dreamtools 1.2.6

Scoring functions for the DREAM / SAGE challenges

Python version:

DREAMTools is supported for Python 2.7, 3.4 and 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 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

Contents

• Overview

  • Motivation

  • Usage

• Installation

  • Familiar with Python ecosystem ?

  • If you are new to Python

• Available challenges, templates and gold standards

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:

1. scoring functions equivalent to those used during past DREAM challenges for end-users via a standalone application (called dreamtools).

2. 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.

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.

Installation

There is a dedicated Installation page on RTD but here is a quick installation guide.

Familiar with Python ecosystem ?

If you are familiar with Python and the pip application and your system is already configured (compilers, development libraries available)), these two commands should install DREAMTools and its dependencies (in unix or windows terminal):

pip install cython
pip install dreamtools

If you do not have dependencies installed yet (e.g pandas, numpy, scipy), this make take a while (e.g., 10-15 minutes). If you are in a hurry, see the Anaconda solution here below.

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 and has dedicated channels. One such channel is called bioconda and complements the default channel (conda) with a set of packages dedicated to life science.

We have included DREAMTools in bioconda. So, once Anaconda is installed, you first need to add bioconda channel to your environment (and R):

conda config --add channels r
conda config --add channels bioconda

This should be done only once. Then, install DREAMTools itself:

conda install dreamtools

This command should install DREAMTools in your default conda environment. If you wish to try DREAMTools in another environment (e.g different python version), you would need to create a new one and then install DREAMTools in that environment:

conda create --name test_dreamtools --python 3.5
source activate test_dreamtools
conda install dreamtools

If there is an issue or wish to install from source, please visit the online documentation on RTD for details.

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 will get the location of the file. For instance:

dreamtools --challenge D6C3 --download-goldstandard
dreamtools --challenge D6C3 --download-template

See online documentation for details.