Debian Science Mathematics packages

4ti2 je balík matematického softvéru na algebraické, geometrické a kombinatorické problémy v lineárnych priestoroch.

Tento balík poskytuje sadu nástrojov 4ti2.

Agda is a dependently typed functional programming language: It has inductive families, which are like Haskell's GADTs, but they can be indexed by values and not just types. It also has parameterised modules, mixfix operators, Unicode characters, and an interactive Emacs interface (the type checker can assist in the development of your code).

Agda is also a proof assistant: It is an interactive system for writing and checking proofs. Agda is based on intuitionistic type theory, a foundational system for constructive mathematics developed by the Swedish logician Per Martin-Löf. It has many similarities with other proof assistants based on dependent types, such as Coq, Epigram and NuPRL.

This is a meta package which provides Agda's emacs mode, executable, standard library and its documentation.

AUTO can do a limited bifurcation analysis of algebraic systems of the form

  f(u,p) = 0,  f,u in Rn
and of systems of ordinary differential equations of the form
  u'(t) = f(u(t),p),  f,u in Rn
subject to initial conditions, boundary conditions, and integral

constraints. Here p denotes one or more parameters. AUTO can also do certain continuation and evolution computations for parabolic PDEs. It also includes the software HOMCONT for the bifurcation analysis of homoclinic orbits. AUTO is quite fast and can benefit from multiple processors; therefore it is applicable to rather large systems of differential equations.

Axiom sa hodí na výskum a vývoj matematických algoritmov. Definuje silne typovú, matematicky korektnú hierarchiu typov. Obsahuje programovací jazyk a zabudovaný kompilátor.

Axiom sa vyvíja od roku 1973 a predával sa ako komerčný produkt. Bol uvoľnený ako slobodný softvér.

Prebiehajú snahy rozšíriť tento softvér:

 a) vyvinúť lepšie používateľské rozhranie
 b) urobiť ho užitočným ako nástroj pri výuke
 c) vyvinúť serverový protokol pre algebru
 d) integrovať ďalšiu matematiku
 e) prebudovať algebru v štýle gramotného programovania (literate
    programming)
 f) integrovať logické programovanie
 g) vyvinúť recenzovaný časopis Axiom Journal

Tento balík obsahuje hlavný binárny súbor programu a všetky predkompilované algebraické a automaticky načítateľné moduly.

Bliss is a backtracking algorithm for computing automorphism groups and canonical forms of graphs, based on individualization and refinement. Its data structures, subroutines, and pruning heuristics are specially designed for fast handling of large and sparse graphs.

This package provides the command line tool bliss.

The algorithm for the computation of sheaf cohomologies for line bundles on toric varieties presented in "Cohomology of Line Bundles: A Computational Algorithm" by Ralph Blumenhagen, Benjamin Jurke, Thorsten Rahn, and Helmut Roschy has been implemented in a convenient and high-performance C/C++ application called cohomCalg.

The optional cohomCalg Koszul extension serves as a Mathematica 7 frontend and allows for the easy computation of hypersurface and complete intersection cohomologies, following the material presented in "Cohomology of Line Bundles: Applications" by the same authors.

Cbc (Coin-or branch and cut) is an open-source mixed integer programming solver written in C++. It can be used as a callable library or as a stand-alone executable.

This package contains cbc executable.

CSDP is a library of routines that implements a predictor corrector variant of the semidefinite programming algorithm of Helmberg, Rendl, Vanderbei, and Wolkowicz. The code runs in parallel on shared memory multi-processor systems, and it makes effective use of sparsity in the constraint matrices.

CSDP is part of the larger COIN-OR initiative (Computational Infrastructure for Operations Research).

This package contains the binaries.

Bonmin (Basic Open-source Nonlinear Mixed INteger programming) is an open-source code for solving general MINLP (Mixed Integer NonLinear Programming) problems.

Bonmin is part of the larger COIN-OR initiative (Computational Infrastructure for Operations Research) and can be used with other COIN-OR packages that make use of cuts, such as the mixed-integer linear programming solver Cbc.

This package contains the header files for developers.

SYMPHONY is an open-source generic mixed-integer linear programs (MILP) solver, callable library, and extensible framework for implementing customized solvers SYMPHONY has a number of advanced capabilities, including the ability to solve multi-objective MILPs, the ability to warm start its solution procedure, and the ability to perform basic sensitivity analyses.

SYMPHONY is part of the larger COIN-OR initiative (Computational Infrastructure for Operations Research).

This package contains the symphony executable.

Coq je asistent dôkazov logiky vyššieho rádu, ktorý umožňuje vývoj počítačových programov v súlade s ich formálnou špecifikáciou. Bol vyvinutý pomocou Objective Caml a Camlp5.

Tento balík poskytuje coqtop, rozhranie príkazového riadka ku Coq.

Grafické rozhranie ku Coq poskytuje balík coqide. Coq je tiež možné používať spolu s ProofGeneral, ktorý umožňuje upravovanie dôkazov pomocou emacs a xemacs. To vyžaduje, aby bol nainštalovaný balík proofgeneral.

CryptoMiniSat is a modern, multi-threaded, simplifying SAT solver.

This package provides a command line interface which reads SAT formulas in conjunctive normal form in the DIMACS format with the extension of XOR clauses and decides whether they are satisfiable.

This package includes several programs to compute with elliptic curves over Q ; most notably mwrank (for 2-descent on elliptic curves over Q) and the modular symbol tools used to create the elliptic curve database.

This package provides tools to prove equational theorems: from a mathematical specification in many-sorted first-order logic with equality and an hypothesis/conjecture, it will look for a proof.

FEniCS is a collection of free software for automated, efficient solution of differential equations.

FEniCS has an extensive list of features, including automated solution of variational problems, automated error control and adaptivity, a comprehensive library of finite elements, high performance linear algebra and many more.

FEniCS is organized as a collection of interoperable components, including the problem-solving environment DOLFIN, the form compiler FFC, the finite element tabulator FIAT, the just-in-time compiler Instant, the code generation interface UFC, the form language UFL and a range of additional components.

This is a metapackage which depends on all FEniCS components.

This is the legacy version of FEniCS. You may want to consider installing the next-generation FEniCS-X (fenicx package).

This package includes William Hart's program to find prime factors of large integers (at least forty digits).

It does so using highly optimized multi-polynomial quadratic sieve.

This is a Symbolic Manipulation System. It reads symbolic expressions from files and executes symbolic/algebraic transformations upon them. The answers are returned in a textual mathematical representation. As its landmark feature, the size of the considered expressions in FORM is only limited by the available disk space and not by the available RAM.

fpLLL is a library for computing reduced (nearly orthogonal) bases for Euclidean lattices using the floating-point LLL algorithm.

fpLLL contains multiple different implementations of the floating-point LLL reduction algorithm, offering multiple different speed/guarantees ratios.

It contains a 'wrapper' that chooses the estimated best sequence of variants in order to provide a guaranteed output as fast as possible. In the case of the wrapper, the succession of variants is oblivious to the user.

This package contains the base tools using libfplll.

FreeFEM is a language adapted to Partial Differential equation. The underlying method used is the Finite Element Method. This tool has been successfully used as a teaching tool and even as a research tool.

FreeFem++ is an implementation of a language dedicated to the finite element method. It enables you to solve Partial Differential Equations (PDE) easily.

Problems involving PDE from several branches of physics such as fluid-structure interactions require interpolations of data on several meshes and their manipulation within one program. FreeFem++ includes a fast quadtree-based interpolation algorithm and a language for the manipulation of these data on multiple meshes. It contains also a powerful mesh generation and adaption tool integrated seamlessly in FreeFem++ called bamg.

FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom allowing for a smooth learning curve.

This package contains the executables of FreeFem++.

FreeMat is a free environment for rapid engineering and scientific prototyping and data processing. It is similar to commercial systems such as MATLAB from Mathworks, and IDL from Research Systems, but is Open Source. FreeMat is available under the GPL license.

Frobby is a software system and project for computations with monomial ideals. Frobby is free software and it is intended as a vehicle for computational and mathematical research on monomial ideals.

The current functionality includes Euler characteristic, Hilbert series, maximal standard monomials, combinatorial optimization on monomial ideals, primary decomposition, irreducible decomposition, Alexander dual, associated primes, minimization and intersection of monomial ideals as well as the computation of Frobenius problems (using 4ti2) with very mmlarge numbers. Frobby is also able to translate between formats that can be used with several different computer systems, such as Macaulay 2, Monos, 4ti2, CoCoA4 and Singular. Thus Frobby can be used with any of those systems.

GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. GAP is used in research and teaching for studying groups and their representations, rings, vector spaces, algebras, combinatorial structures, and more.

This is a dummy package that depends on the standard GAP components.

GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. GAP is used in research and teaching for studying groups and their representations, rings, vector spaces, algebras, combinatorial structures, and more.

This package contains the Character Table Library by Thomas Breuer.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package provides for GAP routines for constructing, classifying, partitioning and studying block designs.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package brings to GAP routines for factoring integers, in particular:

• Pollard's p-1
• Williams' p+1
• Elliptic Curves Method (ECM)
• Continued Fraction Algorithm (CFRAC)
• Multiple Polynomial Quadratic Sieve (MPQS)

It also provides access to Richard P. Brent's tables of factors of integers of the form b^k +/- 1.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This GAP package brings to GAP floating-point numbers with arbitrary precision; it is based on MPFR, MPFI, MPC, CXSC, and FPLLL.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package implements computing with graphs and groups for GAP. GRAPE is primarily designed for constructing and analysing graphs related to groups, finite geometries, and designs; special emphasis is placed on the determination of regularity properties and subgraph structure.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This GAP package brings to GAP computing with error-correcting codes.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

LAGUNA stands for `Lie AlGebras and UNits of group Algebras'.

This package provides GAP with functionality for calculation of the normalized unit group of the modular group algebra of the finite p-group and for investigation of Lie algebra associated with group algebras and other associative algebras.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package allows GAP to import and export mathematical objects encoded in OpenMath, for the purpose of exchanging them with other applications that are OpenMath enabled.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas. In the example text, gap is used to analyse Rubik's Cube using group theory. A kernel implements a Pascal-like language.

This package contains the database of primitive groups.

This is a transitional package. It can be safely removed after the installation is complete.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas. In the example text, gap is used to analyse Rubik's Cube using group theory. A kernel implements a Pascal-like language.

The Small Groups Library is a catalogue of groups of `small' order. This package contains the groups data and identification routines for groups of order up to 1000 except 512, 768 and groups whose order factorises in at most 3 primes.

Note that data for order 512, 768 and between 1000 and 2000 except 1024 are available separately in the gap-small-groups-extra packages.

This is a transitional package. It can be safely removed after the installation is complete.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas. In the example text, gap is used to analyse Rubik's Cube using group theory. A kernel implements a Pascal-like language.

The Small Groups Library is a catalogue of groups of `small' order. This package contains the groups data and identification routines for groups

• of order at most 2000 except 1024.
• of cubefree order at most 50 000.
• of order p^n for n <= 6 and all primes p.
• of squarefree order.
• whose order factorises in at most 3 primes.
• of order q^n * p for q^n dividing 2^8, 3^6, 5^5, 7^4 and p prime different to q

The Small Groups Library provides access to these groups and a method to identify the catalogue number of a given group.

This is a transitional package. It can be safely removed after the installation is complete.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package provides to GAP methods for the construction and analysis of finite nearrings.

GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. GAP is used in research and teaching for studying groups and their representations, rings, vector spaces, algebras, combinatorial structures, and more.

This package contains the GAP Library of Tables of Marks by L. Naughton and G. Pfeiffer.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas.

This package provides for GAP routines for working with toric varieties and dealing with cones and related combinatorial geometric object.

GAP is a system for computational discrete algebra with particular emphasis on computational group theory, but which has already proved useful also in other areas. In the example text, gap is used to analyse Rubik's Cube using group theory. A kernel implements a Pascal-like language.

This package contains the database of transitive groups.

This is a transitional package. It can be safely removed after the installation is complete.

The Mathematics Genealogy Grapher (Geneagrapher) is a software tool to gather the information for building math genealogy trees with data from the Mathematics Genealogy Project. The information extracted is stored in dot file format, which can then be passed to Graphviz to generate a graph.

This package contains the command-line tool.

GeoGebra je program na dynamickú geometriu. Môžete robiť konštrukcie s bodmi, vektormi, úsečkami, priamkami, kužeľosečkami aj funkciami a potom ich dynamicky meniť. Rovnice a súradnice možno zadať aj priamo.

Program podporuje mnohé geometrické konštrukcie a tiež mnohé výpočtové nástroje (derivácie, oskulačné kružnice, ...).

Súbory GeoGebra možno exportovať do mnohých formátov alebo ako interaktívne aplety webových stránok.

Gnomeview je program na prehliadanie interaktívnej geometrie. Hodí sa predovšetkým na výskum a vzdelávanie v oblasti matematiky. Konkrétne je schopný zobraziť predmety v hyperbolickom, sférickom aj eukleidovskom priestore.

Gnomeview používa viaceré na sebe nezávisle ovládateľné objekty a pohľady. Poskytuje interaktívne ovládanie pohybu, vzhľadu (vrátane osvetlenia, tieňovania a materiálov), výber objektu, úroveň hrán či vrcholov, snímky v súbore SGI alebo formáte Renderman RIB a pridávanie/odstraňovanie objektov priamo pomocou myši, ovládacie panely, klávesové skratky. Externé nástroje môžu riadiť požadované uhly pohľadu (čo sa hodí v prípade neustále sa meniacej geometrie alebo na riadenie pohybu určitých objektov), pričom umožňuje úplnú interaktívnu kontrolu nad celou scénou.

Gerris is a system for the solution of the partial differential equations describing fluid flow.

A brief summary of its main (current) features:

• Solves the time-dependent incompressible variable-density Euler, Stokes or Navier-Stokes equations
• Adaptive mesh refinement: the resolution is adapted dynamically to the features of the flow
• Entirely automatic mesh generation in complex geometries
• Second-order in space and time
• Unlimited number of advected/diffused passive tracers
• Flexible specification of additional source terms
• Portable parallel support using the MPI library
• Volume of Fluid advection scheme for interfacial flows

This package has MPI support built in.

GetDP is a general finite element solver using mixed elements to discretize de Rham-type complexes in one, two and three dimensions.

The main feature of GetDP is the closeness between the input data defining discrete problems (written by the user in ASCII data files) and the symbolic mathematical expressions of these problems.

See GetDP's reference manual for a more thorough overview of GetDP's capabilities: http://www.geuz.org/getdp

Gfan is a software package for computing Groebner fans and tropical varieties. These are polyhedral fans associated to polynomial ideals. The maximal cones of a Groebner fan are in bijection with the marked reduced Groebner bases of its defining ideal. The software computes all marked reduced Groebner bases of an ideal. Their union is a universal Groebner basis. The tropical variety of a polynomial ideal is a certain subcomplex of the Groebner fan. Gfan contains algorithms for computing this complex for general ideals and specialized algorithms for tropical curves, tropical hypersurfaces and tropical varieties of prime ideals. In addition to the above core functions the package contains many tools which are useful in the study of Groebner bases, initial ideals and tropical geometry. Among these are an interactive traversal program for Groebner fans and programs for graphical renderings.

For ordinary Groebner basis computations Gfan is not competitive in speed compared to programs such as CoCoA, Singular and Macaulay2.

GiNaC (čo znamená „GiNaC is Not a CAS“ - „GiNaC nie je systém na počítačovú algebru“) je knižnica na vykonávanie symbolických (t.j. nenumerických) výpočtov priamo v programovacom jazyku C++.

Tento balík poskytuje niektoré ďalšie nástroje ako populárny ginsh (interaktívny shell GiNaC) a viewgar (na skúmanie súborov archívov GiNaC).

Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. Its design goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization capabilities. 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.

See Gmsh's reference manual for a more thorough overview of Gmsh's capabilities.

Kreslenie grafov sa zaoberá problémom vizualizácie štrukturálnych informácií zostavením geometrických reprezentácií abstraktných grafov a sietí. Automatická tvorba kresieb grafov má dôležité aplikácie v kľúčových technológiách ako návrh databáz, softvérové inžinierstvo, VLSI a návrh sietí a vizuálnych rozhraní v iných doménach. Medzi situácie, kde tieto nástroje môžu byť obzvlášť užitočné patrí:

• chcete reštrukturalizovať program a najprv chcete pochopiť vzťahy medzi jeho typmi, procedúrami a zdrojovými súbormi,
• potrebujete nájsť úzke miesta na chrbticovej internetovej sieti - nielen jednotlivé spojenia, ale aj ich vzťahy,
• ladíte protokol alebo mikroarchitektúru reprezentovanú konečným stavovým automatom a potrebujete zistiť, ako nastáva istý chybový stav,
• chcete prehliadať schému databázy, bázy znalostí alebo grafickú reprezentáciu distribuovaného programu,
• chcete vidieť prehľad kolekcie navzájom prepojených dokumentov,
• chcete objaviť vzory a záujmové komunity v databáze telefónnych hovorov alebo emailových správ.

Tento balík obsahuje nástroje pre príkazový riadok.

HOL Light is an interactive theorem prover for Higher-Order Logic with a very simple logical core running in an OCaml toplevel. HOL Light is famous for the verification of floating-point arithmetic as well as for the Flyspeck project, which aimed at the formalization of Tom Hales' proof of the Kepler conjecture.

Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. The library, mostly written in Julia itself, also integrates mature, best-of-breed C and Fortran libraries for linear algebra, random number generation, FFTs, and string processing. Julia programs are organized around defining functions, and overloading them for different combinations of argument types (which can also be user-defined).

This package provides a complete Julia installation (JIT compiler, standard library, text-based user interface).

lcalc is a program for computing zeros and values of L-functions. Supported L-functions include the Riemann zeta function, the L-function of the Ramanujan delta function, and L-functions of elliptic curves defined over the rationals.

JGraphT is a free Java class library that provides mathematical graph-theory objects and algorithms. In JGraphT, a graph is defined as a set of vertices connected by a set of edges.

It is possible to define graphs, to modify, compare or generate them, to run many algorithms through them. One may also import or export graphs.

GNU libmatheval is a library comprising of several procedures that make it possible to create an in-memory tree representation of mathematical functions over single or multiple variables and later use this representation to evaluate functions for specified variable values, to create corresponding trees for function derivatives over specified variables or to print textual representations of in-memory trees to a specified string. The library supports arbitrary variable names in expressions, decimal constants, basic unary and binary operators and elementary mathematical functions.

This package contains the runtime shared library.

Problém lineárneho programovania (LP) možno formulovať ako: riešte A.x >= V1, pre ktoré je V2.x maximálne. A je matica, x je vektor (nezáporných) premenných, V1 je vektor pravých strán a V2 je vektor koeficientov účelovej funkcie.

Problém celočíselného lineárneho programovania (CLP) je LP s obmedzením, že všetky premenné sú celé čísla. V zmiešanom celočíselnom lineárnom probléme (ZCLP) sú niektoré premenné celočíselné a iné reálne.

Program lp_solve rieši problémy LP, CLP a MILP. Je o niečo všeobecnejší než sa uvádza vyššie v tom, že každý riadok A (určujúci jedno obmedzenie) môže mať vlastnú (ne)rovnosť <=, >= alebo =. Výsledok určuje hodnoty všetkých premenných.

lp_solve používa pri čistých LP problémoch simplexovú metódu a metódy riedkych matíc. Ak je jedna alebo viac premenných deklarovaných ako celočíselné, simplexová metóda sa iteruje algoritmom vetiev a hraníc, kým sa nenájde požadované optimálne riešenie. lp_solve dokáže čítať vstupné súbory vo formáte MPS.

The "Littlewood-Richardson Calculator" is a package of C programs for computing Littlewood-Richardson coefficients, providing fast calculation of single LR coefficients, products of Schur functions, and skew Schur functions. Its interface uses the same notation as the SF package of John Stembridge, to make it easier to use both packages at the same time.

This package contains the command-line programs.

A convex polyhedron is the set of points satisfying a finite family of linear inequalities. The study of the vertices and extreme rays of such systems is important and useful in e.g. mathematics and optimization. In a dual interpretation, finding the vertices of a (bounded) polyhedron is equivalent to finding the convex hull (bounding inequalities) of an (arbitrary dimensional) set of points. Lrs (lexicographic reverse search) has two important features that can be very important for certain applications: it works in exact arithmetic, and it consumes memory proportional to the input, no matter how large the output is.

Macaulay 2 is a software system for algebraic geometry research, written by Daniel R. Grayson and Michael E. Stillman. Based on Groebner bases, it provides algorithms for computing homological invariants of rings and modules.

This package contains the architecture dependent portion of Macaulay2.

Magnus is a simple screen magnifying glass. It nicely integrates with X11 desktops like MATE or Xfce (probably with others not named here, too).

Visually impaired users may find this tool helpful for zooming into certain screen areas in order to improve readability/visibilty of fonts, icons and other data.

Mathicgb is a program for computing Groebner basis and signature Groebner bases. Mathicgb is based on the fast data structures from mathic.

The paper "Practical Groebner Basis Computation" describes the algorithms in Mathicgb from a high level. It was presented at ISSAC 2012 and is available at http://arxiv.org/abs/1206.6940

This package contains the command line tool.

Mathomatic implements most of the rules of algebra for the mathematical operators +, -, *, /, % (modulus), and power (including roots).

Mathomatic can symbolically:

• combine and solve equations,
• completely simplify and compare expressions and equations,
• do simple calculus transformations and series,
• do standard, complex number, modular, and polynomial arithmetic,
• generate optimized C, Java, and Python language code from simplified equations,
• plot expressions with gnuplot in two or three dimensions,
• do quick calculations, colorize expressions, etc.

Maxima is a fully symbolic computation program. It is full featured doing symbolic manipulation of polynomials, matrices, rational functions, integration, Todd-coxeter methods for finite group analysis, graphing, multiple precision floating point computation. It has a symbolic source level debugger for maxima code. Maxima is based on the original Macsyma developed at MIT in the 1970s. It is quite reliable, and has good garbage collection, and no memory leaks. It comes with hundreds of self tests.

The maxima-sage packages are meant to be used together with SageMath. They contain the version of Maxima that works together with the SageMath version in Debian and use ECL instead of GCL as Lisp compiler. To use Maxima by itself, the more complete and up-to-date maxima package is recommended.

This package contains the main executables and base system files.

The MCL package is an implementation of the MCL algorithm, and offers utilities for manipulating sparse matrices (the essential data structure in the MCL algorithm) and conducting cluster experiments.

MCL is currently being used in sciences like biology (protein family detection, genomics), computer science (node clustering in Peer-to-Peer networks), and linguistics (text analysis).

Napriek tomu, že problém splniteľnosti booleovských funkcií (SAT) je NP-úplný, riešitelia SAT sú často schopní tento problém rozhodnúť v rozumnom časovom rámci. Keďže všetky ostatné NP-úplné problémy sú redukovateľné na SAT, riešitelia sa stali nástrojom na všeobecné účelu pre túto triedu problémov.

MiniSat je minimalistický open source riešiteľ SAT vyvinutý tak, aby pomohol výskumníkom a vývojárom začať pracovať so SAT. MiniSat, ktorý vyhral všetky priemyselné kategórie súťaže SAT 2005, je dobrým východiskovým bodom budúceho výskumy v oblasti SAT a pre aplikácie používajúce SAT.

Model Builder je grafický nástroj na navrhovanie, simulovanie a analýzu Matematického modelu, pozostávajúci zo systému obyčajných diferenciálnych rovníc (ODE).

MUMPS implements a direct solver for large sparse linear systems, with a particular focus on symmetric positive definite matrices. It can operate on distributed matrices e.g. over a cluster. It has Fortran and C interfaces, and can interface with ordering tools such as Scotch.

nauty (No AUTomorphisms, Yes?) is a set of procedures for computing automorphism groups of graphs and digraphs. This mathematical software suite is developed by Brendan McKay and Adolfo Piperno: http://pallini.di.uniroma1.it

nauty computes graph information in the form of a set of generators, the size of the group, and the orbits of the group; it can also produce a canonical label. The nauty suite is written in C and comes with a command-line interface, a collection of command-line tools, and an Application Programming Interface (API).

This package provides the nauty interface named dreadnaut, and a small collection of utilities called gtools.

NETGEN is an automatic 3d tetrahedral mesh generator. It accepts input from constructive solid geometry (CSG) or boundary representation (BRep) from STL file format. NETGEN contains modules for mesh optimization and hierarchical mesh refinement.

Normaliz is a mathematical tool for computations in affine monoids, vector configurations, lattice polytopes, and rational cones.

This dummy package provides the standard installation.

Octave is a (mostly MATLAB® compatible) high-level language, primarily intended for numerical computations. It provides a convenient command-line interface for solving linear and nonlinear problems numerically.

Octave can be dynamically extended with user-supplied C++ files.

This package contains various tools to work with lattice polytopes:

• mori.x computes star triangulations of a polytope
• cws.x creates weight systems and combined weight systems
• class.x classifies reflexive polytopes
• poly.x computes data of a polytope
• nef.x computes Hodge numbers of nef-partitions

PARI/GP je široko používaný systém počítačovej algebry navrhnutý na rýchle výpočty v oblasti teórie čísel (faktorizácie, algebraická teória čísel, eliptické krivky, ...), ale obsahuje aj množstvo iných užitočných funkcií na výpočty s matematickými entitami ako sú matice, polynómy, mocninové rady, algebraické čísla atď. a mnohé transcendentálne funkcie. PARi je tiež dostupný ako knižnica jazyka C umožňujúca rýchlejšie výpočty.

Pôvodne ho vyvinul Henri Cohen a jeho spolupracovníci (University Bordeaux I, France). PARI je dnes licencovaný pod GPL a spravuje ho Karim Belabas za pomoci mnohých dobrovoľníkov.

Tento balík obsahuje kalkulátor GP.

Persalys is a graphical user interface for OpenTURNS, dedicated to the treatment of uncertainty and the management of variabilities. The software is a tool between the computer simulation, probabilistic analyses and the data sciences. The interface is available in French or in English.

Persalys allows one to:

• create mathematical models: analytical, coupling with an external model (finite elements, ...), FMU;
• analyse the variability of one's parameters thanks to many methods and visualisation tools;
• statistically analyse one's measuring data, infer probability distributions or create metamodels.

PHCpack is a software package to solve polynomial systems by homotopy continuation methods.

A polynomial system is given as a sequence of polynomials in several variables. Homotopy continuation methods operate in two stages. In the first stage, a family of polynomial systems (the so-called homotopy) is constructed. This homotopy contains a polynomial system with known solutions. In the second stage, numerical continuation methods are applied to track the solution paths defined by the homotopy, starting at the known solutions and leading to the solutions of the given polynomial system.

This package contains the command line interface to PHCpack.

This package contains a command-line reference implementation of the Edge Addition Planarity Algorithm, which is the best linear-time method to embed a planar graph and isolate planarity obstructions.

Polylib is a free C library for doing computations on polyhedra. The library is operating on objects like vectors, matrices, lattices, polyhedra, Z-polyhedra, unions of polyhedra and other intermediary structures. It provides functions for all important operations on these structures.

This package contains various utilities to perform polyhedral operations.

Proof General is a major mode to turn Emacs into an interactive proof assistant to write formal mathematical proofs using a variety of theorem provers.

This package provides Proof General support for Coq. (There is no other proof assistant that one could sensibly support.)

This package provides the Prover9 resolution/paramodulation theorem prover and the Mace4 countermodel generator.

Prover9 is an automated theorem prover for first-order and equational logic. It is a successor of the Otter prover. Prover9 uses the inference techniques of ordered resolution and paramodulation with literal selection.

The program Mace4 searches for finite structures satisfying first-order and equational statements, the same kind of statement that Prover9 accepts. If the statement is the denial of some conjecture, any structures found by Mace4 are counterexamples to the conjecture.

Mace4 can be a valuable complement to Prover9, looking for counterexamples before (or at the same time as) using Prover9 to search for a proof. It can also be used to help debug input clauses and formulas for Prover9.

DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. It seeks to make algorithms explicit and data structures transparent. It works in perfect harmony with parallelisation mechanism such as multiprocessing and SCOOP.

This package contains the modules for Python3.

DOLFIN is the Python and C++ interface of the FEniCS project for the automated solution of differential equations, providing a consistent PSE (Problem Solving Environment) for solving ordinary and partial differential equations. Key features include a simple, consistent and intuitive object-oriented API; automatic and efficient evaluation of variational forms; automatic and efficient assembly of linear systems; and support for general families of finite elements.

This is the base package depending on specific dolfin builds. By default the version built against the preferred version of PETSc in /usr/lib/petsc is selected (with 32-bit indexing, but the alternative version (64-bit PETSc) can be selected by setting the environment variable PETSC_DIR.

This is the legacy version of DOLFIN, you may want to install the next-generation python3-dolfinx (DOLFIN-X) instead.