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 Github.
Source Code and Full XMLPipeDB Suite
Source code and executable packages are available from the XMLPipeDB project site on Github:
Technical documentation is also available:
- XMLPipeDB Manual (417K PDF)
- 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)
GenMAPP Gene Database for Escherichia coli K12
- Release 20090529
- Read Me (284K PDF, revision 20090529)
GenMAPP Gene Database for Helicobacter pylori str. 26695
- Release 20101130
- Read Me (501K PDF, revision 20101130)
GenMAPP Gene Database for Mycobacterium smegmatis ATCC 700084/mc(2)155
- Release 20110128
- Read Me (248K PDF, revision 20110128)
GenMAPP Gene Database for Mycobacterium tuberculosis ATCC 25618/H37Rv
- Release 20110303
- Read Me (230K PDF, revision 20110303)
GenMAPP Gene Database for Plasmodium falciparum (isolate 3D7)
- Release 20090604
- Read Me (744K PDF, revision 20090604)
GenMAPP Gene Database for Pseudomonas aeruginosa str. PAO1
- Release 20100212
- Read Me (274K PDF, revision 20100212)
GenMAPP Gene Database for Salmonella typhimurium ATCC 700720/SGSC1412/LT2
- Release 20101130
- Read Me (250K PDF, revision 20101130)
GenMAPP Gene Database for Staphylococcus aureus (strain MRSA252)
- Release 20100218
- Read Me (274K PDF, revision 20100218)
GenMAPP Gene Database for Vibrio cholerae O1 biovar El Tor str. N16961 Gene Database
- Release 20101022
- Read Me (246K PDF, revision 20101022)
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 Builder
- Java 6 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
XMLPipeDB Utilities
- Java 6 Runtime Environment
- Relational database with available JDBC driver (only PostgreSQL has been explicitly tested so far)
Database Libraries (UniProtDB, GODB)
- Java 6 Runtime Environment
- Relational database with available JDBC driver (only PostgreSQL has been explicitly tested so far)