns, and so on. Different forms of instructor stations are possible for different areas of instruction. FlightGear has also been used in general education e.g. exhibits in museums^[5] and all sorts of DiY projects. About the project The simulator is created by an international group of volunteers, and released as free, open-source GPL software. The goal of the FlightGear project is to create a sophisticated and open flight simulator framework for use in research or academic environments, pilot training, as an industry engineering tool, for DIY-ers to pursue their favorite interesting flight simulation idea, and last but certainly not least as a fun, realistic, and challenging desktop flight simulator. Being free software, FlightGear has historically received development from the science and engineering community. Many contributors have had an academic background in engineering, maths, physics, or computer-science - in addition to some involvement or interest in aviation like being pilots (hobby, professional, test pilots, or retired). This is true especially among long-term contributors, and the academic insight has shaped the project's simulation standards.^[6] There are many exciting possibilities for an open, free flight sim. It is hoped that this project will be interesting and useful to many people in many areas. History FlightGear started as an online proposal in 1996 by David Murr, living in the United States. He was dissatisfied with proprietary, available, simulators citing motivations of companies not aligning with the simulators' users, and proposed a new flight simulator developed by volunteers over the Internet.^[7] Development of an OpenGL based version was spearheaded by Curtis Olson starting in 1997. FlightGear incorporated other open-source resources, including the LaRCsim flight dynamics engine from NASA, and freely available elevation data. The first working binaries using OpenGL came out in 1997. By 1999 FlightGear had replaced LaRCsim with JSBSim built to the sims' needs, and in 2015 NASA used JSBSim alongside 6 other space industry standards to create a measuring stick to judge future space industry simulation code. The FlightGear project has been nominated by SourceForge, and subsequently chosen as project of the month by the community, in 2015, 2017, and 2019.^[8] ^[9] ^[10]

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.

Fosite: Fosite is a generic framework for the numerical solution of 2D hyperbolic conservation laws in generalized orthogonal coordinates. It is mainly intended for CFD problems with rotational symmetry.

FreeLIMS: FreeLIMS is a Laboratory Information Management System ( LIMS ). Manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. FreeLIMS is Open Source and Free.

FreeMED: FreeMED is a Web-based medical records (EMR) and patient management system with a printing system, patient scheduling, an HL7 interface, a billing system, XML-RPC Web services, and many other features. It has an extensible modular architecture, allowing it to be customized based on individual practices without having to rewrite core components of the system. It is HIPAA compliant.

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.

Freefem++: FreeFem++ is dedicated to the resolution of a large category of partial differential equations in 2D and 3D with complex applications, using finite element discretization and advanced automatic mesh generator. FreeFem++ is written in C++ and it owns documentation in spanich, Japanese and Chinese (http://www.freefem.org/). Finally, FreeFem++ aims the same objectives as Elmer (http://directory.fsf.org/wiki/Elmer) FreeFem++ is free software with LGPL license, developed at Jacques-Louis Lions Laboratory, Pierre and Marie Curie University.

Freesnell: FreeSnell is a program which computes optical properties of multilayer thin-film coatings. Dielectric, metallic, and granular metallic films are supported. The FreeSnell package includes a SCM script (program) "nk" to create, manage, and query a refractive-index spectral database. FreeSnell is an application of the SCM Scheme implementation and the WB B-tree database package.

FroZenLight: FroZenLight connects simple line art and mathematics. The source of light can be positioned so that either symmetric reflection patterns or secret messages (Cryptography) are created. Dozens of example light patterns and some math exercises are provided.

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.

G2q: A very simple Guile-to-OpenQASM 2.0 compiler based on a GNU Guile add-on library that lets you write programs for QASM-based quantum computers and simulators using Scheme.

GAMGI: GAMGI (General Atomistic Modelling Graphic Interface) is a program to build, view, and analyze atomic strucures such as molecules, crystals, glasses, liquids, etc. It aims to be useful for: the scientific community working in Atomistic Modelling that needs a graphic interface to build input data and to view and analyse output data, calculated with Ab-Initio and Molecular Mechanics programs; the scientific community at large studying chemistry, physics, materials science, geology, etc., that needs a graphic interface to view and analyse atomic structural information and to prepare images for presentations in classes and seminars; teaching chemistry and physics in secondary schools and universities; science promotion in schools, exhibitions and science museums.

GAUL: The Genetic Algorithm Utility Library (GAUL) is a programming library designed to assist in the development of code requiring genetic algorithms. The steady-state, generation based and the island model of evolution are supported, using the Darwinian, Lamarkian or Baldwininan evolutionary schemes. Standard mutation, crossover and selection operators are provided, while code hooks additionally allow custom operators. It provides data structures and functions for handling and manipulation of the data required for a genetic algorithm. Additional stochastic algorithms are provided for comparison to the genetic algorithms. Much of the functionality is also available through a simple S-Lang interface.

GDAL: The Geospatial Data Abstraction Library (GDAL) is a unifying C/C++ API for accessing raster geospatial data, and currently includes formats like GeoTIFF, Erdas Imagine, Arc/Info Binary, CEOS, DTED, GXF, and SDTS. It is intended to provide efficient access, suitable for use in viewer applications, and also attempts to preserve coordinate systems and metadata. Python, C, and C++ interfaces are available.

GDC: GDC is a utility to calculate compressible flow (Gas Dynamics Calculator). It provides calculations for isentropic nozzle, isothermal nozzle, isothermal, Fanno, Rayleigh flow, etc. It also provide calculations for shock and oblique shock by direct calculations (no iteration, probably the only one that can do it). The result are in plain text, LaTeX, or a range of values.

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.

GENtle: GENtle is bioinformatics software for everyday molecular biology tasks. It features DNA and amino acid sequence display and editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, primer design, virtual PCR, online database access, and more.

GEOS: 'GEOS' is a C++ implementation of the functions and predicates defined in the OpenGIS "Simple Features for SQL" specification. It includes high quality implementations of all important spatial relationships and operations, robust versions of all functions in the dimensionally extended 9 intersection predicate model, and implementations of the operators Buffer(), Union(), and Intersection() and all other SFSQL functions including Area(), Length(), Centroid(), etc.

GElemental: gElemental is a periodic table viewer that provides detailed information on the chemical elements. It is a port of GPeriodic to C++ and gtkmm, and it offers an improved UI, an updated and corrected data set, a better data format, a list view, and easier coloration.

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.

GMT: Generic Mapping Tools is a collection of ~60 GNU/Linux tools that allow users to manipulate (x,y) and (x,y,z) data sets (including filtering, trend fitting, gridding, projecting, etc.) to produce Encapsulated PostScript File (EPS) illustrations ranging from simple x-y plots through contour maps to artificially illuminated surfaces and 3-D perspective views in black and white, gray tone, hachure patterns, and 24-bit color. GMT supports 25 common map projections plus linear, log, and power scaling, and comes with support data such as coastlines, rivers, and political boundaries. Since the package is quite large, the authors suggest looking at the list of mirrors on the page to ensure that you download from the one closest to you.

GNOME Water Temperature Applet: The GNOME Water Temperature Applet displays water temperatures of rivers, lakes and oceans in your GNOME panel.

GPS: This is a candidate for deletion: Links broken. No links to page. Email to maintainer broken. Poppy-one (talk) 12:14, 31 July 2018 (EDT) Gravitational Particle Simulator uses numerical methods to simulate the behaviour of particles that obey the gravitational laws of motion. The numerical method used to approximate the differential equations is a 4th order Runge Kutta method. Home page is in Italian only, but the README and the comments in the code are in English.

GPSBabel: 'GPSBabel' converts waypoint data between dozens of file formats, including Magellan and Garmin serial, Mapsource, Mapsend, Streets & Trips, Delorme, National Geographics, many Pal formats, and many others. It is endian and word-size safe, includes a GUI, and runs on a variety of operating systems. It also supports Groundspeak GPX extensions for geocaching.

GPStk: 'GPSTk' is a set of both fundamental and advanced GPS processing algorithms. The library provides functions including RINEX I/O, ephemeris calculation, atmospheric refraction models, and positioning algorithms. The applications include cycle slip detection and removal, calculation of the Total Electron Content (TEC) of the ionosphere, bindings to 'octave', and RINEX file manipulation.

GPeriodic: GPeriodic is a periodic table application for GNU/Linux. It allows you to browse through a periodic table of the elements, and view detailed information on each of the elements. 118 elements are currently listed.

GRASS: Commonly referred to as GRASS, this is free Geographic Information System (GIS) software used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many governmental agencies and environmental consulting companies. GRASS is an official project of the Open Source Geospatial Foundation. GRASS contains modules for raster data manipulation (2D and 3D voxels), vector data manipulation, rendering images on the monitor or paper, multispectral image processing, point data management, time series analysis, and general data management, as well as tools for interfacing with digitizers, scanners, and SQL databases as PostgreSQL, and others.

GROMACS: GROMACS simulates molecular dynamics. It is primarily designed for biochemical molecules like proteins and lipids that have many complicated bonded interactions, but since it is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) it is also used for research on non-biological systems, e.g. polymers. GROMACS is user-friendly, with topologies, parameter files, and error messages written in clear text format. There is a lot of consistency checking, but no scripting language: all programs use a simple interface with command line options for input and output files.

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.

Galaxy- Stellar Simulation: This is a candidate for deletion: Links broken. No links to page. Email to maintainer broken. Poppy-one (talk) 12:40, 31 July 2018 (EDT) Galaxy is a computer program which simulates the motion of stars under the influence of gravity. Create a field of random stars to begin with, then watch the stars move as they are accelerated by their mutual gravitational attractions. You can vary the number of stars and the strength of gravity. Watch how the attractive forces accelerate individual stars and send them careening in new directions. Watch how large groups of stars develop into interesting patterns over time, such as clusters and spiral arms.

Gama: Gama is a program for the adjustment of geodetic networks. It is useful in measurements where Global Positioning System (GPS) is not available, such as underground. It features the ability to adjust in local Cartesian coordinates as well as partial support for adjustments in global coordinate systems. Network adjustment in a local coordinate system and its functionality is represented by the program gama-local, which adjusts geodetic (free) networks of observed distances, directions, angles, height differences, 3D vectors and observed coordinates (coordinates with given variance-covariance matrix). Global coordinate network adjustment model is based on geocentric coordinate system (adjustment model on ellipsoid). Its functionality is represented by the program gama-g3.

Gamma: Gamma is designed in the form of a compiler where the final output is geometry, which can be written to file in one of several common formats. It supports multiple language front ends and a great variety of operations for the creation and manipulation of geometry, which are made available to the user as libraries for the supported languages. It is primarily intended as a source code based solid modeling program.

Gammath SPOT: Gammath Stock Price-Opining Toolset (SPOT) is a comprehensive stock technical analysis software that is easy-to-use via its Graphical User Interface (GUI) and Command Line Interface (CLI). It takes watchlist as an input, collects necessary data from the Internet for the stocks on the watchlist, does technical analysis and algorithmically computes a stock analysis score [aka Gammath Score (gScore -- pronounced as "ga Score")] that is between -1 and +1 to indicate the degree to which the algorithm perceives the stock to be trading at a premium or at a discount. SPOT includes tools to compute estimated price projection, multipurpose estimation for Gammath Score and Price, compute useful probabilities, estimate support and resistance level, compute stock news headlines sentiment analysis, generate gscores history, backtest a trading strategy (for short-/long-term and medium-/high risk), screen stocks based on micro-Gammath Scores and run a SPOT trading simulator. [Gammath, SPOT and stylized g(m) are registered trade/service marks.]

Gcx: 'GCX' provides a complete set of data-reduction functions for CCD photometry, with frame WCS fitting, automatic target identification, aperture photometry of target and standard stars, single-frame ensemble photometry data reduction, multi-frame color coefficient fitting, extinction coefficient fitting, and all-sky photometry. 'gcx' also controls CCD cameras and telescopes and implements automatic observation scripting. It controls cameras through a hardware-specific server that it connects to through a TCP socket. It controls telescopes which use the LX200 protocol, and refines pointing by matching images to the GSC catalog position of stars. It also generates FITS files with comprehensive header information.

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.

GenChemLab: 'GenChemLab' is an OpenGL-based application intended to simulate several common general chemistry laboratory exercises. It is meant to be used to help students prepare for actual lab experience. Supported experiments include titration, calorimetry, freezing point depression, vapor pressure, electrochemistry, and spectrophotometry.

Genometools: The GenomeTools genome analysis system is a free collection of bioinformatics tools.

Geo Weather: Geo::Weather is a Perl module used to retrieve weather.com information based on city/state or US zip code. In order for the timeout code to work correctly, you must be using a recent version of libwww-perl and IO::Socket. Geo::Weather was developed with libwww-perl 5.53 and IO::Socket 1.26.

GeoNature: GeoNature is a suite composed of six different tools for the collection, management and distribution of wildlife data, and the administration of users and taxonomy repositories. The purpose of this suite is to build a tool that presents updated information on all sightings of the local species spotted by the national park’s agents.

GeoTIFF Viewer: GeoTIFF Viewer is a simple viewer for GeoTIFF files, which are georeferenced raster images, typically used for maps.

GeoToad: This is a candidate for deletion: Links broken. No archive.org entry. No maintainer response. Poppy-one (talk) 12:35, 5 August 2018 (EDT) 'GeoToad' is a geocaching query tool to help speed up choosing a cache and collecting the data. You can generate any kind of complex query you want, and the program will go and poll the Geocaching query, grab the data, and output it to any format you want. The info can be synced to various devices in over 20 different formats.

Geotrek

Geotrek is an free software solution composed of a Geographic Information System (GIS) mapping tool, a website and a mobile application, for management and support to the development and preservation of the natural territory. The development of Geotrek started as a cooperation between the Écrins National Park and the Mercantour National Park in France, under contract with the software company Makina Corpus. Later, the Alpi Marittime Nature Park joined the project, taking the solution across the border to Italy. As of 2022, close to 20 national parks across France have reused the code and configured their maps with data on the trails and activities. The solution includes three components:

Geotrek-Admin, for the management of the paths by the National Parks and Tourism organisations, with GIS features. The managing parties can draw and manage the hiking trails with sections and topological networks.
Geotrek-Rando, web application for the promotion of activities, for search and display of the hiking trails within the national park. Users can filter the results based on activity, distance, difficulty, and other characteristics.
Geotrek-Mobile, for easy access to Geotrek’s functionalities on the go/while in nature (for both Android and iOS).

Gephi: visualization and exploration software for all kinds of graphs and networks

Ghemical: Ghemical is a molecular modelling software package with a GUI (one for the GLUT library, and another for GNOME), and some nice 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). The geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms are included.

Ghidra: Ghidra is a software reverse engineering (SRE) framework created and maintained by the National Security Agency Research Directorate. This framework includes a suite of full-featured, high-end software analysis tools that enable users to analyze compiled code. Capabilities include disassembly, assembly, decompilation, graphing, and scripting, along with hundreds of other features. Ghidra supports a wide variety of processor instruction sets and executable formats and can be run in both user-interactive and automated modes. Users may also develop their own Ghidra extension components and/or scripts using Java or Python.

Global Village: Global Village is a Gnome application designed to place a front-end, or graphical user interface onto the CLI interface of Xplanet. Originally intended to create and update the desktop wallpaper in a gnome environment, showing a traditional rectangular projection of the planet Earth. Global Village now provides as many of the features of Xplanet as seem reasonable, and with the ability for plugins the scope is nearly limitless.

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.

Gneuralnetwork

Gneural Network is the GNU package which implements a programmable neural network. The current version, 0.9.1, has the following features:

A scripting language is available which allows users to define their own neural network without having to know anything about coding.
Advanced programmers can use the methods/routines inside the code for their own purposes.
When defining the neurons of a network, it is possible to choose among various discriminant and activation functions, etc.
Different methods to train a neural network are available, such as genetic algorithms, multi-scale Monte Carlo optimizers, simulated annealing, and others.
Several training methods can run in parallel on clusters.
Neural networks can be saved once trained for later use.
The code is truly cross platform since it is entirely developed in C and does not depend on any external library.

The network can now learn tasks defined by the user. An example of script defining a simple network which fits a curve is given. We plan to deliver more advanced features very soon. In particular, we are already spending efforts to implement recurrent networks. We also plan to implement learning reinforcement techniques and apply Gneural Network for deep learning applications. We will release the data along with the trained network.

Gnome Flow: Gnome Flow calculates and visualizes simple steady-state fluid flows. It uses the relaxation method, and can calculate flows past symmetric objects. Steady-state means it calculates the flow at a given time and that the physical parameters are constant in time.

Gnotary: Gnotary is an asynchronous peer-to-peer digital notary service based on email. The server polls POP3 mail boxes scanning for specified key words in the subject line. A digital signature of the email body is returned to the sender. The main purpose is to allow medical practitioners to establish a peer-to-peer based notary service for their electronic health records.

Gnowsys: GNOWSYS is an acronym for "Gnowledge Networking and Organizing SYStem." It is a web based object oriented database server with each object provided by an unique URL. GNOWSYS is a tool to construct and store persistently a Gnowledge Base (GB). The GB consists of the following three groups of constructor classes (system and temporal classes under development): PredicateGroup: relationType, relation, functionType, function Object Group: metaType, class, object (with provision to have classes and objects of declarative, procedural, encapsulated, temporal etc.) Structure Group: systemType, system, flowType, flow, processType, process GNOWSYS indexes data and metadata of objects in a catalogue for faster queries. Optionally, data can remain anywhere on the Internet (only the metadata stays in the database). Surrogates of procedures (classes, functions, and system calls) can also be installed in the database as special objects. These procedures execute as web services, so users can design applications without writing program in any programming language by specifying the semantics of a program and mapping the elements of the program to the surrogates of procedures is sufficient for GNOWSYS to test the application design.

Gnuae: GnuAE is a GNOME/GTK compliant GUI for designing photovoltaic and wind powered houses with compliance to the National Electrical Code. As GnuAE has a database of components and current average prices, it can help you judge the total cost of a system by experimenting with different options like using a propane or DV fridge, or more or less reserve days or hours of sun. GnuAE is also designed to make it much easier to wire for NEC code compliance without studying all 800 some pages of the NEC specification. Even for an electrician, the interdependencies between calculations is daunting. While DC wiring is much simpler than AC wiring, most off-grid household systems are both. There is even a built in NEC calculator for people that have a good feel for what they are doing, but want to also experiment with differing conduit sizes, parallel wire runs, and voltage drop.

Gnuastro: The GNU Astronomy Utilities (Gnuastro) is an official GNU package consisting of separate programs and library functions (in C and C++) for the manipulation and analysis of astronomical data. All the various utilities share the same basic command line user interface for the comfort of both the users and developers. GNU Astronomy Utilities is written to comply fully with the GNU coding standards so it integrates finely with the GNU/Linux operating system. This also enables astronomers to expect a fully familiar experience in the source code, building, installing and command line user interaction that they have seen in all the other GNU software that they use.

Gnucap: 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.

Gnumed: GNUmed is a a comprehensive medical management solution written by medical professionals. Its purpose is to enable doctors to keep a medically sound record on their patients’ health. It is intended to become a sophisticated decision support system that will elevate the quality of medical care that can be delivered. GNUmed operates in a client-server environment where the client and the server are physically two different machines. Each software component i.e. Client / Server are distributed separately. It is alongside GNU Health, one of the medical solution of the GNU project.

Gnuskies: The GnuSkies Project is an attempt to create a 'Total Plug In' (TPI) application which will eventually contain many features not yet implemented in xephem.

Gnuspeech

Gnuspeech is a speech synthesis software. The first official release is distributed in two separate packages:

gnuspeechsa, a cross-platform speech synthesis application providing speech output into applications.
gnuspeech, the "core system", consists of a suite of applications, frameworks and services.

Goptical: Goptical is a C++ optical design and simulation library. It provides model classes for optical components, surfaces and materials. It enables building optical systems by creating and placing various optical components in a 3d space and simulates light propagation through the system. Classical optical design analysis tools can be used on optical systems.

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.

Gpivtools: Gpiv-tools is a package that contains command-line driven programs for the so-called (Digital) Particle Image Velocimetry technique (PIV). The programs perform image evaluation, resulting into a velocity field of the flow, validation programs and post-processing programs to manipulate the data or to extract information from the data (statistics, derivatives). There are some additional programs and scripts for data and image format conversions, chain-processing, batch-processing and for generating graphical output. Though the command-line driven tools are mainly intended for non-graphic processing, its outputs may be visualized in a graphical way by displaying with the aid of gnuplot.

Gpsdrive: 'Gpsdrive' is a map-based navigation system. It displays your position on a zoomable map provided from a NMEA-capable GPS receiver. The maps are autoselected for the best resolution, depending of your position, and the displayed image can be zoomed. Maps can be downloaded from the Internet with one mouse click. The program provides information about speed, direction, bearing, arrival time, actual position, and target position. Speech output is also available. All Garmin GPS receivers with a serial output should be usable, as well as other GPS receivers which support the NMEA protocol.

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.

Gravit Sandbox: Gravit is a gravity sandbox made with python and pygame. It is composed of a launcher and a simulator.

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.

Gstat: Gstat is a computer program for geostatistical modelling, prediction and simulation in one, two, or three dimensions. Gstat uses gnuplot (a program for plotting functions) to display sample variograms and variogram functions. The program has a flexible command language. Spatial prediction options range from simple kriging to universal cokriging.

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.

HASAS: HASAS (HydroAcoustic Signal Analysis System) is a modular system for passive sonar signal analysis. It can be used for biological research or surveillance, for example. The soundcard is used as input device, and it currently includes all the very basic functionality; beamforming, direction finding, level histogram, LOFAR/DEMON (narrowband spectrogram), wideband spectrogram, and raw audio.

Health

GNU Health is a program designed for hospitals, offering the following functionalities:

Electronic Medical Record (EMR)
Hospital Information System (HIS)
Health Information System

It has a strong focus on family medicine and primary care, along with socio-economic circumstances. It uses the following disease and medical procedure standards: (ICD-10 / ICD-10-PCS). There are facilities to aid in choosing medicines; prescription writing; patient, hospital finacial, and lab administration tools; a database of 4,200 disease-related genes; epidemiological reporting; and much more. GNU Health is part of GNU Solidario, an NGO offering health and education to the underpriveledged through free software: http://www.gnusolidario.org

HealthBox: HealthBox is a convenient way to manage health information. Instead of each app having to record inforamtion within it's own ecosystem, HealthBox creates a place for developers to centralize health information. Say you have a program that records your steps, one that monitors work outs, and a third program to track your nutrient intake. Typically, if you wanted to access your information, you'd have to use each respective service's interface. With HealthBox, those developers would be able to store all the information in one place, making it much easier for you to compare different health metrics, and share information between services.

Height Map Generator: Height Map Editor edits, generates, and manipulates terrain height maps. These can be used in terrain renderers, which are used in games, applications, and demos. The program itself is small (the entire distribution is smaller than 400 Kb) but it can work with maps up to 10000x10000. Features include 16 levels of zoom, the ability to sink, smooth, or rise the terrain, the ability to put your own objects (ie volcanos, rivers, mountains, craters, etc.) in/on/over existing terrain, multiple brush sizes, flood and tolerance based fills, and the ability to place a height over terrain and add to or excavate from terrain.

Hitchhiker 2000: This is a candidate for deletion: Links broken. Email to maintainer broken. Poppy-one (talk) 15:57, 2 August 2018 (EDT) Hitchhiker 2000 is an astronomical simulation and visualization program. It displays the solar system in a window on your computer; you manipulate the field of view using the mouse. You can rotate a schene, zoom in and out, or view the scene from any angle. You can also control what objects are seen on the screen. You can also create an MPEG-formatted movie based on your current scene.

Holocrunchies: 'Holocrunchies' is a computational holography program that generates diffraction patterns for 2-D images.

Homoeopim: This is a toy homoeopathy software using a database, an expert system and a suit of CGI programs to search for homoeopathic remedies depending on symptoms entered. There is an iteration mode where questions are asked in a attempt to refine the search. This is an ongoing project, but with 47,000+ mapping entries between remedies and symptoms, it should be marginally usable.

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.

ICTester: Program to use EPE Digital IC tester in GNU/Linux systems. It allows to test circuits, build test algorithms, test SRAM or read PROM chips. Both GUI and command-line versions, works in GNU/Linux and Windows (Qt).

IGMT: This is a candidate for deletion: Links broken. Email to maintainer broken. Poppy-one (talk) 18:06, 2 August 2018 (EDT) This program is intended to make working with the Generic Mapping Tools (GMT) easier. iGMT provides a graphical user interface for GMT and is written in the Tcl/Tk computer language. Besides supplying a user friendly way of handling GMT, iGMT comes with built-in support for many different geoscientific data sets, such as topography, gravity, seafloor age, hypocenter catalogs, plate boundary files, hotspot lists, CMT solutions etc. 'iGMT' is used at numerous institutions worldwide for mapping tasks and teaching GMT.

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

Icarus Verilog: Icarus Verilog is a Verilog simulation and synthesis tool. It operates as a compiler, compiling source code writen in Verilog (IEEE-1364) into some target format. For batch simulation, the compiler can generate an intermediate form called vvp assembly. This intermediate form is executed by the ``vvp command. For synthesis, the compiler generates netlists in the desired format. The compiler proper is intended to parse and elaborate design descriptions written to the IEEE standard IEEE Std 1364-2001. The standard proper was released towards the middle of the year 2001, though in a rather pricey electronic form. This is a fairly large and complex standard, so it will take some time for it to get there, but that's the goal. NOTE: Under the Version information please browse the Installation link to find the proper download link.

IceCat/Forecastfox (fix version): Get international weather forecasts from AccuWeather.com and display them in any toolbar or statusbar with this highly customizable and unobtrusive extension.

Ikaros: 'Ikaros' is a framework for writing and running component-based simulators. It is currently used for simulations of brain areas and learning models, but is general enough to be easily used for any discrete-time simulation. A simulation consists of modules connected in the simulator, with connections specified in an XML file. There are socket-based hooks for adding a GUI. The package contains a number of modules and complete documentation for working with the framework.

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.

ImageJ: 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: 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.

IntelHEX: The Intel HEX file format widely used in microprocessors and microcontrollers area as the de-facto standard for representation of code for programming microelectronic devices. This library provides support for reading, modifying, writing Intel HEX files. You also can create new files from the scratch, convert from and/or to binary form, print human-readable dump of data, merge 2 or more files into one, etc. There are several helper scripts: hex2bin, bin2hex, hex2dump and hexmerge.

Interval RPN Calculator: This terminal app runs on PCs or laptops running Windows, OSX or GNU/Linux. It attempts to mimic the functionality of an HP ReversePolishNotation [RPN] calculator with the added enhancement of interval output. So along with your answer, you get a good idea of its trustworthiness.

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.

JavAstro: A collection of astronomy tools written in java: sky map, astronomical events, ephemerides, planet visibility, moon calendar and galilean moons.

Jmol: 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.

KATCP: Karoo Array Telescope Communication Protocol library.

KNIME: 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.

Kci: The kc program is a "kinetic compiler". This means it is able to transform chemical equations into simulation programs.

KiCad: KiCad is electronic design automation (EDA) software made for designing schematics of electronic circuits and printed circuit boards (PCB). KiCad is developed by the KiCad Developers Team, and features an integrated environment with schematic capture, bill of materials list, PCB layout and much more. KiCad is cross-platform, written with WxWidgets and runs on FreeBSD, GNU/Linux, Microsoft Windows and Mac OS X. A lot of component libraries are available. Also migrating tools for components are available (from other EDA software tools). File formats are plain text and well documented, which is good for CVS or Subversion and to make automated component generation scripts. Multiple languages are supported, such as English, Portuguese, Spanish, Czech, Polish, French, German, and Russian. The 3D PCB viewer use 3D model from Wings3D CAD.

Kpl: 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.

Kstars: KStars is a graphical desktop planetarium. It plots the positions of stars, constellations, star clusters, nebulae, galaxies and planets in the night sky for any date, from any location on Earth. The display can be panned and zoomed, and it can even identify and track objects as they move across the sky. KStars is highly configurable, you can control what objects are displayed, and with what colors. Images of any part of the sky can be downloaded from online databases. Our plan is to make KStars an interactive tool for learning about astronomy and the night sky.

L2P: '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.

LLaMA: Based on text from the annoucement blog: LLaMA (Large Language Model Meta AI) is a state-of-the-art foundational large language model designed to help researchers advance their work in this subfield of AI. Smaller, more performant models such as LLaMA enable others in the research community who don’t have access to large amounts of infrastructure to study these models, further democratizing access in this important, fast-changing field.

LLaMA.cpp: Port of Meta's LLaMA model in C/C++ to run on CPU instead of GPU.

Lamprop: 'lamprop' calculates some properties of fiber-reinforced composite laminates. It calculates engineering properties like Ex, Ey, Gxy, thermal properties CTE_x and CTE_y, physical properties like density and laminate thickness, and stiffness and compliance matrices.

Lhendraw: Chemical drawing program for the cdx/cdxml formats. This one tries to be as close and completely as possible to the proprietary reference implementation without forfeiting the KISS principle. It offers a database-less search function and a headless mode for automated editing

LibRadtran: Functions and programs to calculate solar and thermal radiation in the Earth's atmosphere.

LibTAP

'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: '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).

Libgpiv: 'LIBGPIV' is a library for the (Digital) Particle Image Velocimetry technique (PIV), an image analyzing technology that obtains a velocity field from a fluid flow (gas or liquid) that has been seeded with small tracer particles or smoke. 'LIBGPIV' contains the core functions for image evaluation (resulting into estimators of particle image displacements, i.e. PIV data), validation (on peak-locking effects, erroneous vectors or outliers), post-processing, input/output functions, utility functions like memory allocation etc. The project is designed for maximum flexibility for extending and adapting the code for different applications.

Libnova: 'libnova' is a general purpose, double precision, celestial mechanics and astronomical calculation library. It can calculate aberration, nutation, apparent position, dynamical time, Julian day, precession, proper motion, sidereal time, solar coordinates (using VSOP87), coordinate transformations, planetary positions (Mercury - Neptune using VSOP87), planetary magnitude, illuminated disk and phase angle, lunar position (using ELP82), phase angle, elliptic motion of bodies (Asteroid + Comet positional and orbit data), asteroid + comet magnitudes, parabolic motion of bodies (comet positional data), orbit velocities and lengths, atmospheric refraction, rise/set/transit times, and semidiameters of the Sun, Moon, planets, and asteroids.

Libquantum: 'libquantum' is a simulation of a quantum computer. It provides an interface for a quantum register and for all important quantum operations. An efficient model for decoherence allows an analysis of quantum computation in a realistic environment. Features include the simulation of arbitrary algorithms, high performance and low memory consumption and interfaces for quantum error correction (QEC) and the density operator formalism. The package includes implementations of Shor's factoring algorithm and Grover's search algorithm.

Librsb: 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.

Light Speed!: Light Speed! is an OpenGL-based program which illustrates the effects of special relativity on the appearance of moving objects. When an object accelerates past a few million meters per second, these effects begin to grow noticeable, becoming more and more pronounced as the speed of light is approached. These relativistic effects are viewpoint-dependent, and include shifts in length, object hue, brightness and shape. The moving object is, by default, a geometric lattice. 3D Studio and LightWave 3D objects may be imported as well. Best of all, the simulator is completely interactive, rendering the exotic distortions in real-time!

LimeSurvey

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

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.

Lsystem: 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: 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.

MIND: 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.

MIT Photonic Bands: MIT Photonic Bands (MPB) computes the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures, and is applicable both to photonic crystals (photonic band-gap materials) and other optical problems. Its features include: fully-vectorial, 3D computations; a flexible user-interface based upon the GNU Guile scripting language; output in HDF format; and iterative, targeted eigensolver methods to address very large problems by solving for only a few states near a specified frequency.

MLPACK: MLPACK is a C++ machine learning library with emphasis on scalability, speed, and ease-of-use. Its aim is to make machine learning possible for novice users by means of a simple, consistent API, while simultaneously exploiting C++ language features to provide maximum performance and flexibility for expert users. MLPACK contains the following algorithms: Collaborative Filtering, Density Estimation Trees, Euclidean Minimum Spanning Trees, Fast Exact Max-Kernel Search (FastMKS), Gaussian Mixture Models (GMMs), Hidden Markov Models (HMMs), Kernel Principal Component Analysis (KPCA), K-Means Clustering, Least-Angle Regression (LARS/LASSO), Local Coordinate Coding, Locality-Sensitive Hashing (LSH), Logistic regression, Naive Bayes Classifier, Neighbourhood Components Analysis (NCA), Non-negative Matrix Factorization (NMF), Principal Components Analysis (PCA), Independent component analysis (ICA), Rank-Approximate Nearest Neighbor (RANN), Simple Least-Squares Linear Regression (and Ridge Regression), Sparse Coding, Tree-based Neighbor Search (all-k-nearest-neighbors, all-k-furthest-neighbors), Tree-based Range Search.

MPK: MathParseKit is a C++ Library that allows an easy integration of a mathematical functions interpreter.

MapServer: MapServer is a CGI based Web mapping application development tool. It processes user defined configuration files and templates to allow for a wide variety of applications to be developed, including interactive mapping, and spatial query definition and processing. It supports several data formats. Key features include scale dependent map rendering, automatic scalebar and legend building, feature labeling with collision avoidance, logical and thematic classifications, and on-the-fly projection of raster and vector data. The application can also access other WMS servers as a cascading map server.

Marble: 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.

Maryam: OWASP Maryam is an Open-source intelligence(OSINT) and Web-based Footprinting modular framework based on the Recon-ng and written in Python. If you want Extracts Emails, Docs, Subdomains, Social networks from search engines Extracts Links, CSS and JS files, CDN links, Emails, Keywords from Web Source Find and Brute force DNS, TLD and important directs Crawl Web Pages and search your RegExp Identify WebApps, WAF, Interesting and important files Use Maryam

Mastrave: Mastrave is a free software library written to perform vectorized scientific computing and to be as compatible as possible with both GNU Octave and Matlab computing frameworks, offering general purpose, portable and freely available features for the scientific community. Mastrave is mostly oriented to ease complex modeling tasks such as those typically needed within environmental models, even when involving irregular and heterogeneous data series. Semantic array programming The Mastrave project attempts to allow a more effective, quick interoperability between GNU Octave and Matlab users by using a reasonably well documented wrap around the main incompatibilities between those computing environments and by promoting a reasonably general idiom based on their common, stable syntagms. It also promotes the systematic adoption of data-transformation abstractions and lightweight semantic constraints to enable concise and reliable implementations of models following the paradigm of semantic array programming. There are a couple of underlying ideas: library design is language design and vice versa (Bell labs); language notation is definitely a "tool of thought" (version), in the sense that there is a feedback between programming/mathematical notation and the ability to think new scientific insights. And perhaps ethic ones. Science and society Mastrave is free software, which is software respecting your freedom. As many other free scientific software packages, it is offered to the scientific community to also promote the development of a free society more concerned about cooperation rather than competitiveness, heading toward knowledge and culture freedom. Such a vision implies the possibility for motivated individuals to freely access, review and contribute even to the cutting-edge academic culture. This possibility relies on the development of tools and methodologies helping to overcome economic, organizational and institutional barriers (i.e. knowledge oligopolies) while systematically promoting reproducible research. This is a long-term goal to which the free software paradigm can and has been able to actively cooperate.

Matiec: This project has the goal of producing an open source compiler for the programming languages defined in the IEC 61131-3 standard. These programming languages are mostly used in the industrial automation domain, to program PLCs (Programmable Logic Controllers). This standard defines 5 programming languages: - IL : Instructtion List A textual programming language, somewhat similar to assembly. - ST : Structured Text A textual programming language, somewhat similar to Pascal. - FBD: Function Block Diagram A graphical programming language, somewhat similar to an electrical circuit diagram based on small scale integration ICs (Integrated Circuits) (counters, AND/OR/XOR/... logic gates, timers, ...). - LD : Ladder Diagram A graphical programming language, somewhat similar to an electrical circuit diagram based on relays (used for basic cabled logic controllers). - SFC: Sequential Function Chart A graphical programming language, that defines a state machine, based largely on Grafcet. (may also be expressed in textual format). Of the above 5 languages, the standard defines textual representations for IL, ST and SFC. It is these 3 languages that we target, and we currently support all three, as long as they are expressed in the textual format as defined in the standard. Currently the matiec project generates two compilers (more correctly, code translaters, but we like to call them compilers :-O ): iec2c, and iec2iec Both compilers accept the same input: a text file with ST, IL and/or SFC code. The iec2c compiler generates ANSI C code which is equivalent to the IEC 61131-3 code expressed in the input file. The iec2iec compiler generates IEC61131-3 code which is equivalent to the IEC 61131-3 code expressed in the input file. This last compiler should generate and output file which should be almost identical to the input file (some formating may change, as well as the case of letters, etc.). This 'compiler' is mostly used by the matiec project contributors to help debug the lexical and syntax portions of the compilers.

MayaChemTools

MayaChemTools is a growing collection of Perl scripts, modules, and classes to support day-to-day computational discovery needs. The current release of MayaChemtools provides command line scripts for the following tasks:

Manipulation of SD, CSV/TSV, Sequence/Alignments, and PDB files
Analysis of data in SD, CSV/TSV, and Sequence/Alignments files
Information about data in SD, CSV/TSV, Sequence/Alignments, PDB, and fingerprints files
Exporting data from Oracle and MySQL tables into text files
Properties of periodic table elements, amino acids, and nucleic acids
Generation of fingerprints corresponding to atom neighborhoods, atom types, E-state indicies, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs, and topological pharmacophore atom triplets
Generation of fingerprints with atom types corresponding to atomic invariants, DREIDING, E-state, functional class, MMFF94, SLogP, SYBYL, TPSA and UFF
Calculation of similarity matrices using a variety of similarity and distance coefficients
Calculation of physicochemical properties including rotatable bonds, van der Waals molecular volume, hydrogen bond donors and acceptors, logP (SLogP), molar refractivity (SMR), topological polar surface area (TPSA), and so on

McIDAS-V: McIDAS-V is a free, open source, visualization and data analysis software package that is the fifth generation in SSEC's 40 year history of sophisticated McIDAS (Man computer Interactive Data Access System) software packages. McIDAS-V displays weather satellite (including hyperspectral) and other geophysical data in 2- and 3-dimensions, and can be used to analyze and manipulate the data with its powerful mathematical functions.

McStas: McStas lets you very precisely model a neutron scattering instrument described as a series of components, representing the physical elements of the instrument / Beamline. A source component samples the properties of each neutron ray randomly (Monte-Carlo is used to sample spectrum, direction and spatial origin etc.), and the particle is then propagated through the different instrument components. These later act on the neutron characteristics (position, speed, direction, spin, etc.). Further, one can install detectors along the neutron path to monitor the characteristics and flux of the neutron beam. McStas works on a principle of code-generation (LeX-Yacc based grammar), generating a fully portable ISO-C code to run on a variety of platforms and architectures.

Mcl-algorithm: '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.

Meep: Meep is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. It supports distributed-memory parallelism, dispersive and nonlinear materials, PML absorbing boundaries, 1d/2d/3d/cylindrical problems, and arbitrary material and source geometries. It is completely scriptable via either C++ or a Scheme (GNU Guile) interface.

Melting: Melting computes, for a nucleic acid duplex, the enthalpy and entropy of the helix-coil transition, and then its melting temperatures. Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA. The program uses the method of nearest-neighbors. The set of thermodynamic parameters can easily be changed, for instance following an experimental breakthrough.

Mergin Maps: Mergin Maps is used for the collection of data points, lines or polygons along with custom forms in the field. The mobile app allows you to take geotagged photos and save the location of photos.

Metro: '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)

MindForger: Are you drowning in information, but starving for knowledge? Where do you keep your private remarks like ideas, personal plans, gift tips, how-tos, dreams, business vision, finance strategy, auto coaching notes? Loads of documents, sketches and remarks spread around the file system, cloud, web and Post-it notes? Are you affraid of your knowledge privacy? Are you able to find then once you create them? Do you know how are they mutually related when you read or write them? No? MindForger is open, free, well performing Markdown IDE which respects your privacy and enables security. MindForger is actually more than an editor or IDE - it's human mind inspired personal knowledge management tool.

Minfx: The minfx project is a Python package for numerical optimisation, being a large collection of standard minimisation algorithms. This includes the line search methods: steepest descent, back-and-forth coordinate descent, quasi-Newton BFGS, Newton, Newton-CG; the trust-region methods: Cauchy point, dogleg, CG-Steihaug, exact trust region; the conjugate gradient methods: Fletcher-Reeves, Polak-Ribiere, Polak-Ribiere +, Hestenes-Stiefel; the miscellaneous methods: Grid search, Simplex, Levenberg-Marquardt; and the augmented function constraint algorithms: logarithmic barrier and method of multipliers (or augmented Lagrangian method).

Mondo Health Monitor: Mondo is a system health monitor daemon for GNU/Linux, capable of running specific commands whenever alarm conditions get tripped. Mondo can do things like send e-mails and shut your system down if a fan fails, voltage rails start to go haywire, or your system just seems warmer than it should be. It can actually run any command of your choice to handle an alarm condition

Mpc: MPC is a complex floating-point library with exact rounding. It is based on the GNU MPFR floating-point library, which is itself based on the GNU MP library. This is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal.

Msetimon: This program was written to monitor SETI@home activity that may be running on multiple computers or multiple instances on the same computer.

MuTE Toolbox: A challenge for physiologists and neuroscientists is to map information transfer between components of the systems that they study at different scales, in order to derive important knowledge on structure and function from the analysis of the recorded dynamics. We propose a freeware MATLAB toolbox, MuTE (Multivariate Transfer Entropy), that implements four both Granger causality and transfer entropy estimators according to uniform and non-uniform embedding frameworks. The resulting eight methods can be easily compared showing all the pros and cons of the methodologies used to detect the directed dynamical information transfers. The toolbox provides a completely brand-new approach that bridges machine learning and information theory fields. MuTE is also able to perform bivariate and fully multivariate analyses. Furthermore, users can easily implement their own methods or change some features of the already existing approaches due to the modularity of the toolbox.

Munin: '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.

My Knowledge Explorer: My Knowledge Explorer uses the mKR (my Knowledge Representation) language to create, query and update mKB (my Knowledge Base). mKR is a useful mixture of English (subject, verb, object, preposition phrase) and the KornShell (variables, procedures, control structures). mKB can be a local user KB or an internet KB such as OpenCyc. The Redland RDF Library commands can be used to translate mKR to/from standard W3C languages such as Turtle and SPARQL.

Mycroft: Mycroft is the leading free voice assistant. It is private by default and completely customizable.

NMod nBody Modelling Toolkit: nMod nbody toolkit is a collection of tools designed to enable researchers to perform experiments using a particle-particle nBody model that runs on standard home computers.
The toolkit contains a particle-particle model, functions to enable the simulation of spacecraft flight, and an opengl viewer to display the resulting time series data.

NUT nutrition software: This software help you record what you eat and then analyzes your meals for nutrient levels in terms of the USDA "Daily Value" (the standard for food labeling in the US.

Nano-archimedes: 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.

Natural Language Toolkit: The NL Toolkit simplifies the construction of programs that process natural language and defines standard interfaces between the different components of an NLP system. NLTK includes graphical demonstrations, sample data, tutorials, and API documentation.

NeMo: From GitHub README: NVIDIA NeMo is a conversational AI toolkit built for researchers working on automatic speech recognition (ASR), natural language processing (NLP), and text-to-speech synthesis (TTS). The primary objective of NeMo is to help researchers from industry and academia to reuse prior work (code and pretrained models and make it easier to create new conversational AI models.

Network Extraction from Images: NEFI is an extensible computer vision tool that analyzes images that contain networks and extracts the graph. Examples are leaf venations, insect wings, slime molds, mud crack patterns etc. It determines topological information as well as properties such as edge length and width.

NeuroScope: 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.

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