Metadata-Version: 1.1
Name: dreamtools
Version: 1.2.2
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** (or just **dreamtools**) 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
        
        An finally, install **DREAMTools** itself::
        
            pip install dreamtools
        
        Installation from source
        ~~~~~~~~~~~~~~~~~~~~~~~~~
        
        The previous method (using **pip**) install the latest release of
        **DREAMTools**. If you prefer to use the source code, you can also get the latest version as follows::
        
           git clone git@github.com:dreamtools/dreamtools.git
           cd dreamtools
           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
        ------------------------------------------
        
        :Note: Challenges available within DREAMTools provide a mechanism to obtain a template and the gold standard used in the scoring. However, some data have restrictions and require the user to accept conditions of use.  
        :Note about Synapse: In the current version of DREAMTools, you will need to create a login/password on www.synapse.org , which will be used to download some data files. 
        :Restrictions: The first time you run a challenge within DREAMTools, files will be downloaded from Synapse. You may be asked to accept some conditions of use (e.g. D8C1challenge). 
        
        For users, **DREAMTools** package provides an executable called **dreamtools**, which should be installed automatically. 
        
        To obtain some help, type::
        
            dreamtools --help
        
        You should see a list of challenges: D2C1,D2C3, D2C3,... Those are aliases to 
        DREAM challenges. Information about a challenge can be (in general) obtained from the Synapse page of the challenge using the --onweb option::
        
            dreamtools --challenge D6C3 --onweb
        
        Brief information can also be printed in the terminal as follows::
        
            dreamtools --challenge D6C3 --info
        
        Next, you may want to score one of your submission. We provide access to
        templates for each challenge. For instance::
        
            dreamtools --challenge D6C3 --download-template
        
        Now that you have a template, you can fill its contents with your own data and
        score it (let us assume it is called example.zip)::
        
            dreamtools --challenge D6C3 --submission D6C3_template.txt
        
        This command should print some information and the score of the submission for instance for the example above, we get the following results::
        
            {'results': chi2            53.980741
             R-square        34.733565
             Spearman(Sp)     0.646917
             Pearson(Cp)      0.647516
             dtype: float64}
        
        All outputs will contain a json-like output. The synapse page of the challenge
        should give information about the scoring methodology.
        
        Note that some challenges (like the D8C1 challenge) have sub-challenges. For instance in D8C1, there are 4 sub-challenges names (e.g., SC1A). So, you would need to be more specific and to provide the name of a sub-challenge. For instance:: 
        
            dreamtools --challenge D8C1 --download-template --sub-challenge SC1A
        
        .. seealso:: In D8C1, you will also need to accept the conditions of use 
            of the data on a Synapse page, which should pop up.
        
        The sub-challenge names can be obtained using --info option (see here above). Similarly to the simpler case shown above, you can now score that submission as follows::  
        
            dreamtools --challenge D8C1 --sub-challenge SC1A \
                --submission D8C1_example.zip
        
        Again, you should get an output with the results::
        
             Solution for alphabeta-Network.zip in challenge d8c1 (sub-challenge sc1a) is :
             meanAUROC: 0.803628919403
        
        
        Available challenges
        -------------------------
        
        **DREAMTools** includes about 80% of DREAM challenges from DREAM2 to DREAM9.5
        
        
        Gold standards
        -----------------
        
        All gold standards are retrieved automatically. You can obtain the location of a gold standard file as
        follows::
        
            dreamtools --challenge D6C3 --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
