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.
Department of Biology
John David N. Dionisio, Ph.D.
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 Github project.