Scoring functions for the dream / sage challenges
Project description
- Note:
DREAMTools is compatible for Python 2.7, 3.3, 3.4, 3.5
- Contributions:
Please join https://github.com/dreamtools/dreamtools and share your notebooks https://github.com/dreamtools/dreamtools/notebooks
- Online documentation:
- Issues and bug reports:
- 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
Overview
DREAMTools aims at sharing code used in the scoring of DREAM 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 , in which case you will need to register and accept the terms of agreements.
Installation
Python2
DREAMTools depends on a few libraries such as Pandas, Numpy, Matplotlib. They should be automatically installed with DREAMTools using pip executable (note the small caps). However, one package must be installed before (if not already installed), which is called Cython. To install cython, type:
pip install cython
Then, install DREAMTools itself:
pip install dreamtools
From source, download the source code and install the package with Python:
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 version compatible for Python3 and DREAMTools. 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:
# if you do not have cython already installed: pip install cython
and:
pip install dreamtools
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 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 website and follow the instructions. You may need to choose between 2 versions of Python (2.X or 3.5). DREAMTools is tested under Python 2.7 and 3.5 so the version should not matter.
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), it works as follows:
dreamtools --challenge d8c1 --sub-challenge sc1a \
--submission example.zip
It prints 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 with each release.
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