A Project of the LMU Bioinformatics Group
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XMLPipeDB

A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources

Publications

Papers

Dionisio JDN, Dahlquist KD. “Improving the computer science in bioinformatics through open source pedagogy.” ACM SIGCSE Bulletin 40(2):115-119, June 2008. http://doi.acm.org/10.1145/1383602.1383648

Talks/Posters

Brous R, Dahlquist KD, Dionisio JDN. “Implementing Multiple Species Export in XMLPipeDB's GenMAPP Builder.” (talk) Southern California Conference for Undergraduate Research (SCCUR 2011), Mt. San Antonio College, Walnut, California. November 19, 2011.

Parks KC, Dahlquist KD, Dionisio JDN. “Using XMLPipeDB to Create a GenMAPP-Compatible Gene Database for the Analysis of DNA Microarray Data for Staphylococcus aureus MRSA252.” (talk) Beta Beta Beta Western Regional Conference, Azusa Pacific University, Azusa Pacific, California. April 2011.

Murphy DB, Dahlquist KD, Dionisio JDN. “Implementing Support for Multiple Species in XMLPipeDB’s GenMAPP Builder.” (poster) The Third Annual Undergraduate Research Symposium, Loyola Marymount University, Los Angeles, California. March 19, 2011.

Parks KC, Dahlquist KD, Dionisio JDN. “Using XMLPipeDB to Create a GenMAPP-Compatible Gene Database for the Analysis of DNA Microarray Data for Staphylococcus aureus MRSA252.” (talk) The Third Annual Undergraduate Research Symposium, Loyola Marymount University, Los Angeles, California. March 19, 2011.

Murphy DB, Dahlquist KD, Dionisio JDN. “Implementing Support for Multiple Species in XMLPipeDB’s GenMAPP Builder.” (poster) Southern California Conference for Undergraduate Research (SCCUR 2010), Pepperdine University, Malibu, California. November 20, 2010.

Parks KC, Dahlquist KD, Dionisio JDN. “Using XMLPipeDB to Create a GenMAPP-Compatible Gene Database for the Analysis of DNA Microarray Data for Staphylococcus aureus MRSA 252.” (talk) Southern California Conference for Undergraduate Research (SCCUR 2010), Pepperdine University, Malibu, California. November 20, 2010.

Paiz-Ramirez K, Dahlquist KD, Dionisio JDN. “Using XMLPipeDB to Create a GenMAPP-Compatible Gene Database for the Analysis of DNA Microarray Data for Mycobacterium tuberculosis.” (poster) Society for the Advancement of Chicanos and Native Americans in Science National Conference, Anaheim, California. October 2010.

Dahlquist KD, Dionisio JDN. “An Open Source, Open Science Pedagogy for Computational Biology.” Beyond BIO2010 Symposium, National Academy of Sciences, Washington, D.C. May 21–22, 2010.

Parks KC, Hirning AJ, McDonald K, Dionisio JDN, Dahlquist KD. “Extending XMLPipeDB to Create GenMAPP-compatible Gene Databases for the Analysis of DNA Microarray Data from Human Pathogens.” Experimental Biology 2010, Anaheim, California. April 24–28, 2010. http://www.fasebj.org/cgi/content/meeting_abstract/24/1_MeetingAbstracts/669.2

Pak B, Murphy D, Dionisio JDN, Dahlquist KD. “Extending XMLPipeDB with GO Slim to Update the GenMAPP-compatible Gene Database for Budding Yeast, Saccharomyces cerevisiae, for the Analysis of DNA Microarray Data.” Experimental Biology 2010, Anaheim, California. April 24–28, 2010. http://www.fasebj.org/cgi/content/meeting_abstract/24/1_MeetingAbstracts/lb157

Dahlquist KD, Dionisio JDN. “Fostering Interdisciplinary Teamwork in an Undergraduate Biological Databases Course.” 49th Annual American Society for Cell Biology Meeting. San Diego, California, December 2009.

Dahlquist KD, Alphonso A, Smith D, Villaflores C, Dionisio JDN. “XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources.” 10th annual Bioinformatics Open Source Conference (BOSC 2009). Stockholm, Sweden, June 27–28, 2009. http://www.slideshare.net/bosc/dahlquistxmlpipedbbosc2009

Dionisio JDN, Dahlquist KD. “Improving the computer science in bioinformatics through an open source pedagogy.” First RECOMB Satellite Conference on Bioinformatics Education, March 2009.

Alphonso A, Villaflores C, Smith D, Dahlquist KD, Dionisio JDN. “Extending XMLPipeDB to create gene databases for plants and microorganisms for the analysis of DNA microarray data.” First RECOMB Satellite Conference on Bioinformatics Education, March 2009.

Dahlquist KD, Dionisio JDN. “Fostering interdisciplinary teamwork in an undergraduate biological databases course.” First RECOMB Satellite Conference on Bioinformatics Education, March 2009.

Dahlquist KD, Dionisio JDN. “An Open Source Framework for Teaching Bioinformatics.” 8th annual Bioinformatics Open Source Conference (BOSC 2007). Vienna, Austria, July 19–20, 2007.

Dahlquist KD, Nicholas J, Dionisio JDN. “XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources.” 8th annual Bioinformatics Open Source Conference (BOSC 2007). Vienna, Austria, July 19–20, 2007.

Dahlquist KD, Dionisio JDN. “Collaborating Early and Often: Bringing Biology and Computer Science Together Through an Open Source Culture.” LMU Junior Faculty Seminar. Loyola Marymount University, November 14, 2006.

Dahlquist KD, Dionisio JDN. “A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources.” 7th annual Bioinformatics Open Source Conference (BOSC 2006). Fortaleza, Brazil, August 5, 2006.

Dahlquist KD, Barrett J, Boyle J, Carasso A, Hoffman D, Naffas B, Nicholas J, Ruiz R, Spicer S, Dionisio JDN. “A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources.” 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2006). Fortaleza, Brazil, August 6–10, 2006.