Dave Clements

I work on the Galaxy Project for Johns Hopkins University (and formerly at Emory University), where I organize meetings and courses, prepare training materials, and improve Galaxy's documentation, wiki, and web presence.

Prior to working on Galaxy I ran the [GMOD Help Desk](http://gmod.org/wiki/GMOD Help Desk) from 2007-2010, where I did similar work. I am still involved in the GMOD community as a representative of Galaxy. I have a guest faculty appointment at the University of Oregon, and over the years I have telecommuted from the Phillips and Cresko Labs in the Institute of Ecology and Evolution (IE²) and the Toomey Lab in the Department of Earth Sciences.

Details

Background

My background is in computer science. I have been working in bioinformatics 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

• The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update Enis Afgan, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W537–W544, doi:10.1093/nar/gky379. Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Björn Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, and Daniel Blankenberg.
• Community-Driven Data Analysis Training for Biology, Cell Systems, Volume 6, Issue 6, 27 June 2018, Pages 752-758.e1. Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Lariviere, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon, Ryan, Florian Christoph Sigloch, Nicola Soranzo, Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, James Taylor, Rolf Backofen, Anton Nekrutenko, Björn Grüning.
• The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research (2016) doi: 10.1093/nar/gkw343. Enis Afgan, Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Greg Von Kuster, Helena Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, and Jeremy Goecks
• Using Galaxy to Perform Large-Scale Interactive Data Analyses, in Current Protocols in Bioinformatics. 2012 June: Unit 10.5. Jennifer Hillman-Jackson, Dave Clements, Daniel Blankenberg, James Taylor, Anton Nekrutenko, Galaxy Team
• The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data, in Database, 2011; doi: 10.1093/database/bar051, Sook Jung; Naama Menda; Seth Redmond; Robert M. Buels; Maren Friesen; Yuri Bendana; Lacey-Anne Sanderson; Hilmar Lapp; Taein Lee; Bob MacCallum; Kirstin E. Bett; Scott Cain; Dave Clements; Lukas A. Mueller; Dorrie Main
• 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 depth 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.

Organizer

2020's

• 2020 Bioinformatics Community Conference, July 18-25, 2020, Online, Global

2010's

• 2019 Galaxy Community Conference, July 1-8, 2020, Freiburg, Germany.
• GCCBOSC 2018, , Portland, Oregon, United States
• 2017 Galaxy Community Conference (GCC2017), June 26-30, 2017, Montpellier, France
• Galaxy AustralAsia Meeting (GAMe 2017), February 3-9, 2017, Melbourne, Australia
• Galaxy Admin Training 2016, November 7-11, 2016, Salt Lake City, Utah, United States
• 2016 Galaxy Community Conference (GCC2016), June 25-29, 2016, Bloomington, Indiana, United States
• International Plant and Animal Genome XIV (PAGXIV), Computer Demonstration Track, January 9-13, 2016, San Diego, California, United States
• 2015 Galaxy Community Conference (GCC2015), Norwich, United Kingdom
• International Plant and Animal Genome XIII (PAGXIII), Computer Demonstration Track, January 10-14, 2015, San Diego, California, United States

• 2014 Galaxy Community Conference (GCC2014), June 30 - July 2, 2014, Baltimore, Maryland, United States

  • GalaxyAdmins Birds of a Feather Meetup
• May 2014 UK Galaxy Workshop Tour, May 6-12, 2014, Norwich and Edinburgh, United Kingdom
• 2013 Research Triangle Workshop Tour, May 18-22, 2013, Research Triangle Area, North Carolina, United States

• 2013 Galaxy Community Conference (GCC2013), June 30 - July 2, 2013, Oslo, Norway

  • GalaxyAdmins Birds of a Feather Meetup
  • Public Galaxy Server Birds of a Feather Meetup
• Missouri Workshop Tour 2013, April 29 - May 2, 2013, St. Louis and Columbia, Missouri, United States

• 2012 Galaxy Community Conference (GCC2012), July 25-27, Chicago, Illinois, United States

  • Bioinformatics Training and Teaching with Galaxy Breakout Session
• 2011 Galaxy Community Conference (GCC2011), May 25-26, 2011, Lunteren, The Netherlands

• GMOD Americas 2011, March 5-12, 2011, Durham, North Carolina, United States

  • GMOD Satellite Meetings, March 7

    • GMOD in the Sequencing Center Satellite
  • 2011 GMOD Spring Training, March 8-12

• GMOD Europe 2010, September 13-16, 2010, Cambridge, United Kingdom

  • GMOD Satellite Meetings, September 15

    • Post Reference Genome Tools Satellite
    • Community Annotation Satellite
• GMOD Tools for Evolutionary Biology Hackathon, November 8-12, 2010, Durham, North Carolina, United States

2000's

• GMOD Europe 2009, August 3-7, Oxford, United Kingdom

  • 2009 GMOD Summer School - Europe, August 3-6
• 2009 GMOD Summer School - Americas, July 16-19, 2009, Durham, North Carolina, United States
• Database tools for evolutionary genomics workshop, SMBE 2009, June 6, 2009, Iowa City, Iowa, United States
• 2008 GMOD Summer School, July 11-13, 2008, Durham, North Carolina, United States

Presentations, Tutorials, Workshops, Demos and Posters

2020

2019

2018 & 2017

Are coming, the next time I need to do a biosketch.

2016

2015

2014

2013

2012

• Introduction to Galaxy Workshop at Purdue University, October 2012
• Transparent, Accessible, Reproducible Biological Analysis with Galaxy at Indiana University, October 2012
• Introduction to Galaxy Workshop at University of Illinois at Urbana-Champaign, October 2012
• Transparent, accessible, reproducible analysis with Galaxy at the South African Genetics & Bioinformatics Society Conference, Stellenbosch University, South Africa, September 2012
• Galaxy Workshop at the University of Pretoria and Stellenbosch University, South Africa, September 2012
• Galaxy Installation Workshop at the [http://gmod.org/wiki/2012 GMOD Summer School](http://gmod.org/wiki/2012 GMOD Summer School),US National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States
• Introduction to Galaxy Workshops at University of Maryland College Park, Johns Hopkins University, Univeristy of Iowa, and Iowa State University, April 2012
• CloudMan Workshop, Galaxy Project Update, and Community Building lightning talk at [April 2012 GMOD Meeting](http://gmod.org/wiki/April 2012 GMOD Meeting), Washington DC, United States, April 2012
• Galaxy at PAG 2012, San Diego, California, United States, January 2012
  Intro to Galaxy; most of this talk was a live demo.

2011

• Exploit your Data: Galaxy and the GMOD Tool Suite at University of Tasmania, Hobart, Australia, October 2011
  This is a shorter version of the talk presented at AMATA.
• Exploit your Data: Galaxy and the GMOD Tool Suite at AMATA 2011, Canberra, Australia, October 2011.
• Genome Project 101 Workshop with Scott Cain at Arthropod Genomics Symposium, Kansas City, Missouri, United States, June 2011.
• Galaxy Workshop at European Human Genetics Conference 2011 (ESHG), Amsterdam, the Netherlands, May 2011
• Galaxy for high-throughput sequence data analysis at GMOD Americas 2011, Durham, North Carolina, United States, March 2011.

2010

• [GMOD Sustainability and Organization](http://gmod.org/wiki/September 2010 GMOD Meeting#GMOD Sustainability and Organization) at [http://gmod.org/wiki/September 2010 GMOD Meeting](http://gmod.org/wiki/September 2010 GMOD Meeting), Cambridge, United Kingdom, September 2010.
• [Help Desk Update](http://gmod.org/wiki/September 2010 GMOD Meeting#Help Desk Update) at [http://gmod.org/wiki/September 2010 GMOD Meeting](http://gmod.org/wiki/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 [http://gmod.org/wiki/January 2010 GMOD Meeting](http://gmod.org/wiki/January 2010 GMOD Meeting), San Diego, January 2010.
• GMOD Project Update, presentation with Scott Cain at [http://gmod.org/wiki/PAG 2010](http://gmod.org/wiki/PAG 2010), San Diego, January 2010.
• Comparative Genomics Tools in GMOD, poster with Sheldon McKay, Ken Youens-Clark, Ben Faga, Scott Cain, at [http://gmod.org/wiki/PAG 2010](http://gmod.org/wiki/PAG 2010), San Diego, January 2010.

2009

• 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 [http://gmod.org/wiki/August 2009 GMOD Meeting](http://gmod.org/wiki/August 2009 GMOD Meeting), Oxford, UK, August 2009.
• [''Seeing the forest ''and'' the trees: visualizing next generation sequence data''](http://gmod.org/wiki/Image:AGA NGS 2009.pdf), 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](http://gmod.org/wiki/GBrowse syn PAG 2009 Workshop), workshop with Sheldon McKay and Scott Cain at [http://gmod.org/wiki/PAG 2009](http://gmod.org/wiki/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 [http://gmod.org/wiki/PAG 2009](http://gmod.org/wiki/PAG 2009), January 2009.

2008

• 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 2008, Eugene, OR. Highlights GMOD components particularly useful for [comparative genomics](http://gmod.org/wiki/Category:Comparative Genomics): http://gmod.org/wiki/CMap, http://gmod.org/wiki/Sybil, http://gmod.org/wiki/SynView, http://gmod.org/wiki/SynBrowse and http://gmod.org/wiki/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 2008, in Eugene OR. Highlights GMOD tools particularly useful for evolutionary research: http://gmod.org/wiki/GBrowse, http://gmod.org/wiki/Apollo, [http://gmod.org/wiki/Pathway Tools](http://gmod.org/wiki/Pathway Tools), and http://gmod.org/wiki/Chado.

2007 and Before

• 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).