Metadata-Version: 1.1
Name: dreamtools
Version: 1.2.0
Summary: Scoring functions for the dream / sage challenges
Home-page: ['https://github.com/dreamtools/dreamtools']
Author: Thomas Cokelaer
Author-email: cokelaer@gmail.com
License: BSD
Download-URL: ['http://pypi.python.org/pypi/dreamtools']
Description: DREAMTools
        ==========
        
        
        .. image:: https://badge.fury.io/py/dreamtools.svg
            :target: https://pypi.python.org/pypi/dreamtools
        
        .. image:: https://secure.travis-ci.org/dreamtools/dreamtools.png
            :target: http://travis-ci.org/dreamtools/dreamtools
        
        .. image:: https://coveralls.io/repos/dreamtools/dreamtools/badge.png?branch=master
           :target: https://coveralls.io/r/dreamtools/dreamtools?branch=master
        
        .. image:: https://badge.waffle.io/dreamtools/dreamtools.png?label=ready&title=ready
           :target: https://waffle.io/dreamtools/dreamtools
           
        .. image:: https://zenodo.org/badge/18543/dreamtools/dreamtools.svg
           :target: https://zenodo.org/badge/latestdoi/18543/dreamtools/dreamtools
        
        :Note: DREAMTools is compatible for Python 2.7, 3.3, 3.4, 3.5
        :Note about coverage: We do not run the entire test suite on Travis, which
                              reports a 40% test coverage. Note however, that the actual
                              test coverage is about 80%.
        :Contributions: Please join https://github.com/dreamtools/dreamtools and share your notebooks https://github.com/dreamtools/dreamtools/notebooks
        
        :Online documentation: `On pypi website <http://pythonhosted.org/dreamtools/>`_
        :Issues and bug reports: `On github <https://github.com/dreamtools/dreamtools/issues>`_
        :How to cite: Cokelaer T, Bansal M, Bare C et al. DREAMTools: a Python 
            package for scoring collaborative challenges [version 1; referees: 
            awaiting peer review] F1000Research 2015, 4:1030 
            (doi: 10.12688/f1000research.7118.1)
            `F1000 link <http://f1000research.com/articles/4-1030/v1>`_
        
        .. image:: doc/dreamtools_logo.png
            :width: 50%
        
        .. contents::
        
        Overview
        ----------------
        
        **DREAMTools** aims at sharing code used in the scoring of `DREAM <http://dreamchallenges.org>`_ challenges.
        
        The main goals are to provide:
        
        #. scoring functions for the DREAM challenges for **end-users** via the **dreamtools-scoring** standalone
           application.
        #. a place for **developers** involved in the DREAM challenges to share code
        
        **DREAMTools** does not provide code related to aggregation,
        leaderboards, or more complex analysis even though such code
        can be provided (e.g. D8C1 challenge). Note that some functionalities
        may be restricted with some access to synapse platform. Indeed,
        some challenges will require to download public data sets from `Synapse
        <www.synapse.org>`_ , **in which case you will need to register and accept the
        terms of agreements**.
        
        Installation
        ---------------
        
        If you are new to Python
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        If you are not familiar with Python, or have issues with the previous method
        (e.g., compilation failure), or do not have root access, we would recommend to
        use the `Anaconda <https://www.continuum.io/downloads>`_ solution.
        
        Anaconda is a free Python distribution. It includes most popular Python packages
        for science and data analysis. Anaconda will install the software required by
        **DREAMTools**. Since it does not require root access, it should not interfere with your system. 
        
        Please, visit the `Anaconda <https://www.continuum.io/downloads>`_ website 
        and follow the instructions. You may need to
        choose between 2 versions of Python (2.X or 3.5). Since **DREAMTools** is 
        compatible with Python 2.7 and 3.5, the version should not matter.
        
        Whether you use Anaconda or not, Python should provide an utility called **pip**
        that should now be available within a Terminal. 
        
        Before installing **DREAMTools**, please install **cython** as follows::
        
            pip install cython
        
        You may also use::
        
            conda install cython
        
        Python2
        ~~~~~~~~~~~~~~~
        
        **DREAMTools** depends on a few libraries such as Pandas, Numpy, Matplotlib. They should be automatically installed with **DREAMTools** using **pip**::
        
            pip install dreamtools
        
        This will install the last release. However, you can also get the latest code: download the source code and install the package as follows::
        
           git clone git@github.com:dreamtools/dreamtools.git
           cd dreamtools
           sudo python setup.py install
        
        Note for Python3.X
        ~~~~~~~~~~~~~~~~~~~~~~
        **DREAMTools** is compatible with Python2 and Python3. However, 
        **DREAMTools** depends on a package that is currently not available for Python3
        (synapseclient). As a temporary solution, we forked this package and provide
        a compatible version.  You will need to install it manually as follows::
        
            pip install git+https://git@github.com/cokelaer/synapsePythonClient.git@v1.4.0_py3_dreamtools#egg=synapsePythonClient
        
        Then, as above, type::    
        
            pip install dreamtools
        
        
        
        
        The **dreamtools** executable
        ------------------------------------------
        
        For users, **DREAMTools** package provides an executable called **dreamtools**, which should be installed automatically. Knowing the name of the challenge (and possibly sub-challenge), you first need to create a submission file. 
        
        Information about a challenge can be (in general) obtained from Synapse pages as
        follows::
        
            dreamtools --challenge D8C1 --onweb
        
        and templates can be (in general) obtained as follows::
        
            dreamtools --challenge D8C1 --download-template
        
        Note however that some challenges (like the D8C1 challenge) have sub-challenges. For instance in D8C1, there are 4 sub-challenges named (e.g., SC1A). So, you would need to be more specific and to provide the name of a sub-challenge:: 
        
            dreamtools --challenge D8C1 --download-template --sub-challenge SC1A
        
        This should give the path to a template (let us assume it is called
        example.zip). To score that submission example, type::
        
            dreamtools --challenge d8c1 --sub-challenge SC1A \
                --submission example.zip
        
        This command should print some information and the score of the submission for instance for the example above::
        
             Solution for alphabeta-Network.zip in challenge d8c1 (sub-challenge sc1a) is :
             AUROC: 0.803628919403
             Rank LB: 1
        
        
        Available challenges
        -------------------------
        
        **DREAMTools** includes about 80% of DREAM challenges from DREAM2 to DREAM9.5
        
        
        Templates
        -------------
        
        All template location can be retrieved using **dreamtools** executable::
        
            dreamtools --challenge d5c2 --download-template
        
        
        Gold standard
        --------------
        
        All gold standard are retrieved automatically. You can obtain a GS location as
        follows::
        
            dreamtools --challenge d5c2 --download-goldstandard
        
        Issues
        -----------
        
        Please fill bug report in https://github.com/dreamtools/dreamtools/issues
        
        
        Contributions
        ---------------
        
        Please join https://github.com/dreamtools/dreamtools
        
        
        For developers
        ----------------
        
        Please see doc/source/developers.rst
        
        Credits
        -----------
        
        Please see doc/source/credits.rst
        
        
        More documentation ?
        ------------------------
        
        Please see the doc directory, which is processed and posted on 
        `pypi website <http://pythonhosted.org/dreamtools/>`_ with each release.
        
        
Keywords: DREAM challenges,DREAM,System Biology,Leaderboard,ROC,scoring,synapse,statistics
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
