DREAMTools
| Python version: | DREAMTools is supported for Python 2.7, 3.4 and 3.5. Pre-compiled versions are available for Linux and MAC platforms through Anaconda and the bioconda channel. |
|---|---|
| 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 |
| Online documentation: | On readthedocs |
| Issues and bug reports: | On github |
| 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
Motivation
DREAMTools aims at sharing code used in the scoring of DREAM challenges that pose fundamental questions about system biology and translational medicine.
The main goals of DREAMTools are to provide:
- Scoring functions equivalent to those used during past DREAM challenges for end-users via a standalone application (called dreamtools).
- A common 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 may be provided (e.g., in D8C1 challenge).
Note that many scoring functions requires data hosted on Synapse . We therefore strongly encourage you to register to Synapse. Depending on the challenge, you may be requested to accept terms of agreements to use the data.
Installation
For those familiar with Python, you may use the pip executable provided with Python. It will install the latest release of DREAMTools and the dependencies:
pip install cython pip install dreamtools
If you are not familiar with compilation and/or Python, you may use conda since we have pre-compiled packages with a conda channel called bioconda:
conda config --add channels r conda config --add channels bioconda conda install dreamtools
See Installation section on RTD for details.
Usage
DREAMTools can be used by developers as a Python package:
>>> from dreamtools import D6C3
>>> s = D6C3()
>>> s.score(s.download_template())
{'results': chi2 53.980741
R-square 34.733565
Spearman(Sp) 0.646917
Pearson(Cp) 0.647516
dtype: float64}
A standalone application can be used from a terminal. The executable is called dreamtools. Here is an example:
dreamtools --challenge D6C3 --submission path_to_a_file
See online documentation on for more details and examples. The source code also provides a set of IPython/Jupyter notebooks.
Available challenges, templates and gold standards
DREAMTools includes about 80% of DREAM challenges from DREAM2 to DREAM9.5 Please visit F1000 link (Table 1).
All gold standards and templates are retrieved automatically. Once downloaded, you can obtain the location of a gold standard or template as follows:
dreamtools --challenge D6C3 --download-gold-standard dreamtools --challenge D6C3 --download-template
See online documentation on RTD for details.