dreamtools 0.10.1

Scoring functions for the dream / sage challenges

note:

DREAMTools is tested for Python 2.7

Contributions:

Please join https://github.com/dreamtools/dreamtools and share your notebooks https://github.com/dreamtools/dreamtools/notebooks

Online documentation:

On pypi website,

Issues and bug reports:

On github,

Contents

• Overview

• Installation

• The dreamtools-scoring executable

• Available challenges

• Templates

• Gold standard

• Issues

• Contributions

• For developers

• Credits

Overview

DREAMTools aims at sharing code used in the scoring of DREAM challenges.

The main goals are to provide:

1. scoring functions for the Dream challenges for end-users via the dreamtools-scoring standalone application.

2. 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).

Installation

DREAMTools depends on a few libraries such as Pandas, Numpy, Matplotlib. They should be automatically installed with dreamtools using pip executable:

pip install dreamtools

From source, download the source code and install the package with Python:

git clone [e-mail]:dreamtools/dreamtools.git
cd dreamtools
sudo python setup.py install

The dreamtools-scoring executable

For users, DREAMTools 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 submision 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