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

People

XMLPipeDB was created by the Bioinformatics Group at Loyola Marymount University, a collaborative research group founded by Dr. Kam D. Dahlquist (Department of Biology) and Dr. John David N. Dionisio (Department of Electrical Engineering and Computer Science). XMLPipeDB development began in Spring 2006 as a group project in a special studies course in Bioinformatics (CMSI 698/BIOL 498) team-taught by Drs. Dahlquist and Dionisio. Development continued in a second special studies course, Open Source Software Development Workshop (CMSI 698/598) and has transitioned into an undergraduate Biological Databases (CMSI 367, BIOL 367, HNRS 398) course taught in Fall 2008, Fall 2009, and Fall 2010. XMLPipeDB also follows the philosophy of Dr. Dionisio’s Recourse project, which seeks to introduce an open source culture into the computer science curriculum.

Principal Investigators

Kam D. Dahlquist, Ph.D.

http://myweb.lmu.edu/kdahlqui

Department of Biology

John David N. Dionisio, Ph.D.

http://myweb.lmu.edu/dondi

Department of Electrical Engineering and Computer Science

Manager of Laboratory Facilities

Masao Kitamura

Department of Electrical Engineering and Computer Science

Research Assistants

Alexandrea Alphonso, spring 2009 (Vibrio cholerae)

Richard Brous, spring 2011 (Mycobacterium tuberculosis, GenMAPP Builder)

Wesley Citti, summer 2006 (XMLPipeDB logo)

Kelia McDonald, spring 2010 (Pseudomonas aeruginosa)

Kevin McGee, spring 2014 (Leishmania major)

Don Murphy, spring-fall 2010 (Saccharomyces cerevisiae, GenMAPP Builder, GO Slim)

Jeffrey Nicholas, Masters thesis 2007 (Arabidopsis thaliana, GenMAPP Builder, xmlpipedbutils)

Bernadette Pak, spring 2010 (Saccharomyces cerevisiae)

Kevin Paiz-Ramirez, fall 2010 (Mycobacterium tuberculosis)

Kelly Parks, spring-fall 2010, spring 2011 (Staphylococcus aureus)

Mitchell Petredis, spring 2014 (Sinorhizobium meliloti strain 1021)

Andrew Pita, spring 2014 (Streptococcus pneumoniae)

Derek Smith, spring 2009 (GenMAPP Builder, xmlpipedbutils)

Chad Villaflores, spring 2009 (Escherischia coli K12)

Fall 2013 Biological Databases

Team H(oo)KD: Chlamydia trachomatis

Katrina Sherbina, project manager, coder

Hilda Delgadillo, quality assurance

Dillon Williams, GenMAPP user

Team ATK: Streptococcus pneumoniae

Tauras Vilgalys, project manager, coder

Alina Vreeland, quality assurance

Kevin Meilak, GenMAPP user

Off the Leish: Leishmania major

Gabriel Leis, project manager, coder

Lena Hunt, quality assurance

Viktoria Kuehn, GenMAPP user

Kevin McGee, GenMAPP user

Team Name: Sinorhizobium meliloti (strain 1021)

Stephen Louie, project manager, quality assurance

Mitchell Petredis, coder

Lauren Magee, GenMAPP user

Miles Malefyt, GenMAPP user

Fall 2010 Biological Databases

Don Dahlquist’s Angels: Helicobacter pylori

Andrew Forney, project manager, coder

Claudia Campos, GenMAPP user

Salomon Garcia, quality assurance

Team Winner Winner Chicken Dinner: Salmonella typhimurium

Zeb Russo, project manager, quality assurance

Jennifer Okonta, GenMAPP user

Evan Montz, coder

The A Team: Mycobacterium smegmatis

Margie Doyle, project manager, GenMAPP user

Andrew Herman, quality assurance

Richard Brous, coder

Fall 2009 Biological Databases

Speedies: Mycobacterium tuberculosis

Kevin Paiz-Ramirez, project manager

Reid Oldenburg, coder

Cydnee Charles, ID minder

Jaime Bittner, GenMAPP user

Mrs. A: Staphylococcus aureus

Kelly Parks, project manager, GenMAPP user

Andrew Hirning, coder

Michael Piña, ID minder

Ravenclaw: Pseudomonas aeruginosa

Kelia McDonald, project manager, GenMAPP user

Lita Gratrix, coder

Kristen Phifer, ID minder

The Elite Three: Saccharomyces cerevisiae

Bernadette Pak, project manager, GenMAPP user

Don Murphy, coder

Kenny Rodriguez, ID minder

Fall 2008 Biological Databases

Gryffindor: Pseudomonas putida KT2440

Kelsi Busch, project manager, GenMAPP user

Courtney McCrary, coder

Stephanie Kuelbs, ID minder

Hufflepuff: Plasmodium falciparum

Greg Pierce, project manager

Ashley Hunter, coder

Chad Villaflores, ID minder

Sarah Ifrah, GenMAPP user

Ravenclaw: Candida albicans

Molly Bogeberg, project manager

Chester Hawkins, coder

Dan Moore, ID minder

Prestyn Lozano, GenMAPP user

Slytherin: Vibrio cholerae

Amanda Bierbauer, project manager

Derek Smith, coder

Thomas de Guzman, ID minder

Drea Alphonso, GenMAPP user

Summer 2006 Special Studies: Open Source Software Development Workshop

Joey Barrett (UniProtDB, GenMAPP Builder)

David Hoffman (xmlpipedbutils, web site)

Ryan Nakamoto (xmlpipedbutils)

Jeffrey Nicholas (xsd2db, xmlpipedbutils, GenMAPP Builder)

Scott Spicer (xsd2db, GODB, GenMAPP Builder)

Spring 2006 Special Studies: Bioinformatics

Joey Barrett (UniProtDB, GenMAPP Builder)

Joe Boyle (UniProtDB)

Adam Carasso (xsd2db)

David Hoffman (xmlpipedbutils)

Babak Naffas (xmlpipedbutils)

Jeffrey Nicholas (xsd2db, xmlpipedbutils, GenMAPP Builder)

Roberto Ruiz (GODB)

Scott Spicer (xsd2db, GODB, GenMAPP Builder)

If you would like to participate in or contribute to XMLPipeDB, please contact Dr. Dahlquist or Dr. Dionisio either directly or through our SourceForge project.

Acknowledgments

We would like to thank the GenMAPP.org Development Group, especially Bruce R. Conklin, Steven C. Lawlor, Scott W. Doniger, and Kristina Hanspers. We also wish to thank the LMU Departments of Biology and Electrical Engineering & Computer Science for giving us the opportunity to team-teach bioinformatics at LMU, as well as the Seaver College of Science & Engineering for encouraging interdisciplinary research. Thank you also to Caskey Dickson and Andrés Buriticá for all of their technical assistance.