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Acknowledgements

Third Party Software Libraries used in CLUE

The CLUE platform was developed by researchers at the Broad Institute. We gratefully acknowledge a number of code libraries that are used in CLUE.

Python Package Libraries

NameDescriptionVersionLicense Type
BeautifulSoupPython library for pulling data out of HTML and XML files.3.2.1MIT
behavebehave is behaviour-driven development, Python style.1.2.3BSD
BioPythonTools for biological computation1.59Biopython License
blessingsA thin, practical wrapper around terminal coloring, styling, and positioning1.5MIT
botoPython interface to Amazon Web Services2.22.1MIT
chemspipyA simple (and probably ropey) Python wrapper for the ChemSpider API1CC0 1.0 Universal
fuzzywuzzyFuzzy String Matching in Python0.2MIT
htmlSimple, elegant HTML, XHTML and XML generation.1.13BSD
jinja2Jinja2 is a full featured template engine for Python2.7.2BSD
matplotlibPython 2D plotting library1.3.1PSF
mechanizeStateful programmatic web browsing in Python0.2.5BSD or ZPL 2.1
networkxFor the creation, manipulation, and study of the structure, dynamics, and functions of complex networks1.8.1BSD
numpyNumPy is the fundamental package for scientific computing with Python.1.7.0BSD
pandasLlibrary providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language0.13.1BSD
paramikoNative Python SSHv2 protocol library1.12.1GNU
patternPattern is a web mining module for the Python programming language.2.6BSD
pymongoPython distribution containing tools for working with MongoDB2.4.2Apache
pytablesPackage for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data.2.4.0BSD
reportlabAllows rapid creation of rich PDF documents and vector formats2.7BSD
rpy2Provides a low-level interface to R, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions2.3.8Mozilla Public License Version 1.1
scikit-learnMachine Learning in Python0.14.1BSD
scipyPython-based ecosystem of open-source software for mathematics, science, and engineering.0.12.0BSD
SOAPpySOAPpy provides tools for building SOAP clients and servers0.12.5BSD
statsmodelsStatsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests.0.5.0Modified BSD
svglibAn experimental library for reading and converting SVG.0.6.3LGPL 3
svgwritePython library to create SVG drawings.1.1.5MIT
wxPythonBlending of the wxWidgets C++ class library with the Python programming language.2.8.10.1wxWindows

Other Libraries

NameDescriptionVersionLicense Type
Apache POI
FaceJava
Java1.7
libHDF5
m2html
Matlab
matlab_xunit
MongoAPI
MongoDB
mtocpp
pdfTex
PythonGeneral-purpose interpreted language.2.7.1Python Software Foundation License
RFreely available language and environment for statistical computing2.15.2GNU
TomcatServlet container and Web server
Apache VelocityTemplating engine
ApacheFreely available language and environment for statistical computing. Used in clue web server.2.15.2GNU
nginxNGINX is a high performance, open source web application accelerator. Used in clue web server and reverse-proxy.