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← Revision 151 as of 20170807 20:33:20 ⇥
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Replaced some code.google.com links with current links.

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* [[PyGSL]]  http://pygsl.sourceforge.net/  This project provides a python interface for the GNU scientific library (gsl).  * [[NumPyNumPy]]  http://www.numpy.org/  Numerical Python adds a fast, compact, multidimensional array facility to Python. [[NumPyNumPy]] is the successor to both Numeric and Numarray. * '''Deprecated''': [[NumericNumeric]]  Numerical Python adds a fast, compact, multidimensional array language facility to Python. (Note: superseded by [[NumPyNumPy]]) * '''Deprecated''': [[NumArrayNumArray]]  http://stsdas.stsci.edu/numarray/index.html  Numarray is a reimplementation of Numeric which adds the ability to efficiently manipulate large numeric arrays in ways similar to Matlab and IDL. (Note: superseded by [[NumPyNumPy]]) 
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* [[NumPy]]  http://numpy.scipy.org/  Numerical Python adds a fast, compact, multidimensional array facility to Python. NumPy is the successor to both Numeric and Numarray. * '''Deprecated''': [[Numeric]]  http://www.numpy.org/  Numerical Python adds a fast, compact, multidimensional array language facility to Python. (Note: superseded by NumPy) * '''Deprecated''': NumArray  http://stsdas.stsci.edu/numarray/index.html  Numarray is a reimplementation of Numeric which adds the ability to efficiently manipulate large numeric arrays in ways similar to Matlab and IDL. (Note: superseded by NumPy) * SciPy  http://www.scipy.org/ (older info still on http://old.scipy.org) SciPy is an open source library of scientific tools for Python. SciPy supplements the popular NumPy module, gathering a variety of high level science and engineering modules together as a single package. SciPy includes modules for linear algebra, optimization, integration, special functions, signal and image processing, statistics, genetic algorithms, ODE solvers, and others. * !SymPy  http://code.google.com/p/sympy/ !SymPy is a symbolic manipulation package, written in pure Python. Its aim is to become a full featured CAS in Python, while keeping the code as simple as possible in order to be comprehensible and easily extensible. * ScientificPython  http://dirac.cnrsorleans.fr/ScientificPython/  ScientificPython is a collection of Python modules that are useful for scientific computing. In this collection you will find modules that cover basic geometry (vectors, tensors, transformations, vector and tensor fields), quaternions, automatic derivatives, (linear) interpolation, polynomials, elementary statistics, nonlinear leastsquares fits, unit calculations, Fortrancompatible text formatting, 3D visualization via VRML, and two Tk widgets for simple line plots and 3D wireframe models. There are also interfaces to the netCDF library (portable structured binary files), to MPI (Message Passing Interface, messagebased parallel programming), and to BSPlib (Bulk Synchronous Parallel programming). * [[PyACTS]] http://www.pyacts.org  PyACTS is a collection of Python Modules that are very useful to Parallel Computing in a High Performance Computing environment. This packages incorporates several modules like PyBLACS (allows communication data for Linear Algebra), PyPBLAS (distributed Matrix Operations) and PyScaLAPACK (solve linear systems and get the eigenvalue problems). These libraries are part of PyACTS project that provide interfaces to the ACTS Collection. Also is provided a parallel interpreter for using this package that implements messagebased parallel programming using MPI. * [[PyDSTool]]  http://pydstool.sourceforge.net  PyDSTool is an integrated simulation, modeling and analysis package for dynamical systems (including ODEs, DAEs, maps, and hybrid systems) and scientific data. Building on SciPy classes, the package also supports symbolic expression processing, bifurcation analysis, and enhanced arrays for "indexfree" and highly contextualized scientific data manipulation. Model building tools use symbolic expression and hierarchical specification classes to ease the development and analysis of complex models. This includes automated compilation of symbolic representations of models into fast numerical code using enhanced legacy Fortran and C integrators for both stiff and nonstiff systems. * [[escript]]  https://shake200.esscc.uq.edu.au/twiki/bin/view/ESSCC/EsysUser  escript is a python module to define and solve coupled, nonlinear, timedependend partial differential equations (PDEs). The user has to implement highlevel time intergration schemes and iteration schemes to reduce the problem to the solution of steady, linear systems of PDEs which are solved by a suitable PDE solver library. The current version uses the FEM solver library finley but the design is open and other libraries can be used. escript is parallelized for OpenMP (MPI is under construction). It is compatible with NumArray and uses VTK for visualization. * [[PyIMSL]]  http://www.vni.com/products/imsl/pyimsl/overview.php  PyIMSL is a collection of Python wrappers to the mathematical and statistical algorithms in the IMSL C Numerical Library. PyIMSL offers a quality Python interface to the largest collection of portable statistical and analytical algorithms available for Python. Developers can use Python, PyIMSL and the IMSL C Library for rapid prototyping. They can then directly deploy the Python application into production or if they choose to rewrite the application in C/C++ use the same math and stats algorithms in both development environments. [[PyIMSL Studio]]  http://www.vni.com/pyimslstudio is a packaged, supported and documented development environment designed for deploying mathematics and statistics prototype models into production applications. PyIMSL Studio includes the Python language distribution and contains both open source and proprietary components that create a fully supported and documented platform for analytic prototyping and production development. * [[PyGTS]]  http://pygts.sourceforge.net/  PyGTS is a python package used to construct, manipulate, and perform computations on triangulated surfaces. It is a handcrafted and pythonic binding for the GNU Triangulated Surface (GTS) Library (http://gts.sourceforge.net/). 
* [[SciPySciPy]]  http://www.scipy.org/ [[SciPySciPy]] is an open source library of scientific tools for Python. [[SciPySciPy]] supplements the popular [[NumPyNumPy]] module, gathering a variety of high level science and engineering modules together as a single package. [[SciPySciPy]] includes modules for linear algebra, optimization, integration, special functions, signal and image processing, statistics, genetic algorithms, ODE solvers, and others. * Numba  http://numba.pydata.org/ Numba is an open source, NumPyaware Python compiler specifically suited to scientific codes. * [[http://pypi.python.org/pypi/adad]] is an opensource Python package for transparently performing first and secondorder automatic differentiation calculations with any of the base numeric types (int, float, complex, etc.). Utility functions designed for working with [[SciPySciPy]] optimization routines. * APM Python  http://apmonitor.com/wiki/index.php/Main/PythonApp APMonitor is a nonlinear programming and optimization environment with an interface to Python. The software is available as a webservice through Python libraries for the solution of largescale mathematical programming problems. * SymPy  http://www.sympy.org/ SymPy is a symbolic manipulation package, written in pure Python. Its aim is to become a full featured CAS in Python, while keeping the code as simple as possible in order to be comprehensible and easily extensible. * ALGLIB  http://www.alglib.net/  numerical analysis library in C++ and C#, with Python and [[IronPythonIronPython]] interfaces. * Python Data Analysis Library  http://pandas.pydata.org/  pandas is a library providing highperformance, easytouse data structures and data analysis tools for the Python . * [[PyGSLPyGSL]]  http://pygsl.sourceforge.net/  This project provides a python interface for the GNU scientific library (gsl). * FuncDesigner  http://openopt.org/FuncDesigner FuncDesigner is Python module to rapidly build functions and get their derivatives via automatic differentiation. Also you can perform integration, interpolation, interval analysis, uncertainty analysis, solve eigenvalue problems, systems of linear/nonlinear/ODE equations and numerical optimization problems coded in FuncDesigner by OpenOpt. * OpenOpt  http://openopt.org  a framework for numerical optimization and systems of linear/nonlinear equations. Connects to dozens of solvers (some are C or Fortranwritten). Can optimize FuncDesigner models with automatic differentiation. Provides graphic output of convergence, [[http://openopt.org/MultiFactorAnalysismultifactor analysis tool]] for scientific experiments planning and some more numerical optimization "MUST HAVE" features. Also OpenOpt has [[http://openopt.org/StochasticProgrammingStochastic Programming and Optimization addon]] (commercial yet, free for smallscaled academic and research purposes) * SpaceFuncs  http://openopt.org/SpaceFuncs  a tool for 2D, 3D, Ndimensional geometric modeling with possibilities of parametrized calculations, numerical optimization and solving systems of geometrical equations with automatic differentiation. * !NLopt  http://abinitio.mit.edu/nlopt  another library for nonlinear optimization, including many local/global optimization algorithms written in C, with a Python interface (as well as interfaces for several other languages). * [[jHepWorkjHepWork]]  http://jwork.org/jhepwork  a multiplatform dataanalysis framework written in Java. The main programming language is Jython, a clone of Python written in Java. Contains Java libraries for numerical calculations and visualisation of scientific graphs. Contains an interactive Python prompt. * [[ScientificPythonScientificPython]]  http://dirac.cnrsorleans.fr/ScientificPython/  [[ScientificPythonScientificPython]] is a collection of Python modules that are useful for scientific computing. In this collection you will find modules that cover basic geometry (vectors, tensors, transformations, vector and tensor fields), quaternions, automatic derivatives, (linear) interpolation, polynomials, elementary statistics, nonlinear leastsquares fits, unit calculations, Fortrancompatible text formatting, 3D visualization via VRML, and two Tk widgets for simple line plots and 3D wireframe models. There are also interfaces to the netCDF library (portable structured binary files), to MPI (Message Passing Interface, messagebased parallel programming), and to BSPlib (Bulk Synchronous Parallel programming). * [[PyACTSPyACTS]] http://wiki.python.org/moin/PyACTS  PyACTS is a collection of Python Modules that are very useful to Parallel Computing in a High Performance Computing environment. This packages incorporates several modules like PyBLACS (allows communication data for Linear Algebra), PyPBLAS (distributed Matrix Operations) and PyScaLAPACK (solve linear systems and get the eigenvalue problems). These libraries are part of PyACTS project that provide interfaces to the ACTS Collection. Also is provided a parallel interpreter for using this package that implements messagebased parallel programming using MPI. * [[PyDSToolPyDSTool]]  http://pydstool.sourceforge.net  PyDSTool is an integrated simulation, modeling and analysis package for dynamical systems (including ODEs, DAEs, maps, and hybrid systems) and scientific data. Building on [[SciPySciPy]] classes, the package also supports symbolic expression processing, bifurcation analysis, and enhanced arrays for "indexfree" and highly contextualized scientific data manipulation. Model building tools use symbolic expression and hierarchical specification classes to ease the development and analysis of complex models. This includes automated compilation of symbolic representations of models into fast numerical code using enhanced legacy Fortran and C integrators for both stiff and nonstiff systems. * [[https://launchpad.net/escriptfinleyescript]]  https://launchpad.net/escriptfinley  escript is a Python module to define and solve coupled, nonlinear, timedependent partial differential equations (PDEs). The user has to implement highlevel time integration schemes and iteration schemes to reduce the problem to the solution of steady, linear systems of PDEs which are solved by a suitable PDE solver library. The current version uses the FEM solver library finley but the design is open and other libraries can be used. escript is parallelized for OpenMP and MPI. It is compatible with [[NumPyNumPy]] and VTK for visualization. * [[http://www.roguewave.com/products/imslnumericallibraries/pyimslstudio.aspxPyIMSL]]  http://www.roguewave.com/products/imslnumericallibraries/pyimslstudio.aspx  PyIMSL is a collection of Python wrappers to the mathematical and statistical algorithms in the IMSL C Numerical Library. PyIMSL offers a quality Python interface to the largest collection of portable statistical and analytical algorithms available for Python. Developers can use Python, PyIMSL and the IMSL C Library for rapid prototyping. They can then directly deploy the Python application into production or if they choose to rewrite the application in C/C++ use the same math and stats algorithms in both development environments. [[http://www.roguewave.com/products/imslnumericallibraries/pyimslstudio.aspxPyIMSL Studio]] is a packaged, supported and documented development environment designed for deploying mathematics and statistics prototype models into production applications. PyIMSL Studio includes the Python language distribution and contains both open source and proprietary components that create a fully supported and documented platform for analytic prototyping and production development. PyIMSL Studio is available for download at no charge for noncommercial use or for commercial evaluation. * [[PyGTSPyGTS]]  http://pygts.sourceforge.net/  PyGTS is a python package used to construct, manipulate, and perform computations on 3D triangulated surfaces. It is a handcrafted and pythonic binding for the GNU Triangulated Surface (GTS) Library (http://gts.sourceforge.net/). * [[scikitlearnscikitlearn]]  http://scikitlearn.sourceforge.net/  machine learning and data mining in Python, using [[NumPyNumPy]] and [[SciPySciPy]] * [[mlpymlpy]]  https://mlpy.fbk.eu/  Machine Learning PYthon  highperformance Python module for Predictive Modeling. * [[graphtoolgraphtool]]  http://graphtool.skewed.de  A python module for efficient analysis of graphs (aka. networks), with algorithms implemented in C++ with the Boost Graph Library. * [[sppysppy]]  http://packages.python.org/sppy/index.html  A sparse matrix package based on Eigen. * [[QuandlQuandl]]  https://www.quandl.com/tools/python  An API package to access http://quandl.com datasets, as well as upload data to Quandl. 
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* MultiprecisionSoftwareDirectory (http://crd.lbl.gov/~dhbailey/mpdist/index.html)  Python wrapping unknown * [[MAPM]] (http://www.tc.umn.edu/~ringx004/mapmmain.html)  Python wrapping unknown * GmPy (http://gmpy.sourceforge.net/)  GNU Multiple Precision library wrapping * [[mpmath]]  http://code.google.com/p/mpmath/  mpmath is a pure Python library for arbitraryprecision floatingpoint arithmetic, with support for complex numbers. Implements all the transcendental functions from Python's math and cmath modules and a few others. 
* [[MultiprecisionSoftwareDirectoryMultiprecisionSoftwareDirectory]] (http://crd.lbl.gov/~dhbailey/mpdist/index.html)  Python wrapping unknown * [[MAPMMAPM]] (http://www.tc.umn.edu/~ringx004/mapmmain.html)  Python wrapping unknown * [[GmPyGmPy]] (http://gmpy.sourceforge.net/)  GNU Multiple Precision library wrapping * [[mpmathmpmath]]  http://mpmath.org/  mpmath is a pure Python library for arbitraryprecision floatingpoint arithmetic, with support for complex numbers. Implements all the transcendental functions from Python's math and cmath modules and many others. * clnum  http://calcrpnpy.sourceforge.net/clnum.html  Class Library For Numbers wrapping 
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Vector Data Support: Shapefile, PostGIS Layer, Raster Data Support: GeoTIFF Layer, Comfortable Map Navigation, Object Identification and Annotation, Legend Editor and Classification, Table Queries and Joins, Projection Support, Printing and Vector Export, API for AddOns (Extensions), MultiLanguage Support: English, French, German, Hungarian, Italian, Russian and Spanish, User Manual (English) Multiplatform (GNU/Linux, Windows, ...). (Noli Sicad) 
. Vector Data Support: Shapefile, PostGIS Layer, Raster Data Support: GeoTIFF Layer, Comfortable Map Navigation, Object Identification and Annotation, Legend Editor and Classification, Table Queries and Joins, Projection Support, Printing and Vector Export, API for AddOns (Extensions), MultiLanguage Support: English, French, German, Hungarian, Italian, Russian and Spanish, User Manual (English) Multiplatform (GNU/Linux, Windows, ...). (Noli Sicad) 
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* [[http://pysal.orgPySAL Python Spatial Analysis LIbrary]]  an open source crossplatform library of spatial analysis functions written in Python. It is intended to support the development of high level applications for spatial analysis. * [[http://www.cardiff.ac.uk/sdnasDNA]] is freeware spatial network analysis software developed by Cardiff university, and has a [[http://www.cardiff.ac.uk/sdna/sdnaforpythonenthusiasts/Python API]]. 

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* VTK  [[http://vtk.org/]]  is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. It has a very good python interface.  * Bokeh  http://bokeh.pydata.org/  is a Python interactive visualization library for large datasets that natively uses the latest web technologies. * scikitimage  http://scikitimage.org/  is an image processing library written in Python/Cython for use with [[NumPyNumPy]] and [[SciPySciPy]] * VTK  http://vtk.org/  is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. It has a very good python interface. * WrapITK  http://code.google.com/p/wrapitk/  interface ITK http://itk.org and several languages, with a particular focus on python. ITK module used with python interpreter is particulary useful for quick and easy prototyping of image analysis procedures. Some glue classes allow to efficiently pass data to others modules like [[NumPyNumPy]] or VTK. * PIL  http://www.pythonware.com/products/pil  Python Imaging Library provides basic image handling and processing for various image types including jpg, gif, tiff, and bmp. Reads and writes graphics files. Allows pixelbypixel data access and has functions for cropping and transposing an image. Also has various filters builtin. * matplotlib  http://matplotlib.sourceforge.net/  matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell (ala matlab or mathematica), web application servers, and six graphical user interface toolkits. * GR Framework  http://grframework.org/  GR is a universal framework for crossplatform visualization applications. It offers developers a compact, portable and consistent graphics library for their programs. Applications range from publication quality 2D graphs to the representation of complex 3D scenes. GR can be used in imperative programming systems or integrated into modern objectoriented systems, in particular those based on GUI toolkits. The GR framework is especially suitable for realtime environments. * Plotly  https://plot.ly/ is a collaborative graphing and analytics platform. The web app has an online Python sandbox  [[NumPyNumPy]] supported  and grid for data analysis. The [[https://plot.ly/api/pythonPlotly graphing library]] produces graphs that are interactive, publication quality, and browserbased. Graphs can be styled with Python or a GUI, shared, embedded, and exported. * Mayavi  http://code.enthought.com/projects/mayavi/  application and library for interactive visualization in 3D of scientific data. High level and targeted toward the end user/application developer. * VisTrails  http://vistrails.org  VisTrails is an opensource scientific workflow and provenance management system developed at the University of Utah that provides support for data exploration and visualization. * Glumpy  http://glumpy.github.io/  a small python library that uses OpenGL for the rapid vizualization of (mainly two dimensional) numpy arrays. Not so much for nice figures for inclusion in a scientific article, more for rapid vizualization of your running simulation. * pyqtgraph  http://luke.campagnola.me/code/pyqtgraph/  Purepython graphics and GUI library for scientific/angineering applications based on [[PyQtPyQt]] and numpy. This library provides fast plotting and image/video display, multidimensional image slicing, volumetric / isosurface rendering, interactive data manipulation tools, and a variety of Qt widgets including an editable property tree, visual programming flowchart, and gradient editor. 
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* WrapITK  [[http://code.google.com/p/wrapitk/]]  interface ITK [[http://itk.org]] and several languages, with a particular focus on python. ITK module used with python interpreter is particulary useful for quick and easy prototyping of image analysis procedures. Some glue classes allow to efficiently pass data to others modules like NumPy or VTK.  
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* PIL  [[http://www.pythonware.com/products/pil]]  Python Imaging Library provides basic image handling and processing for various image types including jpg, gif, tiff, and bmp. Reads and writes graphics files. Allows pixelbypixel data access and has functions for cropping and transposing an image. Also has various filters builtin.  = Life sciences = 
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* Mayavi  [[https://svn.enthought.com/enthought/wiki/MayaVi]]  application and library for interactive visualization in 3D of scientific data. High level and targeted toward the end user/application developer.  * Biopython  http://biopython.org/wiki/Main_Page  a set of freely available tools for biological computation and bioinformatics. It includes [[http://bonsai.ims.utokyo.ac.jp/~mdehoon/software/cluster/software.htm#pyclusterpycluster]], a binding for the [[http://bonsai.ims.utokyo.ac.jp/~mdehoon/software/cluster/Cluster]] software. * PyCogent  http://pycogent.sourceforge.net/  COmparative GENomic Toolkit. Another popular and extensive library for genomic biology. * track  http://xapple.github.com/track/  Provides easy read/write access to genomic tracks in a fashion that is independent from the underlying format. Implemented formats include: BED; WIG; GFF; GTF; BedGraph; BigWig. * [[PyChemPyChem]]  http://pychem.sf.net/  a crossplatform open source package for multivariate analysis, that includes a graphical user interface. * bxpython  http://bitbucket.org/james_taylor/bxpython/  Library and associated set of scripts to allow for rapid implementation of genome scaleanalyses. Also a fundamental part of the ongoing [[http://g2.bx.psu.edu/Galaxy]] and [[http://www.bx.psu.edu/projects/esperrESPERR]] projects. * p4  http://bmnh.org/~pf/p4.html  Python package for phylogenetics, useful for programmatic manipulation of phylogenetic data and trees, including maximum likelihood and Bayesian inference. * UCSF Chimera  http://www.cgl.ucsf.edu/chimera/  UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. Highquality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, nonprofit, and personal use. * Modeller  http://salilab.org/modeller  used for homology or comparative modeling of protein threedimensional structures. Control scripts are Python based. * PyMol  http://www.pymol.org/  3D molecular viewer, suitable (and widely used) for publications and presentations. Fully scriptable in Python. = Space Sciences = * [[http://astropy.org/Astropy]] aims to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages. * [[http://sunpy.org/SunPy]] project is an effort to create an opensource software library for solar physics using Python. * [[http://spacepy.lanl.gov/Spacepy]] is a set of PythonBased Tools for the Space Science Community. 
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* PyLink is an open source Python module for interfacing with the EyeLink eye tracking hardware. Find it at [[http://www.eyelinkinfo.com/mount_software.phpPyLink]] * SimPy is an opensource discreteevent simulation package in Python. Read more at its [[http://simpy.sourceforge.net/index.htmlHomepage]] * Modeller is used for homology or comparative modeling of protein threedimensional structures. Control scripts are Python based. Read about it at [[http://salilab.org/modellerModeller]] * PyChem is a crossplatform open source package for multivariate analysis, that includes a graphical user interface. Find it at our [[http://pychem.sf.net/website]] * [[http://bonsai.ims.utokyo.ac.jp/~mdehoon/software/cluster/software.htm#pyclusterpycluster]]  binding for the [[http://bonsai.ims.utokyo.ac.jp/~mdehoon/software/cluster/Cluster]] software (apparently oriented towards bioinformatics) 
* [[PyLinkPyLink]] is an open source Python module for interfacing with the [[EyeLinkEyeLink]] eye tracking hardware. Find it at [[http://www.eyelinkinfo.com/mount_software.phpPyLink]] * [[SimPySimPy]] is an opensource discreteevent simulation package in Python. Read more at its [[http://simpy.sourceforge.net/index.htmlHomepage]] * [[http://packages.python.org/uncertainties/uncertainties]] is an opensource Python package for transparently performing calculations with uncertainties (3.14±0.01…). * [[http://pypi.python.org/pypi/soerpsoerp]] is a free and opensource Python package for quickly and transparently performing calculatorstyle secondorder error propagation (utilizes [[http://pypi.python.org/pypi/adad]] for derivatives). * [[http://pypi.python.org/pypi/mcerpmcerp]]: an opensource realtime, latinhypercubebased MonteCarlo alternative to uncertainty/error propagation, but isn't order specific like [[http://pypi.python.org/pypi/soerpsoerp]] and [[http://packages.python.org/uncertainties/uncertainties]]. 
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* [[NumericAndScientific/Plotting]]  * [[NumericAndScientific/Libraries]]  useful libraries * [[NumericAndScientific/Formats]]  modules for reading and writing various file formats * NumericBooks * [[http://seal.web.cern.ch/seal/snapshot/workpackages/scripting/index.htmlCERN SEAL Python Services ]]  Automatic Python/C/C++ binding 
* [[NumericAndScientific/PlottingNumericAndScientific/Plotting]]  * [[NumericAndScientific/LibrariesNumericAndScientific/Libraries]]  useful libraries * [[NumericAndScientific/FormatsNumericAndScientific/Formats]]  modules for reading and writing various file formats * [[NumericBooksNumericBooks]] * [[http://root.cern.ch/drupal/content/pyrootCERN ROOT Python Services]]  Automatic Python/C/C++ binding * [[http://continuum.io/downloadsAnaconda]]  Free distribution with many Scientific Libraries prepackaged. * [[http://numfocus.orgNumfocus]]  Nonprofit supporting NumPy stack and accessible computing for science.  CategoryPythonInScience 
Numeric and Scientific
NumPy  http://www.numpy.org/  Numerical Python adds a fast, compact, multidimensional array facility to Python. NumPy is the successor to both Numeric and Numarray.
Deprecated: Numeric  Numerical Python adds a fast, compact, multidimensional array language facility to Python. (Note: superseded by NumPy)
Deprecated: NumArray  http://stsdas.stsci.edu/numarray/index.html  Numarray is a reimplementation of Numeric which adds the ability to efficiently manipulate large numeric arrays in ways similar to Matlab and IDL. (Note: superseded by NumPy)
SciPy  http://www.scipy.org/ SciPy is an open source library of scientific tools for Python. SciPy supplements the popular NumPy module, gathering a variety of high level science and engineering modules together as a single package. SciPy includes modules for linear algebra, optimization, integration, special functions, signal and image processing, statistics, genetic algorithms, ODE solvers, and others.
Numba  http://numba.pydata.org/ Numba is an open source, NumPyaware Python compiler specifically suited to scientific codes.
ad is an opensource Python package for transparently performing first and secondorder automatic differentiation calculations with any of the base numeric types (int, float, complex, etc.). Utility functions designed for working with SciPy optimization routines.
APM Python  http://apmonitor.com/wiki/index.php/Main/PythonApp APMonitor is a nonlinear programming and optimization environment with an interface to Python. The software is available as a webservice through Python libraries for the solution of largescale mathematical programming problems.
SymPy  http://www.sympy.org/ SymPy is a symbolic manipulation package, written in pure Python. Its aim is to become a full featured CAS in Python, while keeping the code as simple as possible in order to be comprehensible and easily extensible.
ALGLIB  http://www.alglib.net/  numerical analysis library in C++ and C#, with Python and IronPython interfaces.
Python Data Analysis Library  http://pandas.pydata.org/  pandas is a library providing highperformance, easytouse data structures and data analysis tools for the Python .
PyGSL  http://pygsl.sourceforge.net/  This project provides a python interface for the GNU scientific library (gsl).
FuncDesigner  http://openopt.org/FuncDesigner FuncDesigner is Python module to rapidly build functions and get their derivatives via automatic differentiation. Also you can perform integration, interpolation, interval analysis, uncertainty analysis, solve eigenvalue problems, systems of linear/nonlinear/ODE equations and numerical optimization problems coded in FuncDesigner by OpenOpt.
OpenOpt  http://openopt.org  a framework for numerical optimization and systems of linear/nonlinear equations. Connects to dozens of solvers (some are C or Fortranwritten). Can optimize FuncDesigner models with automatic differentiation. Provides graphic output of convergence, multifactor analysis tool for scientific experiments planning and some more numerical optimization "MUST HAVE" features. Also OpenOpt has Stochastic Programming and Optimization addon (commercial yet, free for smallscaled academic and research purposes)
SpaceFuncs  http://openopt.org/SpaceFuncs  a tool for 2D, 3D, Ndimensional geometric modeling with possibilities of parametrized calculations, numerical optimization and solving systems of geometrical equations with automatic differentiation.
!NLopt  http://abinitio.mit.edu/nlopt  another library for nonlinear optimization, including many local/global optimization algorithms written in C, with a Python interface (as well as interfaces for several other languages).
jHepWork  http://jwork.org/jhepwork  a multiplatform dataanalysis framework written in Java. The main programming language is Jython, a clone of Python written in Java. Contains Java libraries for numerical calculations and visualisation of scientific graphs. Contains an interactive Python prompt.
ScientificPython  http://dirac.cnrsorleans.fr/ScientificPython/  ScientificPython is a collection of Python modules that are useful for scientific computing. In this collection you will find modules that cover basic geometry (vectors, tensors, transformations, vector and tensor fields), quaternions, automatic derivatives, (linear) interpolation, polynomials, elementary statistics, nonlinear leastsquares fits, unit calculations, Fortrancompatible text formatting, 3D visualization via VRML, and two Tk widgets for simple line plots and 3D wireframe models. There are also interfaces to the netCDF library (portable structured binary files), to MPI (Message Passing Interface, messagebased parallel programming), and to BSPlib (Bulk Synchronous Parallel programming).
PyACTS http://wiki.python.org/moin/PyACTS  PyACTS is a collection of Python Modules that are very useful to Parallel Computing in a High Performance Computing environment. This packages incorporates several modules like PyBLACS (allows communication data for Linear Algebra), PyPBLAS (distributed Matrix Operations) and PyScaLAPACK (solve linear systems and get the eigenvalue problems). These libraries are part of PyACTS project that provide interfaces to the ACTS Collection. Also is provided a parallel interpreter for using this package that implements messagebased parallel programming using MPI.
PyDSTool  http://pydstool.sourceforge.net  PyDSTool is an integrated simulation, modeling and analysis package for dynamical systems (including ODEs, DAEs, maps, and hybrid systems) and scientific data. Building on SciPy classes, the package also supports symbolic expression processing, bifurcation analysis, and enhanced arrays for "indexfree" and highly contextualized scientific data manipulation. Model building tools use symbolic expression and hierarchical specification classes to ease the development and analysis of complex models. This includes automated compilation of symbolic representations of models into fast numerical code using enhanced legacy Fortran and C integrators for both stiff and nonstiff systems.
escript  https://launchpad.net/escriptfinley  escript is a Python module to define and solve coupled, nonlinear, timedependent partial differential equations (PDEs). The user has to implement highlevel time integration schemes and iteration schemes to reduce the problem to the solution of steady, linear systems of PDEs which are solved by a suitable PDE solver library. The current version uses the FEM solver library finley but the design is open and other libraries can be used. escript is parallelized for OpenMP and MPI. It is compatible with NumPy and VTK for visualization.
PyIMSL  http://www.roguewave.com/products/imslnumericallibraries/pyimslstudio.aspx  PyIMSL is a collection of Python wrappers to the mathematical and statistical algorithms in the IMSL C Numerical Library. PyIMSL offers a quality Python interface to the largest collection of portable statistical and analytical algorithms available for Python. Developers can use Python, PyIMSL and the IMSL C Library for rapid prototyping. They can then directly deploy the Python application into production or if they choose to rewrite the application in C/C++ use the same math and stats algorithms in both development environments. PyIMSL Studio is a packaged, supported and documented development environment designed for deploying mathematics and statistics prototype models into production applications. PyIMSL Studio includes the Python language distribution and contains both open source and proprietary components that create a fully supported and documented platform for analytic prototyping and production development. PyIMSL Studio is available for download at no charge for noncommercial use or for commercial evaluation.
PyGTS  http://pygts.sourceforge.net/  PyGTS is a python package used to construct, manipulate, and perform computations on 3D triangulated surfaces. It is a handcrafted and pythonic binding for the GNU Triangulated Surface (GTS) Library (http://gts.sourceforge.net/).
scikitlearn  http://scikitlearn.sourceforge.net/  machine learning and data mining in Python, using NumPy and SciPy
mlpy  https://mlpy.fbk.eu/  Machine Learning PYthon  highperformance Python module for Predictive Modeling.
graphtool  http://graphtool.skewed.de  A python module for efficient analysis of graphs (aka. networks), with algorithms implemented in C++ with the Boost Graph Library.
sppy  http://packages.python.org/sppy/index.html  A sparse matrix package based on Eigen.
Quandl  https://www.quandl.com/tools/python  An API package to access http://quandl.com datasets, as well as upload data to Quandl.
Multi precision math
MultiprecisionSoftwareDirectory (http://crd.lbl.gov/~dhbailey/mpdist/index.html)  Python wrapping unknown
MAPM (http://www.tc.umn.edu/~ringx004/mapmmain.html)  Python wrapping unknown
GmPy (http://gmpy.sourceforge.net/)  GNU Multiple Precision library wrapping
mpmath  http://mpmath.org/  mpmath is a pure Python library for arbitraryprecision floatingpoint arithmetic, with support for complex numbers. Implements all the transcendental functions from Python's math and cmath modules and many others.
clnum  http://calcrpnpy.sourceforge.net/clnum.html  Class Library For Numbers wrapping
The Grid
Grid is a type of parallel and distributed system that enables the sharing, selection, and aggregation of resources distributed across "multiple" administrative domains based on their (resources) availability, capability, performance, cost, and users' qualityofservice requirements.
PyGlobus  Globus toolkit bindings for python
PEG  Python Extensions for the Grid
Ganga  Grid job management interface.
DIANE  Python userlevel middleware layer for Grids.
Geographic Information System (GIS), Mapping, Image Processing and Analysis
Thuban is a Python Interactive Geographic Data Viewer with the following features:
 Vector Data Support: Shapefile, PostGIS Layer, Raster Data Support: GeoTIFF Layer, Comfortable Map Navigation, Object Identification and Annotation, Legend Editor and Classification, Table Queries and Joins, Projection Support, Printing and Vector Export, API for AddOns (Extensions), MultiLanguage Support: English, French, German, Hungarian, Italian, Russian and Spanish, User Manual (English) Multiplatform (GNU/Linux, Windows, ...). (Noli Sicad)
Python Cartographic Library, OWSLib, GeoJSON, and Rtree  packages for GIS programming and a cartographic application framework.
PySAL Python Spatial Analysis LIbrary  an open source crossplatform library of spatial analysis functions written in Python. It is intended to support the development of high level applications for spatial analysis.
sDNA is freeware spatial network analysis software developed by Cardiff university, and has a Python API.
Image analysis and visualization
Bokeh  http://bokeh.pydata.org/  is a Python interactive visualization library for large datasets that natively uses the latest web technologies.
scikitimage  http://scikitimage.org/  is an image processing library written in Python/Cython for use with NumPy and SciPy
VTK  http://vtk.org/  is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. It has a very good python interface.
WrapITK  http://code.google.com/p/wrapitk/  interface ITK http://itk.org and several languages, with a particular focus on python. ITK module used with python interpreter is particulary useful for quick and easy prototyping of image analysis procedures. Some glue classes allow to efficiently pass data to others modules like NumPy or VTK.
PIL  http://www.pythonware.com/products/pil  Python Imaging Library provides basic image handling and processing for various image types including jpg, gif, tiff, and bmp. Reads and writes graphics files. Allows pixelbypixel data access and has functions for cropping and transposing an image. Also has various filters builtin.
matplotlib  http://matplotlib.sourceforge.net/  matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell (ala matlab or mathematica), web application servers, and six graphical user interface toolkits.
GR Framework  http://grframework.org/  GR is a universal framework for crossplatform visualization applications. It offers developers a compact, portable and consistent graphics library for their programs. Applications range from publication quality 2D graphs to the representation of complex 3D scenes. GR can be used in imperative programming systems or integrated into modern objectoriented systems, in particular those based on GUI toolkits. The GR framework is especially suitable for realtime environments.
Plotly  https://plot.ly/ is a collaborative graphing and analytics platform. The web app has an online Python sandbox  NumPy supported  and grid for data analysis. The Plotly graphing library produces graphs that are interactive, publication quality, and browserbased. Graphs can be styled with Python or a GUI, shared, embedded, and exported.
Mayavi  http://code.enthought.com/projects/mayavi/  application and library for interactive visualization in 3D of scientific data. High level and targeted toward the end user/application developer.
VisTrails  http://vistrails.org  VisTrails is an opensource scientific workflow and provenance management system developed at the University of Utah that provides support for data exploration and visualization.
Glumpy  http://glumpy.github.io/  a small python library that uses OpenGL for the rapid vizualization of (mainly two dimensional) numpy arrays. Not so much for nice figures for inclusion in a scientific article, more for rapid vizualization of your running simulation.
pyqtgraph  http://luke.campagnola.me/code/pyqtgraph/  Purepython graphics and GUI library for scientific/angineering applications based on PyQt and numpy. This library provides fast plotting and image/video display, multidimensional image slicing, volumetric / isosurface rendering, interactive data manipulation tools, and a variety of Qt widgets including an editable property tree, visual programming flowchart, and gradient editor.
Life sciences
Biopython  http://biopython.org/wiki/Main_Page  a set of freely available tools for biological computation and bioinformatics. It includes pycluster, a binding for the Cluster software.
PyCogent  http://pycogent.sourceforge.net/  COmparative GENomic Toolkit. Another popular and extensive library for genomic biology.
track  http://xapple.github.com/track/  Provides easy read/write access to genomic tracks in a fashion that is independent from the underlying format. Implemented formats include: BED; WIG; GFF; GTF; BedGraph; BigWig.
PyChem  http://pychem.sf.net/  a crossplatform open source package for multivariate analysis, that includes a graphical user interface.
bxpython  http://bitbucket.org/james_taylor/bxpython/  Library and associated set of scripts to allow for rapid implementation of genome scaleanalyses. Also a fundamental part of the ongoing Galaxy and ESPERR projects.
p4  http://bmnh.org/~pf/p4.html  Python package for phylogenetics, useful for programmatic manipulation of phylogenetic data and trees, including maximum likelihood and Bayesian inference.
UCSF Chimera  http://www.cgl.ucsf.edu/chimera/  UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. Highquality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, nonprofit, and personal use.
Modeller  http://salilab.org/modeller  used for homology or comparative modeling of protein threedimensional structures. Control scripts are Python based.
PyMol  http://www.pymol.org/  3D molecular viewer, suitable (and widely used) for publications and presentations. Fully scriptable in Python.
Space Sciences
Astropy aims to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages.
SunPy project is an effort to create an opensource software library for solar physics using Python.
Spacepy is a set of PythonBased Tools for the Space Science Community.
Miscellaneous
PyLink is an open source Python module for interfacing with the EyeLink eye tracking hardware. Find it at PyLink
SimPy is an opensource discreteevent simulation package in Python. Read more at its Homepage
uncertainties is an opensource Python package for transparently performing calculations with uncertainties (3.14±0.01…).
soerp is a free and opensource Python package for quickly and transparently performing calculatorstyle secondorder error propagation (utilizes ad for derivatives).
mcerp: an opensource realtime, latinhypercubebased MonteCarlo alternative to uncertainty/error propagation, but isn't order specific like soerp and uncertainties.
Links
NumericAndScientific/Libraries  useful libraries
NumericAndScientific/Formats  modules for reading and writing various file formats
CERN ROOT Python Services  Automatic Python/C/C++ binding
Anaconda  Free distribution with many Scientific Libraries prepackaged.
Numfocus  Nonprofit supporting NumPy stack and accessible computing for science.