Model Development Kit (MDK)

The MDK is a modular Java open source library for simplifying procedures when handling metabolic models and metabolomes. The kit was written at EMBL-EBI by John May and Pablo Moreno. The library was previously named CheMet after the Cheminformatics and Metabolism group but was renamed as it's function became more defined. The name MDK is derived from The Chemistry Development Kit (CDK) which is one of the major constituent and used throughout the library to handle chemical structure.

Key Features

• intuitive object model for handling metabolic network/model chemistry (CDK) and gene/proteins (BioJava)
• service framework using WebServices and NoSQL local storage
• semantic annotation of cross-references
• fast read/write of models
• import/resolution of multiple formats including SBML, KGML, Excel
• incubation/testing for tools prior to deployment in CDK
• core library used by Metingear: The Metabolic Development Environment (GitHub project)

Extra Dependencies

To build this project you need to install CAF (https://www.github.com/jwmay/caf) and MacWidgets. You need to install MacWidgets manually as follows:

$ curl https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/macwidgets/mac_widgets-0.10.0.zip -O mac_widgets-0.10.0.zip
$ unzip mac_widgets-0.10.0.zip
$ mvn install:install-file -Dfile=MacWidgets.jar -Dpackaging=jar -DartifactId=macwidgets -DgroupId=com.explodingpixels -Dversion=0.10.0 -DgeneratePom=true

License

The MDK is licensed under Lesser General Public License 3.0.

Getting the library

Maven

The easiest way to use the library is with the Apache Maven build automation tool and adding a module dependency in the pom.xml. The example below shows adding the lucene service module, any required dependencies that the defined module needs will automatically be downloaded by maven.

<dependency>
    <groupId>uk.ac.ebi.mdk</groupId>
    <artifactId>mdk-service-lucene</artifactId>
    <version>1.4.0</version>
</dependency>

The MDK modules are currently deployed to the EBI Maven Repository and the following should be defined in the <repositories> section:

<repository>
    <id>ebi-repo</id>
    <name>EBI maven repository</name>
    <url>http://www.ebi.ac.uk/~maven/m2repo</url>
</repository>

Jar

Coming soon