AMBIT libraries

AMBIT is implemented in Java, uses a MySQL database as backend, and relies on The Chemistry Development Kit for cheminformatics functionality.

The OpenTox API implementation introduces two additional major dependencies, namely, the Restlet library for implementation of REST services, and the Jena RDF API. Apache Maven is used for software project management (organizing dependencies and building of executables).

The source code is available in a Subversion repository at the SourceForge site.

There are two top level Maven projects, ambit2-all (libraries) and ambit2-apps (applications), consisting of several sub-modules. The first is used to organize and build libraries, while the second uses these modules as dependencies to build the end user applications and web services.

The Toxtree source code also includes dependencies on some of the ambit2-all modules. On the other hand, Toxtree itself a dependency of the end user applications and web services, in which it has been incorporated, such as AmbitXT and AMBIT REST web services.

More details about (javadoc, code examples) at ambit modules web pages.

License

LGPL
http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt

Please note the license of AMBIT Applications and web services is GPL

The code

Libraries (multi-module Maven project)

Applications (multi-module Maven project)

tags

Maven artifacts

http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases/ambit/

Artifacts

<dependency>
  <groupId>ambit</groupId>
  <artifactId>ambit2-*</artifactId>
  <version>2.4.2</version>
</dependency>

Repository

   <repository>
        <id>ambit-plovdiv-releases</id>
        <url>http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases</url>
    </repository>

Publications

AMBIT REST
Jeliazkova N., Jeliazkov V. AMBIT RESTful web services: an implementation of the OpenTox application programming interface, Journal of Cheminformatics 2011, 3:18, doi:10.1186/1758-2946-3-18.
AMBIT Substructure search
Jeliazkova N., Kochev N. Ambit-SMARTS: Efficient Searching Of Chemical Structures And Fragments, Mol. Inf., 2011, 30, 2 - 15 (in print)
AMBIT, AMBITXT
Jeliazkova N., Jaworska J., Worth A. (2010) Chapter 17. Open Source Tools for Read-Across and Category Formation, In M. Cronin, & Madden J. (Eds.), In Silico Toxicology : Principles and Applications (pp. 408-445). Cambridge, UK: RSC Publishing