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,

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).

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 git@github.com:dreamtools/dreamtools.git
cd dreamtools
sudo python setup.py install

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

DREAMTools includes about 80% of DREAM challenges from DREAM2 to DREAM9.5

All template location can be retrieved using dreamtools executable:

dreamtools --challenge d5c2 --download-template

All gold standard are retrieved automatically. You can obtain a GS location as follows:

dreamtools --challenge d5c2 --download-goldstandard

Please fill bug report in https://github.com/dreamtools/dreamtools/issues

Please join https://github.com/dreamtools/dreamtools

Please see doc/source/developers.rst

Please see doc/source/credits.rst

Please see the doc directory, which is processed and posted on pypi website with each release.