XMLPipeDB

Download

Regular GenMAPP users can go straight to downloading Gene Databases for their species of interest. Software developers in bioinformatics (or other areas) that wish to automate the creation of relational databases from XML sources will be interested in the releases available from SourceForge.

Source Code and Full XMLPipeDB Suite

Source code and executable packages are available from the XMLPipeDB project site on SourceForge:

• All XMLPipeDB file releases
• GenMAPP Builder
• XSD-to-DB

Technical documentation is also available:

• XMLPipeDB Manual (417K PDF)
  • Direct from this site
  • SourceForge mirror
• UniProtDB relational database schema as generated by XSD-to-DB
  • Click here to view Schema Spy results
• GODB relational database schema as generated by XSD-to-DB
  • Click here to view Schema Spy results
• GenMAPPBuilder relational database schema
  • Click here to view Schema Spy results

Gene Databases

GenMAPP Gene Database for Arabidopsis thaliana

• Release 20090610
• Read Me (268K PDF, revision 20090610)
  • Direct from this site
  • SourceForge mirror

GenMAPP Gene Database for Escherichia coli K12

• Release 20090529
• Read Me (284K PDF, revision 20090529)
  • Direct from this site
  • SourceForge mirror

GenMAPP Gene Database for Plasmodium falciparum (isolate 3D7)

• Release 20090604
• Read Me (744K PDF, revision 20090604)
  • Direct from this site
  • SourceForge mirror

GenMAPP Gene Database for Vibrio cholerae O1 biovar El Tor str. N16961 Gene Database

• Release 20090622
• Read Me (264K PDF, revision 20090622)
  • Direct from this site
  • SourceForge mirror

System Requirements

Recommended Hardware

• For Gene Databases, GenMAPP, and exporting Gene Databases with GenMAPP Builder, a Microsoft Windows machine is required.
• At least 1G of memory is recommended. The software may run with less memory, but its performance and stability will degrade.
• For all other functions, XMLPipeDB software will run on any machine that can run Java and PostgreSQL.

Gene Databases

• GenMAPP software

GenMAPP Builder

• Java 5 Runtime Environment
• Relational database with available JDBC driver (only PostgreSQL has been explicitly tested so far)
• Microsoft Jet Database Engine (for exporting Gene Databases); included with Microsoft Windows

XSD-to-DB

• Java 5 Runtime Environment

XMLPipeDB Utilities

• Java 5 Runtime Environment
• Relational database with available JDBC driver (only PostgreSQL has been explicitly tested so far)

Database Libraries (UniProtDB, GODB)

• Java 5 Runtime Environment
• Relational database with available JDBC driver (only PostgreSQL has been explicitly tested so far)