Scoring functions for the dream / sage challenges
Project description
- 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:
- Issues and bug reports:
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
Code related to aggregation, leaderboards, or more complex analysis are not guaranteed to be found in dreamtools even though it may be in some challenges (e.g. D8C1). Some functionalities may be restricted with some access to synapse. 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 git@github.com:dreamtools/dreamtools.git cd dreamtools sudo python setup.py install
The dreamtools-scoring executable
For users, dreamtools provide one executable called dreamtools-scoring, which should be installed automatically when installing dreamtools. Knowing the name of the challenge (and possibly sub-challenge), it works as follows:
dreamtools-scoring --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 software does not include all scoring functions but more will be implemented in the future. Here is the list of challenges available
DREAM9.5
D9dot5C1 olfaction challenge
DREAM8
D8C1 (HPN breat cancer) sub challenges named sc1a, sc1b, sc2a, sc2b. See Synapse page D8C1 for details
D8C2 (Toxoxicology) sub challenges named sc1, sc2. See Synapse page D8C2 for details
D8C3 coming soon
DREAM7
D7C1 (Network Parameter Estimation)
DREAM6
D6C1 (Network Parameter Estimation) WONT be included (see D7C1 instead)
DREAM5
D5C2 (transcription factor)
DREAM4
D4C1 (Peptide Recognition Domain (PRD) Specificity Prediction)
DREAM4 In Silico Network Challenge
D4C3 (Predictive Signaling Network Modeling)
DREAM3
D3C1 (Signaling Cascade Challenge)
D3C2 (Signaling Response Prediction)
Format of the template for each challenge should be found in the README of each subchallenge. For instance, for Dream8 Challenge1, please see ./dreamtools/dream8/D8C1/README.rst
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
Project details
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