BDVal for MPS is an MPS plugin designed to help you configure BDVal projects. BDVal for MPS makes it easier to develop and validate predictive models in high-throughput datasets.

Usage

BDVal for MPS facilitates the configuration and running of BDVal projects. Below is a snapshot of a BDVal Project in MPS. MPS provides an interactive user interface with support for auto-completion and a smooth editing experience. Error highlighting provides immediate feedback when some configuration item is incorrectly set. Once configured, a BDVal project can be compiled to  generate input files for BDVal. Running the generated file can be done without leaving MPS. The interface updates to show the result of previous runs and the performance of the models measured by cross-validation.

Screen Shot 2014-08-14 at 4.37.24 PM

Installation

MPS

Install MPS on your computer. If you have never used MPS, we recommend your read the free chapters of the MPS Language Workbench, distributed here, which describe and explain the main MPS user interface elements.

BDVal Plugin

Install the BDVal plugin (full name: org.campagnelab.BDval). To do so, open the MPS Preferences menu, select the Plugins category, type BDVal in the search box. See the snapshot below:

Preferences_BDVal_Plugin

 

Note that the BDVal plugin requires other plugins developed by our lab. Download and install the plugin’s dependencies as well. After a restart, create an empty project. You should see the org.campagnelab.bdval language under the Modules Pool.

Sample Projects

You are ready to start using the Sample projects. First download the archive:

Unzip this file on your computer. We suggest to put it under ~/MPSProjects, such as ~/MPSProjects/BDVal_Samples

Open the project in MPS (File > Open > Choose ~/MPSProjects/BDVal_Samples, click Ok).

BDVal

The plugin requires a local installation of BDVal. Download a binary distribution (version 1.3 or higher), or clone a BDVal Git repository. Both options are described on the BDVal Download page

Follow the instructions in the following slides to see how to use the sample or to create a new project:

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MPS for BDVal User Guide 2.42 MB 200 downloads

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    Apache Ant

    Ant is required to run BDVal scripts. You can download a binary distribution here.

    MPS Plugin Code

    The MPS BDVal Plugin is open-source (perhaps better referred as open-code, since it does not contain any text source code). You can obtain the source code for the project at GitHub.

    Preprint

    Credits

    BDVal for MPS was developed by Victoria Benson during her 2014 summer internship in the laboratory. Victoria was a Sophomore at Cornell University who had no prior experience with MPS before starting her 3 month internship in the lab.