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MyDasTemplate-1.0.2.zip mydas-1.0.2.jar mydas-javadoc-1.0.2.jar mydas-sources-1.0.2.jar
MyDasTemplate-1.0.2.zip mydas-1.0.2.jar mydas-javadoc-1.0.2.jar mydas-sources-1.0.2.jar
 | A Java Distributed Annotation System (DAS) Server with a Simple API for Developing DAS Sources |  |
Index | Introduction: Obtaining and configuring the MyDas code to start building your data source ->
This project offers an easy-to-extend Java DAS server framework with several advantages:
- Implementing data sources is very easy but also flexible and powerful
- Data caching is built into the system, with access to the caching mechanism made available to the data sources.
- All aspects of the server are highly configurable, including selecting options where the DAS 1.53 specification offers choices to the implementor.
- The latest Java technologies have been used throughout the system to optimise performance and simplify data source development.
- Wherever possible the same terminology is used in the API as in the DAS specification and XML - again, making data source development more easy.
If you would like to see an example of MyDas in action, please take a look at the UniProt DAS Annotation Server at the EBI, which is a popular DAS Reference server with six data sources.
More details of the DAS protocol, DAS servers and DAS clients can be found at http://www.biodas.org/wiki/Main_Page.
The first version of this server is a complete implementation of Distributed Sequence Annotation System (DAS) Version 1.53. If you are interested in learning more about DAS 1.53, this specification is highly recommended as a concise and complete description of the DAS protocol.
We now plan to implement the functionality of the DAS 1.53E specification, as described in BMC Bioinformatics:
Prlić A, Down TA, Kulesha E, Finn RD, Kähäri A, Hubbard TJ. Integrating sequence and structural biology with DAS. BMC Bioinformatics. 2007 Sep 12;8:333 (PMID: 17850653)
All the source code is available from subversion. (Click on the 'Source' tab above to access this.)
Please see the documentation for building a mydas data source plugin for details of how to start implementing a plugin (This documentation is a work in progress).
This code is being developed using the following platform, tools and APIs:
| Development OS | Both Windows Vista and Suse Linux 10.1 | |
| IDE | IntelliJ IDEA Version 6 | http://www.jetbrains.com/idea/ |
| Sun Java SDK | jdk1.5.0_11 | http://java.sun.com |
| Build and Project Management Tool | Maven 2.0.6 | http://maven.apache.org/ |
| Test Framework | JUnit 4.3.1 | http://www.junit.org/index.htm |
| Logging | Log4J 1.2.14 | http://logging.apache.org/log4j/docs/ |
| Logging | commons-logging 1.1 | http://jakarta.apache.org/commons/logging/ |
| XML Marshalling and Unmarshalling | MXP XMLPullParser API 1.1.3.4.M | http://www.extreme.indiana.edu/xgws/xsoap/xpp/mxp1/ |
| Caching Framework | Open Symphony OSCache 2.3 | http://www.opensymphony.com/oscache/ |
| Java Collections Framework Extensions | commons-collections 3.2 | http://jakarta.apache.org/commons/collections/ |
Note that the Maven build tool downloads all jar dependencies for the project - it will not be necessary to download these individually.
 | This project is led by Philip Jones with contributions from Antony Quinn. Both Philip and Antony are software developers in the Proteomics Service Team at the EMBL-European Bioinformatics Institute. Philip Jones designed and developed the mydas DAS servlet and associated Java API and is responsible for the mydas project documentation. Antony Quinn is developing a configurable XSLT transformation of the DAS XML to allow it to be viewed in a human-readable format in an internet browser : effectively a simple DAS client built into the DAS server. | |
