Open Source Mathematics Software - Page 4
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. We thank the support from Claudia Adams Barr Program in Innovative Basic Cancer Research and NIH/NHGRI to develop MAGeCK. -
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XonGrid
Excel interpolation add-in
XonGrid is a free Excel library of functions to perform 1D, 2D, 3D, 4D and arbitrary dimension (ND) interpolations from scattered data. -
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calc: C-style arbitrary precision system
Calc: arbitrary precision C-like arithmetic & calculator
Calc is arbitrary precision C-like arithmetic system that is a calculator, an algorithm prototyper and mathematical research tool. Calc comes with a rich set of builtin mathematical and programmatic functions. -
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FriCAS is an advanced computer algebra system. Its capabilities range from calculus (integration and differentiation) to abstract algebra. It can plot functions and has integrated help system.
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Linear Program Solver
Solve linear programming problems
Linear Program Solver (LiPS) is an optimization package oriented on solving linear, integer and goal programming problems. The main features of LiPS are: ● LiPS is based on the efficient implementation of the modified simplex method that solves large scale problems. ● LiPS provides not just an answer, but a detailed solution process as a sequence of simplex tables, so you can use it for studying/teaching linear programming. ● LiPS gives sensitivity analysis procedures, which allow us to study the behaviour of the model when you change its parameters, including: analysis of changes in the right sides of constraints, analysis of changes in the coefficients of the objective function, analysis of changes in the column/row of the technology matrix. Such information may be extremely useful for the practical application of LP Models. ● LiPS provides methods of goal programming, including lexicographic and weighted GP methods, which are oriented on multi-objective optimisation. -
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Java Universal Network/Graph Framework
Java graph/network library
JUNG provides a common and extendible language for the modeling, analysis, and visualization of data that can be represented as a graph or network. New version now available on GitHub: https://github.com/jrtom/jung/releases/tag/jung-2.1 -
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AlphaPlot
Interactive scientific graphing and data analysis software.
Alpha Plot can generate different types of 2D and 3D plots (such as line, scatter, bar, pie, and surface plots) from data that is either imported from ASCII files, entered by hand, or calculated using formulas. The data is held in spreadsheets which are referred to as tables with column-based data (typically X and Y values for 2D plots) or matrices (for 3D plots). The spreadsheets as well as graphs and note windows are gathered in a project and can be organized using folders. The built-in analysis operations include column/row statistics, (de)convolution, FFT and FFT-based filters. Scripting Console support in-place evaluation of mathematical expressions and scrtipting interface to ECMAScript like dynamic scripting language(java script). The GUI of the application uses the Qt toolkit. Periodic test builds are available here http://alphaplot.sourceforge.net/test-build.html -
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ASCEND is a modelling environment and solver for large or small systems of non-linear equations, for use in engineering, thermodynamics, chemistry, physics, mathematics and biology. Solvers for both steady and dynamic (NLA & DAE) problems, are provid
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JuMP
Modeling language for Mathematical Optimization
JuMP is a modeling language and collection of supporting packages for mathematical optimization in Julia. JuMP makes it easy to formulate and solve a range of problem classes, including linear programs, integer programs, conic programs, semidefinite programs, and constrained nonlinear programs. JuMP is used to solve large-scale inventory routing problems at Renault, schedule trains at Thales Inc., plan power grid expansion at PSR, and route school buses. -
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KrylovKit.jl
Krylov methods for linear problems, eigenvalues, and singular values
A Julia package collecting a number of Krylov-based algorithms for linear problems, singular value and eigenvalue problems and the application of functions of linear maps or operators to vectors. -
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LazySets.jl
Scalable Symbolic-Numeric Set Computations
LazySets.jl is a Julia package for calculus with convex sets. The aim is to provide a scalable library for solving complex set-based problems, such as those encountered in differential inclusions or reachability analysis techniques in the domain of formal verification. Typically, one is confronted with a set-based recurrence with a given initial set and/or input sets, and for visualization purposes, the final result has to be obtained through an adequate projection onto low dimensions. This library implements types to construct set formulas and methods to efficiently and accurately approximate the projection in low dimensions. -
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Mathematics Dataset
This dataset code generates mathematical question and answer pairs
The Mathematics Dataset, developed by Google DeepMind, is a synthetic dataset designed to evaluate and train machine learning models on mathematical reasoning and symbolic manipulation. It generates question-and-answer pairs across a wide range of mathematical topics typically found in school-level curricula, testing a model’s ability to reason about algebra, arithmetic, calculus, probability, and more. Each question is programmatically generated with structured templates to ensure clear logic and reproducibility. The dataset enables models to learn mathematical problem-solving through examples that involve both numeric and symbolic reasoning. Version 1.0 includes over 2 million examples per category, with training splits labeled as “easy,” “medium,” and “hard,” supporting curriculum-based learning strategies. The data can be accessed via PyPI or generated locally using provided Python scripts, with outputs formatted for direct use in training or evaluation pipelines. -
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statsmodels
Statsmodels, statistical modeling and econometrics in Python
statsmodels is a Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration. An extensive list of result statistics are available for each estimator. The results are tested against existing statistical packages to ensure that they are correct. The package is released under the open source Modified BSD (3-clause) license. Generalized linear models with support for all of the one-parameter exponential family distributions. Markov switching models (MSAR), also known as Hidden Markov Models (HMM). Vector autoregressive models, VAR and structural VAR. Vector error correction model, VECM. Robust linear models with support for several M-estimators. statsmodels supports specifying models using R-style formulas and pandas DataFrames. -
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A symbolic framework for C++, Python and Octave implementing automatic differentiation by source code transformation in forward and reverse modes on sparse matrix-valued computational graphs.
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rw
rw calculates rank-width and rank-decompositions.
rw calculates rank-width and rank-decompositions. It is based on ideas from "Computing rank-width exactly" by Sang-il Oum, "Sopra una formula numerica" by Ernesto Pascal, "Generation of a Vector from the Lexicographical Index" by B.P. Buckles and M. Lybanon and "Fast additions on masked integers" by Michael D. Adams and David S. Wise. On 2009's computers it works quite well up to graph sizes of about 28 nodes. Runtime and memory usage are exponential in the graph size. -
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EqualX
The LaTeX Equation Editor
EqualX makes you easily write equations in LaTeX and preview them in real-time. repository: https://gitlab.com/q-quark/equalx -
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pgfplots - A TeX package to draw normal and/or logarithmic plots directly in TeX in two and three dimensions with a user-friendly interface and pgfplotstable - a TeX package to round and format numerical tables. Examples in manuals and/or on web site. ATTENTION: As of February 2020, the development has been moved to https://github.com/pgf-tikz/pgfplots ! Please refer to the new page for downloads and change requests! This page is kept in read-only mode.
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wxMathPlot is an add-on library for wxWidgets which provides a framework for easy plotting of mathematical functions, sampled data and generic 2D plots.
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Madagascar is a software package for geophysical data processing and reproducible numerical experiments. The package mission is to provide a convenient environment for researchers working with digital image and data processing in geophysics and related fields.
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CompPad is a LibreOffice extension that provides live mathematical and engineering calculations within a Writer document. It is intended to provide a free / open-source alternative to Mathcad .
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JMulTi is an interactive software designed for univariate and multivariate time series analysis. It has a Java graphical user interface that uses an external engine for statistical computations. It uses the framework JStatCom.
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Benchee
Easy and extensible benchmarking in Elixir
Library for easy and nice (micro) benchmarking in Elixir. Benchee allows you to compare the performance of different pieces of code at a glance. It is also versatile and extensible, relying only on functions. There are also a bunch of plugins to draw pretty graphs and more! Benchee runs each of your functions for a given amount of time after an initial warmup, it then measures their run time and optionally memory consumption. It then shows different statistical values like average, standard deviation etc. The aforementioned plugins like benchee_html make it possible to generate nice-looking HTML reports, where individual graphs can also be exported as PNG images. first runs the functions for a given warmup time without recording the results, to simulate a "warm"/running system. Plugin/extensible-friendly architecture so you can use different formats to display benchmarking results as HTML, markdown, JSON, and more. -
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CGAL
The Computational Geometry Algorithms Library
CGAL or the Computational Geometry Algorithms Library is a C++ library that gives you easy access to a myriad of efficient and reliable geometric algorithms. These algorithms are useful in a wide range of applications, including computer aided design, robotics, molecular biology, medical imaging, geographic information systems and more. CGAL features a great range of data structures and algorithms, including Voronoi diagrams, cell complexes and polyhedra, triangulations, arrangements of curves, surface and volume mesh generation, spatial searching, alpha shapes, geometry processing, and many more. The use of these result in beautiful, visually complex and accurate representations. -
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CUTLASS
CUDA Templates for Linear Algebra Subroutines
CUTLASS is a collection of CUDA C++ template abstractions for implementing high-performance matrix-multiplication (GEMM) and related computations at all levels and scales within CUDA. It incorporates strategies for hierarchical decomposition and data movement similar to those used to implement cuBLAS and cuDNN. CUTLASS decomposes these "moving parts" into reusable, modular software components abstracted by C++ template classes. These thread-wide, warp-wide, block-wide, and device-wide primitives can be specialized and tuned via custom tiling sizes, data types, and other algorithmic policy. The resulting flexibility simplifies their use as building blocks within custom kernels and applications. To support a wide variety of applications, CUTLASS provides extensive support for mixed-precision computations, providing specialized data-movement and multiply-accumulate abstractions for half-precision floating point (FP16), BFloat16 (BF16), Tensor Float 32 (TF32), etc. -
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FourierFlows.jl
Tools for building fast, hackable, pseudospectral equation solvers
This software provides tools for partial differential equations on periodic domains using Fourier-based pseudospectral methods. A central intent of the software's design is also to provide a framework for writing new, fast solvers for new physical problems. The code is written in Julia.
