User:Clements

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Dave Clements

I work on the Galaxy Project for Emory University, where I organize meetings and courses, prepare training materials, and improve Galaxy's documentation, wiki, and web presence. I'm also hoping to touch the (Python!) code.

Prior to working on Galaxy I ran the GMOD Help Desk from 2007-2010, where I did similar work. I am still involved in the GMOD community as a representative of Galaxy, and in planning GMOD Americas 2011. I telecommute from the Phillips Lab in the Center for Ecology and Evolutionary Biology (CEEB) at the University of Oregon.

Contact Details

E-mail	clementsgalaxy@gmail.org
Phone	1 541 914 6324 (9-5 Pacific time)

Background

My background is in computer science. I have been working in biological databases since 2000.

Prior to working on Galaxy, and for NESCent and GMOD before that, I worked as the database manager at the European Renal Genome project (EuReGene), as a member of the Edinburgh Mouse Atlas Project (EMAP). This project studied kidney development and disease. My work focused on gene expression patterns, and anatomy ontologies.

Prior to EuReGene I worked for ZFIN, the zebrafish model organism database at the University of Oregon for 5 years as a database administrator and software engineer.

My pre-bioinformatics career included

• 4 years at an artificial intelligence lab at the University of Oregon,
• 6 years at database management system vendors,
• 2 years as a database administrator at General Mills,
• Temporary positions (6 to 12 months) working on
  • teaching database courses at the University of Oregon
  • a data warehouse for inventory control in semiconductor manufacturing (HP),
  • a test harness for a network controller OS (IBM), and
  • query tools for credit unions (EDS)
• A master's degree in Computer Science from the University of Minnesota. My research focused on transaction management in federated databases,
• A bachelor's degree in Computer Science from Iowa State University.

Publications

• Organization of the pronephric kidney revealed by large-scale gene expression mapping; in Genome Biology, 2008, 9:R84. Daniela Raciti, Luca Reggiani, Lars Geffers, Qiuhong Jiang, Francesca Bacchion, Astrid E Subrizi, Dave Clements, Christopher Tindal, Duncan R Davidson, Brigitte Kaissling, and André W Brändli

• A high-resolution anatomical ontology of the developing murine genitourinary tract; in Gene Expression Patterns, 7(6), pp. 680-699 (June 2007). Melissa H. Little, Jane Brennan, Kylie Georgas, Jamie A. Davies, Duncan R. Davidson, Richard A. Baldock, Annemiek Beverdam, John F. Bertram, Blanche Capel, Han Sheng Chiu, Dave Clements, Luise Cullen-McEwen, Jean Fleming, Thierry Gilbert, Doris Herzlinger, Derek Houghton, Matt H. Kaufman, Elena Kleymenova, Peter A. Koopman, Alfor G. Lewis, Andrew P. McMahon, Cathy L. Mendelsohn, Eleanor K. Mitchell, Bree A. Rumballe, Derina E. Sweeney, M. Todd Valerius, Gen Yamada, Yiya Yang and Jing Yu

• The Zebrafish Information Network: the zebrafish model organism database; in Nucleic Acids Research 34:D581-585 (2006); Sprague, J., Bayraktaroglu, L., Clements, D., Conlin, T., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Mani, P., Ramachandran, S., Schaper, K., Segerdell, E., Song, P., Sprunger, B., Taylor, S., Van Slyke, C.E., and Westerfield, M.

• The Zebrafish Information Network (ZFIN): the zebrafish model organism database; in Nucleic Acids Research 31(1):241-243 2003); Sprague, J., Clements, D., Conlin, T., Edwards, P., Frazer, K., Schaper, K., Segerdell, E., Song, P., Sprunger, B., and Westerfield, M.

• The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research; in Nucleic Acids Research 29(1):87-90 (2001); Sprague, J., Doerry, E., Douglas, S., Westerfield, M., and ZFIN Group, (Conlin, T., Clements, D., Edwards, P., Frazer, K., Schaper, K., Segerdell, E.)

• Squeaky Wheel Optimization; in Journal of Artificial Intelligence Research, 10, 353-373 (May 1999); D. Joslin and D. Clements. This material was covered in less detail in Squeaky Wheel Optimization; in Proceedings of the 15th National Conference on Artificial Intelligence (AAAI-98).

• Cyclic Scheduling; in Proceedings of the 16th International Joint Conference on Artificial Intelligence (IJCAI-99), D. Draper, A. Jonsson, D. Clements, and D. Joslin.

• Heuristic Optimization: A hybrid AI/OR approach. at Workshop on Industrial Constraint-Directed Scheduling, held in conjunction with CP'97, Schloss Hagenberg, Austria (1997); D. Clements, J. Crawford, D. Joslin, G. Nemhauser, M. Puttlitz and M. Savelsbergh.

• Myriad: Design and Implementation of a Federated Database Prototype; in Software - Practice and Experience, 25(5), 533-562 (May 1995); E.P. Lim, S.Y. Hwang, J. Srivastava, D. Clements and M. Ganesh.

Presentations, Tutorials, Workshops, Demos and Posters

• GMOD Sustainability and Organization at September 2010 GMOD Meeting, Cambridge, United Kingdom, September 2010.

• Help Desk Update at September 2010 GMOD Meeting, Cambridge, United Kingdom, September 2010.

• GMOD for Evolutionary Biology, presentation with Rob Buels at iEvoBio 2010, Portland, Oregon, June 2010.

• Help Desk Report, presentation at January 2010 GMOD Meeting, San Diego, January 2010.

• GMOD Project Update, presentation with Scott Cain at PAG 2010, San Diego, January 2010.

• Comparative Genomics Tools in GMOD, poster with Sheldon McKay, Ken Youens-Clark, Ben Faga, Scott Cain, at PAG 2010, San Diego, January 2010.

• Database Tools for Biologists, workshop at Department of Biochemistry and Biophysics, Texas A&M University, December 2009

• GMOD for Comparative Genomics, presentation at Information Systems for Insect Pests (ISyIP), Rennes, France, November 2009

• Database Tools for Biologists: A Half-Day GMOD Workshop, at Bioinformatics Australia 2009 (BA2009), Melbourne, Australia, October 2009

• Visualizing Next Generation Sequence Data with GBrowse and SAMtools, poster at Bioinformatics Australia 2009 (BA2009), Melbourne, Australia, October 2009

• Visualising NGS Data in GBrowse 2, presentation at August 2009 GMOD Meeting, Oxford, UK, August 2009.

• Seeing the forest and the trees: visualizing next generation sequence data, presentation at Next Generation Genome Analysis in Non-Model Organisms, University of Connecticut, June 2009

• Using GMOD for evolutionary genomics and next generation sequence data, presentation as a part of Database Tools for Evolutionary Genomics: An introduction to GMOD software for managing, annotating and visualizing genomic data workshop at SMBE 2009, Iowa City, IA.

• Visualizing and Integrating Next Generation Sequence Data using GMOD, workshop at Evolutionary Genetics - the impact of next generation sequencing technologies, Lutherstadt-Wittenberg, Germany, April 2009.

• Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your syntenic data with GBrowse_syn, workshop with Sheldon McKay and Scott Cain at PAG 2009, January 2009.

• Managing Next Generation Sequence Data with GMOD, poster with Scott Cain, Paul Hohenlohe, Nicholas Stiffler, Eric Johnson, and William Cresko, at PAG 2009, January 2009.

• GMOD: Managing genomic data from emerging model organisms, poster with Hilmar Lapp and Todd Vision at ISMB 2008, July 2008.

• GMOD: Genomics Resources for Emerging Model Organisms, poster with Hilmar Lapp and Todd Vision at American Genetic Association Annual Symposium, upcoming, June 2008.

• Chado - A Database Schema for Integrating Biological Data, workshop with Scott Cain at the 2nd Annual Arthropod Genomics Symposium, April 2008.

• GMOD: Database Resources for Emerging Model Organisms, poster with Hilmar Lapp and Todd Vision at the 2nd Annual Arthropod Genomics Symposium, April 2008.

• GMOD Tools for Comparative Genomics, poster with, David Riley, Ben Faga, Hervé Tettelin, Sam Angiuoli, and Jonathan Crabtree. Presented at the IGERT Symposium on Evolution, Development, and Genomics, April 4-6, Eugene, OR. Highlights GMOD components particularly useful for comparative genomics: CMap, Sybil, SynView, SynBrowse and GBrowse_syn.

• GMOD: Informatics Resources for Evolutionary Research, poster with Hilmar Lapp and Todd Vision. Presented at the IGERT Symposium on Evolution, Development, and Genomics, April 4-6, 2008, in Eugene OR. Highlights GMOD tools particularly useful for evolutionary research: GBrowse, Apollo, Pathway Tools, and Chado.

• Digesting the Genome Glut: Promoting the Use and Extension of GMOD To Emerging Model Organisms, poster with Brian Osborne, Hilmar Lapp, Xianhua Liu, W. Owen McMillan, Nassib Nassar, and Todd J. Vision, at the 2007 Genome Informatics conference. An overview of GMOD highlighting components, the new web site, and using GMOD for evolution research.

• Gene Expression Databases: Where and When, presentation given at NESCent in April 2007. Describes common issues with gene expression databases focusing on anatomy ontology issues. Uses 4 websites to demonstrate different ways to deal with these issues.

• Worldwide Aeronautical Route Planner, demonstration with Charles B. McVey, and Andrew J. Parkes at the 16th National Conference on Artificial Intelligence (AAAI-99).

• Squeaky Wheel Optimization, demonstration with David Joslin at the 15th National Conference on Artificial Intelligence (AAAI-98).