dreamtools 1.2.4

Scoring functions for the DREAM / SAGE challenges

Similarly for For Windows:

1. Download Anaconda2 (Python2) for windows

2. Open an Anaconda prompt (from the Start->All program->Anaconda2->Anaconda Prompt

3. Download conda_install.bat

4. Execute the script:

   sh conda_install.sh python=2

The dreamtools executable

DREAMTools provides functions to obtain the template and gold standard(s) used in a given challenge. Some challenge have restrictions of data access and require the user to accept conditions of use. Such data are stored on http://www.synapse.org. You will need to create a login/password on www.synapse.org website. The first time you run a challenge within DREAMTools, files will be downloaded from Synapse. You may be asked to accept some conditions of use (e.g. D8C1 challenge) directly on the website.

For users, DREAMTools package provides an executable called dreamtools, which should be installed automatically.

To obtain some help, type:

dreamtools --help

You should see a list of challenges: D2C1,D2C3, D2C3,… Those are aliases to DREAM challenges. Information about a challenge can be (in general) obtained from the Synapse page of the challenge using the –onweb option:

dreamtools --challenge D6C3 --onweb

Brief information can also be printed in the terminal as follows:

dreamtools --challenge D6C3 --info

Next, you may want to score one of your submission. We provide access to templates for each challenge. For instance:

dreamtools --challenge D6C3 --download-template

This command prints the location of the template on your system. Copy that file in local/temporary place. Now that you have a copy of the template, you can fill its contents with your own data and score it (let us assume it is called D6C3_template.txt):

dreamtools --challenge D6C3 --submission D6C3_template.txt

This command should print some information and the score of the submission for instance for the example above, we get the following results:

{'results': chi2            53.980741
 R-square        34.733565
 Spearman(Sp)     0.646917
 Pearson(Cp)      0.647516
 dtype: float64}

All outputs will contain a json-like output. The synapse page of the challenge should give information about the scoring methodology.

Note that some challenges (like the D8C1 challenge) have sub-challenges. For instance in D8C1, there are 4 sub-challenges names (e.g., SC1A). So, you would need to be more specific and to provide the name of a sub-challenge. For instance:

dreamtools --challenge D8C1 --download-template --sub-challenge SC1A

Note

In D8C1, you will also need to accept the conditions of use of the data on a Synapse page, which should pop up.

The sub-challenge names can be obtained using –info option (see here above). Similarly to the simpler case shown above, you can now score that submission as follows:

dreamtools --challenge D8C1 --sub-challenge SC1A \
    --submission D8C1_example.zip

Again, you should get an output with the results:

Solution for alphabeta-Network.zip in challenge d8c1 (sub-challenge sc1a) is :
meanAUROC: 0.803628919403

Available challenges

DREAMTools includes about 80% of DREAM challenges from DREAM2 to DREAM9.5 Please visit F1000 link (Table 1).

Gold standards

All gold standards are retrieved automatically. You can obtain the location of a gold standard file as follows:

dreamtools --challenge D6C3 --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

More documentation ?

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