AMBRE is part of a collection of tools devoted to the evaluation of Mellin-Barnes integrals collected at HEPFORGE.

ANT - ANalytic loopTools - is a Mathematica package implementing all Passarino-Veltman functions up to boxes as defined by FormCalc and LoopTools in the limit of vanishing external momenta. Additionally, it includes all first derivatives of B0, B1, C0, C1, C2 as well as C00 in the limit of vanishing external momenta.

This Mathematica package facilitates the integration of notebooks to the Documentation Center, without needing to use the Wolfram Workbench.

Commerical Mathematica toolbox for calculations in modern differential geometry and its applications. Provides of options to control aspects of the project from initial problem formulation to manipulation and visualization of results.

A package for Mathematica 6 and later that facilitates analytic and numerical density-matrix calculations in atomic and related systems.

The package contains more than 820 tools which eliminate restrictions of a number of standard tools of the Mathematica system, and expand its software with new tools. In this context, the package can serve as a certain additional tool of modular programming, especially useful in the numerous applications where certain nonstandard evaluations have to accompany programming. At that, tools presented in the given package have a direct relationship to certain principal questions of procedure–functional programming in the Mathematica system, not only for the decision of applied problems, but, first of all, for creation of software extending frequently used facilities of... Read more.

A Mathematica toolbox for solving system of differential equations, fitting coefficients, convolution, and more, with application for modeling Linear and Nonlinear Biokinetic Systems. It includes the current ICRP biokinetic models. It can be applied in pharmacokinetic, internal dosimetry, bioassay evaluations, nuclear medicine and more. This toolbox consist of Mathematica packages and tutorials.

Connect Bluetooth Low Energy/Smart/4.0 devices to Mathematica using this package. Dynamically update data, display device information, and make custom connections to unsupported device profiles.

Last updated September 9, 2015
bluetooth

Fast vectorized evaluation of conditional expressions over arrays, with a simple notation. Inspired by MATLAB's advanced logical matrix indexing.

Simplifies the creation of online bootstrap installer scripts.

Last updated September 8, 2015

Visualizes the content of BVH files. BVH files contain recorded motion data, and are visualized by a skeleton reproducing the recorded movements.

Simulates cellular automata using the notion of templates introduced in Representing Families of Cellular Automata Rules.

CifImport imports a Crystallographic Information File (CIF). It also applies the symmetry operations of the crystal structure to the atoms in the file in order to construct the complete crystal structure.

CMBquick is a package for Mathematica in which tools are provided to compute the spectrum and bispectrum of Cosmic Microwave Background (CMB). It is unavoidably slow, but the main goal is not to design a tool which can be used for systematic exploration of parameters in cosmology, but rather a toy CMB code which is transparent and easily modified.

A code formatter and pretty printer written in Mathematica, for Mathematica.

Last updated September 9, 2015
code formatting

ColorBar is an interactive ColorFunction designer for Mathematica. It allows you to easily modify existing color functions, change colors or vary the blending fraction and get the final result in other applications. You can also use it directly inside a plotting function.

ColorMath is a Mathematica package for symbolically performing color summed calculations in SU(Nc). It is based on advanced pattern matching and uses a syntax which is very similar to how QCD color structure is written on paper.

CompileNoting is a fancy formatter for Mathematica. It generates a sidenoted Input Cell of the inputted CompiledFunction.
Please refer to the [documentation] CompileNotingTools.nb for detailed usage and examples.

Last updated September 19, 2015
CompiledFunction

Simple package for replacing combinations of constants with single constants.

Last updated March 12, 2016
symbolic

Crystallica is an application for crystal and molecular structures. The user can manipulate structures and create plots with a variety of elements like atoms, bonds, lattice planes, and coordination polyhedra. Design and layout can be adjusted through various options.

Last updated February 5, 2016
crystal structure

CurvesGraphics6 is a package for drawing parametric, contour or stream curves, or text, on any surface in 3D. It can also place arrowhead on curves produced by various builtin plotting functions.

This is a Mathematica Application Project. Packages in this project extend Wolfram Language with commands that are related to data management. There is a basic Utilities Package that is used in transformations between Wolfram Language constructs such as List, Rule, Association, and Dataset, and external serialization standards such as JSON and comma-separated values (CSV) files. On top of that package we are porting RESTful APIs from various web services through URLFetch into Wolfram Language building commands with arguments that specify options with rules of the form name->value. An example of such a RESTful API is the OrientDB HTTP API and... Read more.

The DebugTrace package is an attempt to design a better alternative to the built-in debugger .

DebugTrace uses no special hooks into Mathematica, instead it modifies the source code as it is presented to the kernel, to add the necessary hooks to allow the debugger to operate. This process imposes much less run-time overhead than TraceScan (used by M-Debug).

Discrete is a Mathematica package providing tools for model building with discrete symmetries. Its main features are

- the calculation of arbitrary Kronecker products;
- an interface to the group catalogues within GAP, e.g. the SmallGroups library with all discrete groups up to order 2000 (with the exception of groups of order 1024) and many more;
- calculation of Clebsch-Gordan coefficients (They are calculated on demand and are stored internally, in order to improve the performance);
- the possibility to reduce covariants to a smaller set of independent covariants;

This is a port of DistMesh to the Wolfram Language complete with Documentation.

Last updated October 28, 2015
Mesh generation

Can create a continuous diverging color map starting from any two RGB colors, by converting to linear-RGB, then XYZ, then CIELAB, and finally into Msh, a polar-coordinate version of CIELAB. These color palettes are useful for visualizing data where both large low and high values are interesting, with a well-defined midpoint.

Dynamo is a suite of Mathematica notebooks that contain code visualizing phase diagrams, vector fields and other graphics related to evolutionary game dynamics.

A Mathematica package that provides explicit matrix expressions for group theoretic calculations in E6.

This is a collection of function that may be useful for common tasks in macrorconomic analysis. Some of the included funcitons are: an interface to ARIMA-X13 binary, functions to estiamte VAR and identify SVAR.

A collection of fourteen packages that extend the core of Wolfram Language, packages for studying cellular automata, binary trees and more.

The AbstractAlgebra package is a freely available complement to the book *Exploring Abstract Algebra with Mathematica*. The package supports working with (finite) groups, rings, fields, and morphisms and functions related to each of these objects. There are a large number of built-in groups (including such standard groups as $Z_n$, $U_n$ (units of $Z_n$), $S_n$, and $D_n$, as well as direct products and quotients of these) and rings (including $Z_n$, Boolean rings and lattice rings, as well as polynomial, matrix and function extension rings). One can also create functions between groups or rings and investigate if these are morphisms.

ExportTable is a faster implementation of Mathematica's `Export[..., "Table"]`

for matrices of real numbers.

FeynArts is a package for the generation and visualization of Feynman diagrams and amplitudes.

FeynCalc is a Mathematica package for symbolic evaluation of Feynman diagrams and algebraic calculations in quantum field theory and elementary particle physics.

FIESTA stands for Feynman Integral Evaluation. It is a package that evaluates integrals by using the sector decomposition approach.

FIRE stands for Feynman Integral Reduction. It is a package for performing reduction of Feynman integrals to master integrals.

This is the development page for the FlexibleSUSY project. FlexibleSUSY provides Mathematica and C++ code to create fast and modular spectrum generators for supersymmetric and non-supersymmetric models. It is based on SOFTSUSY and SARAH.

This package extends Mathematica's built-in format rules. Assignments to expressions and lists are now possible. The package adds definitions Assign, CAssign and FortranAssign and MapleAssign. Many shortcomings of the built-in formatting code have also been addressed, such as the limit on continuation lines in FORTRAN77 and assignments to Expressions. Code optimization is possible via the auxiliary function Experimental`OptimizeExpression and the option AssignOptimize. The options of Experimental`OptimizeExpression, such as OptimizationLevel, can also be passed to the Assign functions. The functions are primarily intended for use with the Splice command. When using Splice, the option FormatType->OutputForm should be specified. Interactive output within a Mathematica session is also possible (see also the AssignToFile option). All expressions are written... Read more.

FormCalc is a Mathematica package for the calculation of tree-level and one-loop Feynman diagrams. It reads diagrams generated with FeynArts and returns the results in a way well suited for further numerical and analytical evaluation.

FormFlavor is a Mathematica based tool for computing a broad list of flavor and CP observables in general new physics models. Based on the powerful machinery of FeynArts and FormCalc, FormFlavor calculates the one-loop Wilson coefficients of the dimension 5 and 6 Standard Model effective Lagrangian entirely from scratch. These Wilson coefficients are then evolved down to the low scale using one-loop QCD RGEs, where they are transformed into flavor and CP observables. The last step is accomplished using a model-independent, largely stand-alone package called FFObservables that is included with FormFlavor. The SM predictions in FFObservables include up-to-date references and... Read more.

Mathematica package for Clifford (geometric) algebra calculations.

Main features: Textbook notation and precedences of products (without Mathematica palettes) Algebraic operations in orthonormal frame (additive representation, symbolic coefficients) Switching between multiple algebras in same Mathematica session Matrix representations of Cl(p,q) algebras Idempotents with different base element sorting Main involutions and general multivector inverse

Grassmann algebra is a mathematical system which predates vector algebra, and yet is more powerful, subsuming and unifying much of the algebra used by engineers and physicists. It has remained relatively unknown since its discovery around 1832, yet is now emerging as a potential mathematical system for describing such diverse applications as robotic manipulators and fundamental physical theories.
The GrassmannAlgebra package is a computer algebra package written in Mathematica's programming language. It is accompanied by an extensive guide. The package contains useful palettes for quick entry of expressions.

Last updated September 10, 2015
Grassmann algebra

An Open Source Mathematica Package that provides a platform independent way to import HDF5 (.h5) file's datasets with compound datatypes while hiding much of the HDF5 implementation from the user.

HadoopLink provides a framework for delegating the work of a map-reduce job to Mathematica kernels running on your Hadoop cluster and a suite of tools for working with your Hadoop cluster from a Mathematica notebook.

Last updated September 9, 2015
Hadoop

Makes it easy to write Mathematica packages in Haskell. Just write some functions and provide a package specification in a simple DSL that mimics that of Mathematica's mprep utility.

The HolonomicFunctions package allows to deal with multivariate holonomic functions and sequences. For this purpose the package can compute annihilating ideals and execute closure properties (addition, multiplication, substitutions) for such functions. An annihilating ideal represents the set of linear differential equations, linear recurrences, q-difference equations, and mixed linear equations that a given function satisfies. Summation and integration of multivariate holonomic functions can be performed via creative telescoping. As subtasks, the following functionalities have been implemented in HolonomicFunctions: computations in Ore algebras (noncommutative polynomial arithmetic with mixed difference-differential operators), noncommutative Gröbner bases, and solving of coupled linear systems of differential or... Read more.

Updated implementation of the Hodrick-Prescott filter in Mathematica - based on original code by Johannes Ludsteck, code improvements by Ekkehart Schlicht. Updated for version 9+ compatibility and one-sided implementation by Luci Ellis

Expands hypergeometric JFJ-1 functions around their parameters. Detailed descriptions are available at hep-ph/0507094 and arXiv:0708.2443 .

This package contains a Mathematica importer for CERN ROOT data files. The importer uses a MathLink program to dynamically load and use the ROOT libraries. In this package, we include the source files as well as Mathematica notebooks documenting the usage of this importer.

The IMTEK Mathematica Supplement, or IMS for short is an open source Mathematica add-on and provides a wealth of packages and tutorials from a variety of application areas, but with a strong focus on Finite Element Computations. The IMS is a continuous project at the Chair for Microsystem Simulation, Department for Microsystem Engineering (IMTEK), University of Freiburg, Germany. Website (not Github like the main link).

IntU is a package for Mathematica computer algebra system, which allows calculating polynomial integrals over the unitary group with respect to the Haar measure. he preprint of the paper describing the package is available at Z. Puchała, J.A. Miszczak, Symbolic integration with respect to the Haar measure on the unitary group in Mathematica, arXiv:1109.4244.

Last updated May 23, 2017
Haar measure; unitary group

Mathematica code for joint inference of identities by descent along multiple chromosomes from population samples.

The KnotTheory package is the main tool used to create the Knot Atlas.

Last updated September 25, 2015
knots

A Mathematica-package for OPEs in vertex algebras. The package Lambda is designed for calculating λ-brackets in both vertex algebras, and in SUSY vertex algebras. This is equivalent to calculating operator product expansions in two-dimensional conformal field theory. For an introduction, see http://arxiv.org/abs/1004.5264 .

Finds analytical and numerical polynomial approximations of solutions to initial value problems, boundary value problems and more.

Last updated March 15, 2017
approximations

A simple C++11 toolkit that automates the boring boilerplate that is needed to write functions for Mathematica LibraryLink.

LieART (Lie Algebras and Representation Theory) is a Mathematica application for computations frequently encountered in Lie algebras and representation theory, such as tensor product decomposition and subalgebra branching of irreducible representations. LieART can handle all classical and exceptional Lie algebras. It computes root systems of Lie algebras, weight systems and several other properties of irreducible representations. LieART's user interface has been created with a strong focus on usability and thus allows the input of irreducible representations via their dimensional name, while the output is in the textbook style used in most particle-physics publications. The unique Dynkin labels of irreducible representations... Read more.

LiteRed is a Mathematica package performing the IBP reduction of the multiloop integrals. It also contains the tools for the construction of the differential equations and dimensional recurrence relations.

The LTemplate package simplifies developing LibraryLink code by automatically generating much of the needed boilerplate code based on "templates" that describe a class interface.

A package for decompressing LZW compressed data. It can read data compressed using the Unix `compress`

command, i.e. `.Z`

files, and integrates into `Import[]`

.

Many packages, some of them generating plots and visualizations, others related to statistics. Several of the packages are related to Monte Carlo methods.

A package for using LaTeX in Mathematica graphics, legends, plot labels, etc. Ideal for publication quality figures or for matching the style of figure labels with that of LaTeX-generated documents.

Transfrom almost everything in you notebook, including text, graphics, formula, citations etc, nicely into a TeX source and precompile it to PDF. Previews are shown inside of the notebook.

A Mathematica package for differential analysis of metabolite profiles. MathDAMP facilitates the visualization of differences between metabolite profiles acquired by hyphenated mass spectrometry techniques. Differences are highlighted by applying arithmetic operations to all corresponding signal intensities from whole raw (automatically preprocessed and normalized) datasets on a datapoint-by-datapoint basis. The results are visualized using density plots.

A Mathematica package to make up for Mathematica's abysmal built-in auto-save functionality. Once loaded, it will automatically backup any open notebook at user-defined intervals. Configurable, works well...

The package file, NotebookBackup.m, should be saved to the Mathematica user "Applications" folder; for Unix systems (including OS X) this is ~/.Mathematica/Applications. In Windows Vista/7 it's something like C:\Users\[you]\AppData\... The package can then be loaded by entering <<NotebookBackup` into Mathematica. More instructions are inside the file; note that it may need to be configured for the particular system (paths, etc.) before being used. Mathematica 7+.

This is a Mathematica package to access HEYEX Raw files which can e.g. created from Optical Coherence Tomography scans of Heidelberg Spectralis products.
The package incorporates its functionality directly into the Import-framework of Mathematica. Therefore, Heyex Raw files can be loaded by calling Import as specified in the Usage section.

A Mathematica interface for the WEKA 2.0 data mining software.

Last updated September 27, 2015
machine learning

Mathematica package containing a general-purpose Markov chain Monte Carlo routine. Includes various examples and documentation.

Features:

- Convenience wrapper for fitting models to arbitrary-dimensional data with Gaussian errors
- Handles both real-valued and discrete-valued model parameters
- Uses Metropolis algorithm with decaying exponential proposal distribution
- Progress monitor; support for auto save/resume

Usage examples are available on Mathematica.StackExchange:

Last updated February 12, 2017
MCMC

It is an easy to install plugin for almost all IntelliJ IDEA based IDEs, which turns them into a powerful development tool for Mathematica and Wolfram Language code. The plugin and the Community Edition of IDEA is open-source and therefore completely free of charge.

This package provides Mathematica syntax highlighting for the Textmate text editor. It can also be converted to work with the SublimeText and Atom editors.

The Mathematica.jl package provides an interface for using Wolfram Mathematica from the Julia language. It is based on MathLink.jl, a MathLink interface for Julia.

Wolfram Language implementations of machine learning algorithms that are used or can be used for prediction and personalization systems.

Last updated September 8, 2015
machine learning

MathematicaStan is an interface for Stan, which is a probabilistic language for Bayesian inference, with MCMC sampling, approximate Bayesian inference, with variational sampling, and penalized maximum likelihood methods with optimizations.

MathGR is a package for GR calculation, written in Mathematica. The manual of the package is available at http://arxiv.org/abs/1306.1295.

MathIOmica provides a framework for graphical, numerical and symbolic work for omics analyses. The code cross-platform, open source and includes full integrated documentation.

This package provides access to Mathematica's MathLink library from Julia, with convenient wrappers for import Mathematica functions, seamless data conversion etc. It is used as the bases of the Mathematica.jl Julia package.

MathPSfrag is a Mathematica package providing a graphics export function that automatically replaces Mathematica expressions in a graphic by the corresponding LaTeX constructs and positions them correctly. It thus facilitates the creation of publication-quality Enscapulated PostScript (EPS) graphics. It can also create LaTeX independent EPS and PDF files for processing with other programs or pdfLaTeX.

The MathToolBox package is further essential development of the AVZ_Package package and contains more than 950 means of different purpose which eliminate restrictions of a number of standard tools of the Mathematica system, and expand its software with new tools. In this context, the package can serve as a certain additional tool of procedural and functional programming, especially useful in the numerous appendices where certain nonstandard evaluations have to accompany programming. At that, tools presented in the given package have a direct relationship to certain principal questions of procedural and functional programming in the Mathematica system, not only for the... Read more.

Seven different packages related to mathematical physics; a package for GR-type tensor algebra, one for Virasoro algebra, one for algebra with Grassman variables, a package for Polchinski theta-function conventions, a package specialized at inverting diagonal matrices by inverting each diagonal entry separately, and two packages that deal with approximations to the Ricci-flat metric on the algebraic Calabi-Yau manifold.

A package implementing multidimensional scaling.

Last updated September 24, 2015
multidimensional scaling

mPower.m is a Mathematica package that interfaces with *qhull* and *Power Diagram* binaries to provide convex hull, Delaunay and Voronoi tessellations in 2D, 3D and higher dimensions, regular tetrahedralizations in 3D and computing vertices of power diagrams in 3D.

Last updated September 27, 2015
geometry

The main contribution of MTools is to allow object oriented programming in Mathematica in a very natural way .

The package also contains:

- Generic classes for manipulating trees of objects and displaying them
- Automatic interface generation for displaying and editing objects
- Functions for doing asynchronous evaluation easily using parallel kernels (MSync)
- Tools for accessing Couchbase, serializing and deserializing objects.

Last updated July 3, 2016
OOP

Organic molecules can have single, double or triple bonds between atoms. The multiBondPlot function uses the bond multiplicity as found in ChemicalData[] or in a MOL file, and returns a 3D plot of the molecule with multiple bonds.

A suite of non-commutative algebra packages for Mathematica. Features include noncommutative inequalities, linear systems and control, semidefinite programming, computing non-commutative Groebner bases, etc.

An all-compiled-code Nelder-Mead minimizer. See the description on Mathematica.SE.

NetLogo is a modelling environment for agent-based modelling using the Logo programming language. It comes with a Mathematica link that makes it possible to run and analyse models directly from Mathematica.

This package contains routines and tools for obtuse angle shadowing networks and distance-based interpolation between scattered, multidimensional points. Four variants of distance-based interpolation can be compared with (coordinate-based) 2D Delaunay interpolation. The Obtuse package adds five interpolation methods to the Mathematica Interpolation command: Delaunay interpolation, Voronoi interpolation, Shepard interpolation, RBF interpolation, ObtuseAngle interpolation.

Various tools for working with data from the On-Line Encyclopedia of Integer Sequences.

Framework simplifying validation of options.

It provides functions registering arbitrary tests for values of options, of given symbols, with names matching given patterns. Test of relations between different options can be also registered.

Registered tests can be automatically used in various different strategies of option value testing. Tests can be performed while evaluating body of function when option values are accessed, or they can be performed upfront while matching function pattern. When tests fail - function can either return a value denoting failure, or can remain unevaluated.

Package-X is a Mathematica package to obtain compact analytic expressions for one-loop integrals in higher order calculations of relativistic quantum field theory in 4 spacetime dimensions.

Read and convert Newick trees, hierarchical cluster objects and tree graphs to evolutionary cladograms (with explicit branching distances) and back. The package has various functions to work with trees and cladograms directly: it can extract internal and terminal nodes, paths and measure distances of nodes. Latest version: v1.1.0 (2017 01. 31.)

Enhances PLY support in Mathematica.

Current version adds support for exporting Points (currently only for point-only Graphics3D data).

Rich set of carefully designed shapes allowing flexible creation of publication quality

`PlotMarkers`

. See full description on Mathematica.SE.

`ProjectInstaller`

is a simple web installer for Mathematica projects. The projects can be stored on the web or on the local machine, in .zip or .tar.gz formats. It attempts to download and install a given project into a specified project directory.

The most up-to-date lexer and highlighter for Mathematica/Wolfram Language source code using the pygments engine.

Sometimes computations in Mathematica require more memory than is available. QLink solves this problem by making it possible to work on objects stored directly on the hard-drive, in a so called Tokyo Cabinet database.

A free Mathematica add-on for Dirac Bra-Ket Notation, Quantum Algebra, Quantum Computing and the QHD approximation to the Heisenberg Equations of Motion.

QuantumUtils for Mathematica is a software library for quantum information scientists. Features include: Multi-partite tensor manipulations; Quantum system modelling including qudits, circuits, spins, and cavities; Symbolic Lie algebra simplification for spin and cavity systems; Quantum channels in multiple representations; Numerical and symbolic simulators for open and closed quantum system evolution; An implementation of GRadient Ascent Pulse Engineering including distortions; Perturbative expansion tools such as the Magnus series, the Zassenhaus formula, and matrix power series; Visualization functions for displaying matrices, quantum states, data etc.

Last updated September 9, 2015
quantum information

RadarChart Mathematica Package The RadarChart mathematica package incorporates Radar Charts (also known as Spider Charts, Web Charts and Star Plots) as a new set of visualization tools into the mathematica environment.

Last updated December 21, 2015
Data Visualization

REAP (Renormalization group Evolution of Angles and Phases) is a Mathematica package for solving the renormalization group equations (RGE) of the quantities relevant for neutrino masses, for example the dimension-5 neutrino mass operator, the Yukawa matrices and the gauge couplings.

The package MPT (Mixing Parameter Tools) allows to extract the lepton masses, mixing angles and CP phases from the mass matrices of the neutrinos and the charged leptons. Thus, the running of the neutrino mass matrix calculated by REAP can be translated into the running of the mixing parameters and the mass eigenvalues.

This package introduces definitions for tensor calculations in Riemannian Geometry.

RISCErgoSum is a collection of packages created at the Research Institute for Symbolic Computation (RISC), Linz, Austria. The included packages are: Asymptotics for computing asymptotic series expansions of univariate holonomic sequences; Dependencies for computing algebraic relations of C-finite sequences and multi-sequences; Engel is an implementation of q-Engel Expansion; fastZeil, the Paule/Schorn Implementation of Gosper’s and Zeilberger’s Algorithms; GeneratingFunctions for manipulations of univariate holonomic functions and sequences; GenOmega, Guo-Niu Han’s general Algorithm for MacMahon’s Partition Analysis; Guess for guessing multivariate recurrence equations; HolonomicFunctions for dealing with multivariate holonomic functions, including closure properties, summation, and integration; MultiSum for proving hypergeometric multi-sum... Read more.

Last updated September 25, 2015
symbolic

SARAH is a Mathematica package for building and analyzing SUSY and non-SUSY models. It calculates all vertices, mass matrices, tadpoles equations, one-loop corrections for tadpoles and self-energies, and two-loop RGEs for a given model. SARAH writes model files for FeynArts, CalcHep/CompHep, which can also be used for dark matter studies using MicrOmegas, the UFO format which is supported by MadGraph 5 and for WHIZARD and OMEGA. SARAH is also the first available spectrum-generator-generator: based on the derived, analytical expression it creates source code for SPheno. In that way, it is possible to implement new models in SPheno without the need to... Read more.

A package for creating publication quality figures with Mathematica, created by Mark Caprio. SciDraw is the successor of LevelScheme and excels at creating multipanel figures and various diagrams (including special support for energy level diagrams).

Drop shadows and specular highlights for 2D graphics. See examples on Mathematica.SE.

Last updated September 16, 2015
graphics

This packages is for interfacing with the Singular computer algebra system. Singular is an open-source computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory.

SNA is a Mathematica toolbox for stoichiometric network analysis. Among other things, it supports flux balance analysis and the enumeration of the elementary vectors of the flux and the conversion cone.

Last updated October 19, 2015
bioinformatics

SNEG library is a Mathematica package that provides a framework for performing calculations using the operators of the second quantization with an emphasis on the anti-commuting fermionic operators in the context of solid-state and atomic physics. It consists of a collection of transformation rules that define the algebra of operators and a comprehensive library of utility functions. SNEG library is the foundation of the NRG Ljubljana package, however it can also be used as a stand-alone package.

Last updated September 13, 2016
physics

A package to read definitions of in-memory Mathematica functions with ease. It does approximately the same thing as

`GeneralUtilities`PrintDefinitions`

, which however is only available for Mathematica 10 and later.

Last updated September 9, 2015
spelunking

A collection of packages useful for demonstrating concepts in computer-music theory.

Last updated September 27, 2015
music

TensoriaCalc tackles (semi-)Riemannian tensor calculus problems encountered in general relativity, cosmology, and field theory. Currently, it calculates geometric objects – Christoffel symbols, the Riemann curvature tensor, Ricci tensor and scalar, etc. – given a metric and the relevant coordinates; and performs basic operations such as covariant derivatives of tensors.

A System for Computer Supported Mathematical Theorem Proving and Theory Exploration
Theorema was conceived and initiated around 1995 by Bruno Buchberger and reflects his view of "doing mathematics". It is being developed under his guidance by the Theorema Working Group at the Research Institute for Symbolic Computation, Johannes Kepler University, Linz – Hagenberg, Austria.

Last updated September 9, 2015

TIDES is a free software to integrate numerically Ordinary Differential Equations by using a Taylor Series method. It consists on a C (Fortran) library, libTIDES, and a Mathematica package, MathTIDES.

Tunnel is a set of scripts that simplify launching remote Mathematica kernels where all established MathLink connections are automatically tunneled through a secure shell connection (SSH).

Unzips zip archives. Unzip is similar to the Mathematica

`ExtractArchive`

function, except that Unzip prints the file names (using `Print`

or `PrintTemporary`

) while unzipping.

Last updated September 10, 2015
compression

The package UserHelp` is aimed to simplify work with the user help pages that includes generating the user package documentation and examples of the Wolfram Mathematica system objects, searching within user documentation, and editing and rebuilding of the user help pages.

Last updated September 30, 2016
User Help Pages

VaspImport imports crystal structures from various file types associated with the Vienna Ab-Initio Simulation Package (VASP). The package recognizes the following formats: POSCAR, CONTCAR, OUTCAR, XDATCAR, vasprun.xml. More information about VASP can be found on the official website, www.vasp.at.

A package for carrying out vector calculus calculations. Related paper: http://arxiv.org/abs/1309.2561.

A package for web browsing automation. It makes it possible to control Google Chrome and other browsers from within Mathematica.

A collection of many packages that make it easier to work with with Wolfram Language.

Last updated September 8, 2015

This is a google-code-prettify extension for highlighting Wolfram Language (Mathematica) source code on the web.

This is a standalone parser library for Mathematica (Wolfram Language). The code for the parser is extracted from the Mathematica IntelliJ Plugin. All dependencies to the IntelliJ Platform are included and it can be used as command-line program without a running IntelliJ IDEA.

A Wolfram Language client for the XML-RPC WordPress API.

Set of packages enhancing capabilities of Wolfram Workbench. Features include, inter alia, creating cross-version compatible documentation and including, in build scripts, test suite runs in multiple Mathematica versions.

xAct is a suite of free packages for tensor computer algebra in Mathematica. xAct implements state-of-the-art algorithms for fast manipulations of indices and has been modelled on the current geometric approach to General Relativity. It is highly programmable and configurable. Since its first public release in March 2004, xAct has been intensively tested and has solved a number of hard problems in GR.

xCellerator is a Mathematica package designed to aide biological modeling via the automated conversion of chemical reactions into ODEs and their subsequent solution via numerical integration.

A Mathematica package that contains functions for performing triangle-wye (also delta-wye or ΔY) and wye-triangle (also wye-delta or YΔ) transforms on simple undirected graphs.

Last updated October 31, 2015
graphs