BDVAL/Install

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BDVAL is an open source project for biomarker discovery in high-throughput datasets and is distributed under the GNU General Public License (GPL). The BDVal package is available as precompiled files and also in source code form. Distribution types are described in the following sections.

Contents

Binary Distribution

The binary distribution is intended for end users who wish to create and evaluate models for datasets they are interested in. The binary distribution of the BDVAL package contains two files as described as follows:

bdval_latest-bdval.zip
This includes all the external classes and sample data needed to run BDVAL
bdval.jar
This (optional) jar includes all the project classes and will require external libraries and data files to use either in standalone mode or embedded within your own projects.

Older releases can be found at the BDVal Download page for your reference.

Dependencies

In order to make use of the BDVal package, the following packages are also required.

Installation Notes

BDVal is written using Java and has been used extensively on both Unix and Windows operating systems. The notes here presume some knowledge of how to install software and set environment variables.

In general spaces in the names of files or directories should be avoided whenever possible. Since BDVal deals with many files at the same time, spaces may be interpreted by BDVal as separators between two filenames rather than a single filename and produce unexpected results.

BDVal

The binary distribution of BDVal is a single zip file. It can be extracted to a directory of your choosing. Throughout the documentation, this location will be referred to as the "<install-dir>"

Java

A Java virtual machine is required for BDVal. The JDK should not be required for the binary distribution. The examples assume the java executable is on the system path.

R

BDVAL uses R and Rserve in order to perform calculations. Rserve is essentially serves a "bridge" between the BDVAL package and R. At least one Rserve process must be running in for BDVal to work properly. BDVal also requires the ROCR package.

ROCR

To install ROCR type the following via the R command line

 install.packages('ROCR')
Rserve

To install Rserve type the following via the R command line

 install.packages('Rserve',,'http://www.rforge.net/')

Note that if you do not specify the rforge url, you will likely get an older version of the Rserve package.

To start the Rserve process type the following via the R command line

 library("Rserve")
 Rserve()

Apache Ant

Apache ant is used throughout the examples included with the BDVal distribution. While this is typically a tool used for software development with Java, it is used here as a method of chaining tasks in BDVal together. It is not strictly required for the binary distribution but it is highly recommend. The ant binary is assumed to be on the system path.

Source Distribution

The source distribution of the BDVAL package contains the Java source code along with supporting files that are used to compile and test the package. See the BDVal page to download the latest release of the source code.

Subversion Access

This project's Subversion repository can be checked out through SVN with the following instruction set:

 svn co https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/bdval

Additionally you can browse the bdval project source code in the Subversion repository.

NOTE: Use username "guest" and your email address at the login prompt if you do not have an account with the ICB.

Dependencies

In addition to the packages in the Binary Distribution the following Java packages are required in order to build and use BDVal.

Updating from a previous release

Every effort has been made to keep the software backwards compatible, however this section describes any issues or workarounds associated with updating the BDVal software from prior versions.

New Binary Model Format

Recent versions of BDVal have introduced a new binary model format. Models created with older versions of BDVal will require conversion. See BDVAL/NewModelFormat for details.

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