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[[Image:Clements.jpg|right|thumb|175px|Dave and Naomi storming the castle]]
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= Dave Clements =
 
= Dave Clements =
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[[File:Clements.jpg|right|175px|Dave Clements looking cheeky]]
  
 
__NOTOC__
 
__NOTOC__
  
I work for the [http://nescent.org/ National Evolutionary Synthesis Center (NESCent)] and since September 2007 I run the [[GMOD Help Desk]].  I telecommute from the [http://www.uoregon.edu/~pphil/index.html Phillips Lab] in the [http://ceeb.uoregon.edu/ Center for Ecology and Evolutionary Biology (CEEB)] at the [http://uoregon.edu University of Oregon].  See the [[GMOD Help Desk]] page for an explanation of what I do for the GMOD project.
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I work on the [[Galaxy]] Project for Johns Hopkins University, where I organize meetings and courses, prepare training materials, and improve
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[http://wiki.galaxyproject.org/ Galaxy's documentation wiki], and web presence.  I'm also hoping to touch the (Python!) code.
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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.  From 2013-2018 I telecommuted from the [http://pages.uoregon.edu/drt/ Toomey Lab] in the [https://earthsciences.uoregon.edu/ Department of Earth Sciences] at the [http://uoregon.edu University of Oregon].  From 2007 through 2012 I telecommuted from the [http://www.uoregon.edu/~pphil/index.html Phillips Lab] in the [http://ceeb.uoregon.edu/ Center for Ecology and Evolutionary Biology (CEEB)], also at Oregon.
  
 
== Contact Details ==
 
== Contact Details ==
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|-
 
|-
 
! E-mail
 
! E-mail
| [mailto:help@gmod.org help@gmod.org] (Help Desk)<br /> [mailto:clements@nescent.org clements@nescent.org] (Other)
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| [mailto:clements@galaxyproject.org clements@galaxyprojet.org]
 
|-
 
|-
! Phone
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! URL
| 1 541 914 6324 (9-5 Pacific time)
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| [https://galaxyproject.org/people/dave-clements/ My home page]
 
|}
 
|}
  
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My background is in computer science.  I have been working in biological databases since 2000.
 
My background is in computer science.  I have been working in biological databases since 2000.
  
Prior to working for [http://nescent.org NESCent] on GMOD I worked as the database manager at the [http://www.euregene.org/ European Renal Genome project (EuReGene)], as a member of the [http://genex.hgu.mrc.ac.uk/ Edinburgh Mouse Atlas Project (EMAP)].  This project studied kidney development and disease.  My work focused on gene expression patterns, and anatomy ontologies.
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Prior to working on [[Galaxy]], and for [http://nescent.org NESCent] and GMOD before that, I worked as the database manager at the [http://www.euregene.org/ European Renal Genome project (EuReGene)], as a member of the [http://genex.hgu.mrc.ac.uk/ 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 [http://zfin.org ZFIN, the zebrafish model organism database] at the [http://uoregon.edu University of Oregon] for 5 years as a database administrator and software engineer.
 
Prior to EuReGene I worked for [http://zfin.org ZFIN, the zebrafish model organism database] at the [http://uoregon.edu University of Oregon] for 5 years as a database administrator and software engineer.
  
 
My pre-bioinformatics career included
 
My pre-bioinformatics career included
* 4 years at an [http://www.cs.uoregon.edu/~clements/ artificial intelligence lab],
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* 4 years at an artificial intelligence lab at the [http://www.uoregon.edu/ University of Oregon],
 
* 6 years at database management system vendors,
 
* 6 years at database management system vendors,
 
* 2 years as a database administrator at [http://generalmills.com General Mills],
 
* 2 years as a database administrator at [http://generalmills.com General Mills],
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** a test harness for a network controller OS ([http://ibm.com IBM]), and
 
** a test harness for a network controller OS ([http://ibm.com IBM]), and
 
** query tools for credit unions ([http://eds.com EDS])
 
** query tools for credit unions ([http://eds.com EDS])
* A master's degree in [http://www.cs.umn.edu Computer Science from the University of Minnesota].  My research focused on transactions management in federated databases,
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* A master's degree in [http://www.cs.umn.edu Computer Science from the University of Minnesota].  My research focused on transaction management in federated databases,
 
* A bachelor's degree in [http://cs.iastate.edu Computer Science from Iowa State University].
 
* A bachelor's degree in [http://cs.iastate.edu Computer Science from Iowa State University].
  
 
== Publications ==
 
== Publications ==
  
* [http://dx.doi.org/10.1016/j.modgep.2007.03.002 A high-resolution anatomical ontology of the developing murine genitourinary tract]; in ''[http://www.elsevier.com/locate/modgep 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
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See the current list at my [http://wiki.galaxyproject.org/DaveClements Galaxy home page].
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== GMOD Era Presentations, Tutorials, Workshops, Demos and Posters ==
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Work done during my time at GMOD.  See my [http://wiki.galaxyproject.org/DaveClements Galaxy home page] for other presentations.
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* ''[[September 2010 GMOD Meeting#GMOD Sustainability and Organization|GMOD Sustainability and Organization]]'' at [[September 2010 GMOD Meeting]], Cambridge, United Kingdom, September 2010.
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* ''[[September 2010 GMOD Meeting#Help Desk Update|Help Desk Update]]'' at [[September 2010 GMOD Meeting]], Cambridge, United Kingdom, September 2010.
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* ''[[Media:GMODForIEvoBio2010.pdf|GMOD for Evolutionary Biology]]'', presentation with [[User:RobertBuels|Rob Buels]] at [http://ievobio.org iEvoBio 2010], Portland, Oregon, June 2010.
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* ''[[Media:Jan2010HelpDesk.pdf|Help Desk Report]]'', presentation at [[January 2010 GMOD Meeting]], San Diego, January 2010.
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* ''[[Media:PAG2010GMODProjectUpdate.pdf|GMOD Project Update]]'', presentation with [[User:Scott|Scott Cain]] at [[PAG 2010]], San Diego, January 2010.
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* ''[[Media:PAG2010ComparativeGenomicsToolsInGMOD.pdf|Comparative Genomics Tools in GMOD]]'', poster with [[User:Mckays|Sheldon McKay]], Ken Youens-Clark, [[User:Faga|Ben Faga]], [[User:Scott|Scott Cain]], at [[PAG 2010]], San Diego, January 2010.
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* ''[[Media:GMODTAMUWorkshop.pdf|Database Tools for Biologists]]'', workshop at Department of Biochemistry and Biophysics, Texas A&M University, December 2009
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* ''[[Media:ISyIPGMODforComparativeGenomics.pdf|GMOD for Comparative Genomics]]'', presentation at [http://colloque.inra.fr/isyip Information Systems for Insect Pests (ISyIP)], Rennes, France, November 2009
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* ''[[BA2009|Database Tools for Biologists: A Half-Day GMOD Workshop]]'', at [http://www.ausbiotech2009.com.au/bia/bia-home Bioinformatics Australia 2009 (BA2009)], Melbourne, Australia, October 2009
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* ''Visualizing Next Generation Sequence Data with GBrowse and SAMtools'', poster at [http://www.ausbiotech2009.com.au/bia/bia-home Bioinformatics Australia 2009 (BA2009)], Melbourne, Australia, October 2009
  
* [http://dx.doi.org/10.1093/nar/gkj086 The Zebrafish Information Network: the zebrafish model organism database]; in ''[http://nar.oxfordjournals.org/ 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.
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* ''[ftp://ftp.gmod.org/pub/gmod/Meetings/2009/August/Aug2009NGSinGBrowse.pdf Visualising NGS Data in GBrowse 2]'', presentation at [[August 2009 GMOD Meeting]], Oxford, UK, August 2009.
  
* [http://dx.doi.org/10.1093/nar/gkg027 The Zebrafish Information Network (ZFIN): the zebrafish model organism database]; in [http://nar.oxfordjournals.org/ ''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.
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* [[Media:AGA NGS 2009.pdf|''Seeing the forest ''and'' the trees: visualizing next generation sequence data'']], presentation at  [http://www.regonline.com/Nextgeneration Next Generation Genome Analysis in Non-Model Organisms], University of Connecticut, June 2009
  
* [http://dx.doi.org/10.1093/nar/29.1.87 The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research]; in ''[http://nar.oxfordjournals.org/ 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.)
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* ''[[Media:GMODGBrowseSMBE2009.pdf|Using GMOD for evolutionary genomics and next generation sequence data]]'', presentation as a part of ''[http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 Database Tools for Evolutionary Genomics: An introduction to GMOD software for managing, annotating and visualizing genomic data]'' workshop at [http://ccg.biology.uiowa.edu/smbe/ SMBE 2009], Iowa City, IA.
  
* [http://www.jair.org/papers/paper561.html Squeaky Wheel Optimization]; in ''[http://www.jair.org/ Journal of Artificial Intelligence Research]'', 10, 353-373 (May 1999);  [http://www.seattleu.edu/scieng/comsci/Fac_Staff/Joslin/joslin_pg.asp D. Joslin] and D. Clements.  This material was covered in less detail in [http://www.cs.uoregon.edu/~clements/squeakyAaai.ps Squeaky Wheel Optimization]; in ''Proceedings of the [http://www.aaai.org/Conferences/AAAI/aaai98.php 15th National Conference on Artificial Intelligence (AAAI-98)]''.
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* ''[[Media:NGSWithGMODWorkshop.pdf|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.
  
* [http://www.cs.uoregon.edu/~clements/cyclic.ps Cyclic Scheduling]; in ''Proceedings of the [http://www.ijcai.org/past/ijcai-99/ 16th International Joint Conference on Artificial Intelligence (IJCAI-99)]'', D. Draper, A. Jonsson, D. Clements, and [http://www.seattleu.edu/scieng/comsci/Fac_Staff/Joslin/joslin_pg.asp D. Joslin].
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* ''[[GBrowse syn PAG 2009 Workshop|Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your syntenic data with GBrowse_syn]]'', workshop with [[User:Mckays|Sheldon McKay]] and [[User:Scott|Scott Cain]] at [[PAG 2009]], January 2009.
  
* [http://www.cs.uoregon.edu/~clements/hopt.ps Heuristic Optimization: A hybrid AI/OR approach.'] at ''Workshop on Industrial Constraint-Directed Scheduling'', held in conjunction with [http://www.mpi-inf.mpg.de/conferences/CP97/ CP'97], Schloss Hagenberg, Austria (1997); D. Clements, J. Crawford, [http://www.seattleu.edu/scieng/comsci/Fac_Staff/Joslin/joslin_pg.asp D. Joslin], G. Nemhauser, M. Puttlitz and M. Savelsbergh.
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* ''[[Media:PAG2009NextGenSeqPoster.pdf‎|Managing Next Generation Sequence Data with GMOD]], poster with [[User:Scott|Scott Cain]], Paul Hohenlohe, Nicholas Stiffler, Eric Johnson, and William Cresko, at [[PAG 2009]], January 2009.
  
* [http://www.cs.uoregon.edu/~clements/myriad.ps Myriad: Design and Implementation of a Federated Database Prototype]; in ''[http://www3.interscience.wiley.com/journal/112769988/home Software - Practice and Experience],'' 25(5), 533-562 (May 1995); E.P. Lim, S.Y. Hwang, J. Srivastava, D. Clements and M. Ganesh.
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* ''[[Media:ISMB2008PosterManagingGenomicData.pdf|GMOD: Managing genomic data from emerging model organisms]]'', poster with Hilmar Lapp and Todd Vision at [http://www.iscb.org/ismb2008/ ISMB 2008], July 2008.
  
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* ''[[Media:GenomicsResourcesForEmergingModelOrganismsPoster.pdf|GMOD: Genomics Resources for Emerging Model Organisms]]'', poster with Hilmar Lapp and Todd Vision at [http://www.agasymposium2008.org/ American Genetic Association Annual Symposium], upcoming, June 2008.
  
== Presentations, Tutorials, Workshops, Demos and Posters ==
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* ''[[Media:ChadoWorkshopArthopod2008.pdf|Chado - A Database Schema for Integrating Biological Data]]'', workshop with [[User:Scott|Scott Cain]] at the [http://www.k-state.edu/agc/symposium.shtml 2nd Annual Arthropod Genomics Symposium], April 2008.
  
* Workshop: ''Chado - A Database Schema for Integrating Biological Data'', with [[User:Scott|Scott Cain]] at the [http://www.k-state.edu/agc/symposium.shtml 2nd Annual Arthropod Genomics Symposium], 2008. (Upcoming)
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* ''[[Media:DatabaseResourcesForEmergingModelOrganismsPoster.pdf|GMOD: Database Resources for Emerging Model Organisms]]'', poster with Hilmar Lapp and Todd Vision at the [http://www.k-state.edu/agc/symposium.shtml 2nd Annual Arthropod Genomics Symposium], April 2008.
  
* Poster: ''GMOD: Database Resources for Emerging Model Organisms'', with Hilmar Lapp and Todd Vision at the [http://www.k-state.edu/agc/symposium.shtml 2nd Annual Arthropod Genomics Symposium], 2008(Upcoming)
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* ''[[Media:GMODToolsForComparativeGenomicsIGERTPoster.pdf|GMOD Tools for Comparative Genomics]]'', poster with, David Riley, [[User:Faga|Ben Faga]], Hervé Tettelin, Sam Angiuoli, and Jonathan Crabtree. Presented at the [http://evodevo.uoregon.edu/symposium.html IGERT Symposium on Evolution, Development, and Genomics], April 4-6, Eugene, ORHighlights GMOD components particularly useful for [[:Category:Comparative Genomics|comparative genomics]]: [[CMap]], [[Sybil]], [[SynView]], [[SynBrowse]] and [[GBrowse_syn]].
  
* Poster: ''[[Media:2007GenomeInformaticsGMODPoster.pdf|Digesting the Genome Glut: Promoting the Use and Extension of GMOD To Emerging Model Organisms]]'', with [[User:bosborne|Brian Osborne]], Hilmar Lapp, Xianhua Liu, W. Owen McMillan, Nassib Nassar, and Todd J. Vision, at the [http://meetings.cshl.edu/meetings/info07.shtml 2007 Genome Informatics conference].  An overview of GMOD highlighting components, the new web site, and using GMOD for evolution research.
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* ''[[Media:InformaticsResourcesForEvolutionaryResearchIGERTPoster.pdf|GMOD: Informatics Resources for Evolutionary Research]], poster with Hilmar Lapp and Todd Vision. Presented at the [http://evodevo.uoregon.edu/symposium.html IGERT Symposium on Evolution, Development, and Genomics], April 4-6, 2008, in Eugene ORHighlights GMOD tools particularly useful for [[:Category:Evolution|evolutionary]] research: [[GBrowse]], [[Apollo]], [[Pathway Tools]], and [[Chado]].
  
* Presentation: ''[[Media:GeneExpressionIWhenWhere.ppt|Gene Expression Databases: Where and When]]'', at [http://nescent.org 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.
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* ''[[Media:2007GenomeInformaticsGMODPoster.pdf|Digesting the Genome Glut: Promoting the Use and Extension of GMOD To Emerging Model Organisms]]'', poster with [[User:bosborne|Brian Osborne]], Hilmar Lapp, Xianhua Liu, W. Owen McMillan, Nassib Nassar, and Todd J. Vision, at the [http://meetings.cshl.edu/meetings/info07.shtml 2007 Genome Informatics conference]An overview of GMOD highlighting components, the new web site, and using GMOD for evolution research.
  
* Demonstration: ''Worldwide Aeronautical Route Planner'', with Charles B. McVey, and [http://www.cs.nott.ac.uk/~ajp/ Andrew J. Parkes] at the [http://www.aaai.org/Conferences/AAAI/aaai99.php 16th National Conference on Artificial Intelligence (AAAI-99)].
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* ''[[Media:GeneExpressionIWhenWhere.ppt|Gene Expression Databases: Where and When]]'', presentation given at [http://nescent.org 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.
  
* Demonstration: ''Squeaky Wheel Optimization'', with [http://www.seattleu.edu/scieng/comsci/Fac_Staff/Joslin/joslin_pg.asp David Joslin] at the [http://www.aaai.org/Conferences/AAAI/aaai98.php 15th National Conference on Artificial Intelligence (AAAI-98)].
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[[Category:Galaxy]]

Latest revision as of 21:39, 31 December 2018

Dave Clements

Dave Clements looking cheeky


I work on the Galaxy Project for Johns Hopkins 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. From 2013-2018 I telecommuted from the Toomey Lab in the Department of Earth Sciences at the University of Oregon. From 2007 through 2012 I telecommuted from the Phillips Lab in the Center for Ecology and Evolutionary Biology (CEEB), also at Oregon.

Contact Details

E-mail clements@galaxyprojet.org
URL My home page

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

Publications

See the current list at my Galaxy home page.


GMOD Era Presentations, Tutorials, Workshops, Demos and Posters

Work done during my time at GMOD. See my Galaxy home page for other presentations.

  • 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.