[[Science::+]]

ID	select_type	table	type	possible_keys	key	key_len	ref	rows	Extra
1	SIMPLE	t2	ALL	PRIMARY				3	Using temporary; Using filesort
1	SIMPLE	t1	ref	s_id,p_id,s_id_2	p_id	4	wikidb.t2.id	3227
1	SIMPLE	t0	eq_ref	PRIMARY,smw_id,smw_iw,smw_iw_2	PRIMARY	4	wikidb.t1.s_id	1	Using where

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.

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