XMLPipeDB is an open source suite of Java-based tools for automatically building relational databases from an XML schema (XSD). XMLPipeDB provides functionality for managing, querying, importing, and exporting information to and from XML data with minimum manual processing of the data. While its applicability is fairly general, the original motivation for XMLPipeDB was to create a solution for the management of biological data from different sources that are used to create Gene Databases for GenMAPP (Gene Map Annotator and Pathway Profiler), software for viewing and analyzing DNA microarray and other genomic and proteomic data on biological pathways.
News
June 23, 2008
SIGCSE Bulletin June 2008 Paper
ACM’s SIGCSE Bulletin has published our paper on how open source pedagogy was instrumental to the XMLPipeDB project. The article can be found here, with full citation details listed in the Publications page.
August 21, 2007
BOSC 2007 Slides Now Available Online
Slides from our two BOSC 2007 talks are now available online. They aren't file downloads, but “play back” directly within their respective pages:
- An Open Source Framework for Teaching Bioinformatics
- XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources
Citation details for these presentations are available from the Publications page.
March 2, 2007
Affymetrix IDs Added to E. coli K12 Gene Database
GenMAPP.org has added Affymetrix probe set identifiers for all Affymetrix Escherichia coli microarrays (E_coli_2 Array, E. coli Genome Sense Array, E. coli Genome Antisense Array) to the 20060731 release of the E. coli K12 Gene Database. These Affymetrix probe set identifiers were related to both UniProt and Blattner identifiers.
This version of the database is now available as Ec-K12-Std_External_20060731x.
November 14, 2006
LMU Junior Faculty Seminar Presentation
The XMLPipeDB project, and the computer science courses that facilitated it, were presented at an interdisciplinary LMU junior faculty seminar today. Slides from the talk, entitled “Collaborating Early and Often: Bringing Biology and Computer Science Together Through an Open Source Culture” (4.7M PDF), are available from the Publications page.
October 23, 2006
Gladstone Visit
Drs. Dahlquist and Dionisio visited the GenMAPP group at the Gladstone Institute in San Francisco today. They presented the XMLPipeDB project and discussed possible points of collaboration.
September 28, 2006
Minor E. coli K12 Gene Database Update
For consistency with GenMAPP.org naming, the filename for the E. coli K12 Gene Database has been changed, and its Read Me file has also been revised. The data itself remains exactly the same.
September 25, 2006
ISMB/BOSC 2006 Materials Now Available
The XMLPipeDB poster (1.7M PDF) and talk slides (3.6M PDF) presented at ISMB and BOSC 2006, respectively, are now available for download as PDF files. Full citations can be found in the newly-added Publications page.
August 28, 2006
New URL: http://xmlpipedb.cs.lmu.edu
The LMU Computer Science lab infrastructure has undergone some upgrades; as a result, the new URL for the project’s home page is now http://xmlpipedb.cs.lmu.edu.
July 31, 2006
Escherichia coli K12 Gene Database Now Available
Our first GenMAPP Gene Database release for E. coli K12 is now available for download.
July 13, 2006
XMLPipeDB at BOSC and ISMB2006
Dr. Kam D. Dahlquist will give a platform presentation at the BOSC (Bioinformatics Open Source Conference) held in conjunction with the ISMB (Intelligent Systems for Molecular Biology) Conference in Fortaleza, Brazil, August 3-10, 2006. She will also present a poster at the main ISMB meeting.