I am a Community Manager for the Galaxy Project at Johns Hopkins University (and formerly at Emory University). I organize meetings and courses, prepare training materials, and improve Galaxy's documentation, community website, and web presence. As a community manager I am part of a team that makes sure that the Galaxy Project and the Galaxy Community are the same thing. Galaxy is its community.
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. 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.
|clements AT galaxyproject DOT org|
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.
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 operating system (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.
- Ramsey, J., McIntosh, B., Renfro, D., Aleksander, S. A., LaBonte, S., Ross, C., Zweifel, A. E., Liles, N., Farrar, S., Gill, J. J., Erill, I., Ades, S., Berardini, T. Z., Bennett, J. A., Brady, S., Britton, R., Carbon, S., Caruso, S. M., Clements, D., … Hu, J. C. (2021). Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PLOS Computational Biology, 17(10), e1009463. DOI: 10.1371/journal.pcbi.1009463
- Serrano-Solano, B., Föll, M. C., Gallardo-Alba, C., Erxleben, A., Rasche, H., Hiltemann, S., Fahrner, M., Dunning, M. J., Schulz, M. H., Scholtz, B., Clements, D., Nekrutenko, A., Batut, B., & Grüning, B. A. (2021). Fostering accessible online education using Galaxy as an e-learning platform. PLOS Computational Biology, 17(5), e1008923. DOI: 10.1371/journal.pcbi.1008923
- Ostrovsky, A., Hillman‐Jackson, J., Bouvier, D., Clements, D., Afgan, E., Blankenberg, D., Schatz, M. C., Nekrutenko, A., Taylor, J., Team, the G., & Lariviere, D. (2021). Using Galaxy to Perform Large-Scale Interactive Data Analyses—An Update. Current Protocols, 1(2), e31. DOI: 10.1002/cpz1.31
- Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. DOI: 10.1093/nar/gkaa434
- Tekman, M., Batut, B., Ostrovsky, A., Antoniewski, C., Clements, D., Ramirez, F., Etherington, G. J., Hotz, H.-R., Scholtalbers, J., Manning, J. R., Bellenger, L., Doyle, M. A., Heydarian, M., Huang, N., Soranzo, N., Moreno, P., Mautner, S., Papatheodorou, I., Nekrutenko, A., … Grüning, B. (2020). A single-cell RNA-sequencing training and analysis suite using the Galaxy framework. GigaScience, 9(10). DOI: 10.1093/gigascience/giaa102
- Jalili, V., Clements, D., Gruning, B., Blankenberg, D., & Goecks, J. (2020). Adding software to package management systems can increase their citation by 280%. BioRxiv, 2020.11.16.385211. DOI: 10.1101/2020.11.16.385211
- Afgan, E., Baker, D., Batut, B., van den Beek, M., Bouvier, D., Čech, M., Chilton, J., Clements, D., Coraor, N., Grüning, B. A., Guerler, A., Hillman-Jackson, J., Hiltemann, S., Jalili, V., Rasche, H., Soranzo, N., Goecks, J., Taylor, J., Nekrutenko, A., & Blankenberg, D. (2018). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Research, 46(W1), W537–W544. DOI: 10.1093/nar/gky379
- Batut, B., Hiltemann, S., Bagnacani, A., Baker, D., Bhardwaj, V., Blank, C., Bretaudeau, A., Brillet-Guéguen, L., Čech, M., Chilton, J., Clements, D., Doppelt-Azeroual, O., Erxleben, A., Freeberg, M. A., Gladman, S., Hoogstrate, Y., Hotz, H.-R., Houwaart, T., Jagtap, P., … Grüning, B. (2018). Community-Driven Data Analysis Training for Biology. Cell Systems, 6(6), 752-758.e1. DOI: 10.1016/j.cels.2018.05.012
- Afgan, E., Baker, D., van den Beek, M., Blankenberg, D., Bouvier, D., Čech, M., Chilton, J., Clements, D., Coraor, N., Eberhard, C., Grüning, B., Guerler, A., Hillman-Jackson, J., Von Kuster, G., Rasche, E., Soranzo, N., Turaga, N., Taylor, J., Nekrutenko, A., & Goecks, J. (2016). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. DOI: 10.1093/nar/gkw343
- Hillman-Jackson, J., Clements, D., Blankenberg, D., Taylor, J., Nekrutenko, A., & Team, G. (2012). Using Galaxy to Perform Large-Scale Interactive Data Analyses. Current Protocols in Bioinformatics, Chapter 10. DOI: 10.1002/0471250953.bi1005s38
- Goecks, J., Li, K., Clements, D., & Taylor, J. (2011). The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool. Biological Data Visualization (BioVis), 2011 IEEE Symposium On, 39–46. DOI: 10.1109/biovis.2011.6094046
- Bolser, D. M., Chibon, P. Y., Palopoli, N., Gong, S., Jacob, D., Del Angel, V. D., Swan, D., Bassi, S., González, V., Suravajhala, P., Hwang, S., Romano, P., Edwards, R., Bishop, B., Eargle, J., Shtatland, T., Provart, N. J., Clements, D., Renfro, D. P., Bhak, D., … Bhak, J. (2012). MetaBase--the wiki-database of biological databases. Nucleic Acids Research, 40(Database issue), D1250–D1254. DOI: 10.1093/nar/gkr1099
- Jung, S., Menda, N., Redmond, S., Buels, R. M., Friesen, M., Bendana, Y., Sanderson, L. A., Lapp, H., Lee, T., MacCallum, B., Bett, K. E., Cain, S., Clements, D., Mueller, L. A., & Main, D. (2011). The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data. Database : the Journal of Biological Databases and Curation, 2011, bar051. DOI: 10.1093/database/bar051
- Raciti, D., Reggiani, L., Geffers, L., Jiang, Q., Bacchion, F., Subrizi, A. E., Clements, D., Tindal, C., Davidson, D. R., Kaissling, B., & Brändli, A. W. (2008). Organization of the pronephric kidney revealed by large-scale gene expression mapping. Genome Biology, 9(5), R84. DOI: 10.1186/gb-2008-9-5-r84
- Little, M. H., Brennan, J., Georgas, K., Davies, J. A., Davidson, D. R., Baldock, R. A., Beverdam, A., Bertram, J. F., Capel, B., Chiu, H. S., Clements, D., Cullen-McEwen, L., Fleming, J., Gilbert, T., Herzlinger, D., Houghton, D., Kaufman, M. H., Kleymenova, E., Koopman, P. A., Lewis, A. G., … Yu, J. (2007). A high-resolution anatomical ontology of the developing murine genitourinary tract. Gene Expression Patterns : GEP, 7(6), 680–699. DOI: 10.1016/j.modgep.2007.03.002
- 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., & Westerfield, M. (2006). The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Research, 34(Database issue), D581–D585. DOI: 10.1093/nar/gkj086
- Sprague, J., Clements, D., Conlin, T., Edwards, P., Frazer, K., Schaper, K., Segerdell, E., Song, P., Sprunger, B., & Westerfield, M. (2003). The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Research, 31(1), 241–243. DOI: 10.1093/nar/gkg027
- Sprague, J., Doerry, E., Douglas, S., & Westerfield, M. (2001). The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research. Nucleic Acids Research, 29(1), 87–90. DOI: 10.1093/nar/29.1.87
- McVey, C. B., Clements, D. P., Massey, B. C., & Parkes, A. J. (1999). Worldwide Aeronautical Route Planner. AAAI-99 Proceedings, 3.
- Draper, D. L., Jonsson, A. K., Clements, D. P., & Joslin, D. E. (1999). Cyclic scheduling. Proceedings of the 16th International Joint Conference on Artificial Intelligence - Volume 2, 1016–1021.
- Joslin, D. E., & Clements, D. P. (1999). Squeaky Wheel Optimization. Journal of Artificial Intelligence Research, 10, 353–373. DOI: 10.1613/jair.561
- Clements, D, Crawford, J., Joslin, D., Nemhauser, G., Puttlitz, M., & Savelsbergh, M. (1997). Heuristic Optimization: A hybrid AI/OR approach. Workshop on Industrial Constraint-Directed Scheduling held in conjunction with Constraint Programming 97 (CP-97).
- Lim, E.-P., Hwang, S.-Y., Srivastava, J., Clements, D., & Ganesh, M. (1995). Myriad: Design and implementation of a federated database prototype. Software: Practice and Experience, 25(5), 533–562. DOI: 10.1002/spe.4380250505
- 2022 Galaxy Community Conference, July 17-23, 2022, Minneapolis, Minnesota, United States
- Informatics Technology for Cancer Research (ITCR) Training & Outreach Working Group, Chair, September 2021-present, Monthly, Online, United States
- Galaxy Resources Webinar Series, Spring 2021, Online, Global
- 2021 Galaxy Community Conference, June 28-July 10, 2021, Online, Global
- Galaxy Papercuts CoFest Days, October 2020-present, Monthly, Online, Global
- 2020 Bioinformatics Community Conference, July 18-25, 2020, Online, Global
- 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
- 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
- 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
- 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 Europe 2010, September 13-16, 2010, Cambridge, United Kingdom
- GMOD Tools for Evolutionary Biology Hackathon, November 8-12, 2010, Durham, North Carolina, United States
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
- Galaxy: A global ecosystem for data intensive science, Pre-Conference Workshop on Galaxy Community, Tools and Workflows for Cheminformatics and NGS Data; Inbix2021 : Indian Conference on Bioinformatics 2021, Online, India. November 9, 2021.
- Resources and Communities for Outreach and Training, ITCR Training and Outreach Working Group, Online, United States. Video, Slides. September 9, 2021.
- Introduction to Sequencing, Assembly, and Galaxy on AnVIL, Virtual Applied Data Science Training Institute (VADSTI), Online, Howard University, Washington DC, United States. Video. April 23 2021.
- Galaxy Resources for Researchers, Galaxy Resources Webinar Series, Online, Global. Video, Slides. April 21, 2021.
- Your First Galaxy Analysis, GTN Smörgåsbord: A Global Galaxy Course, Online, Global. Video, Slides, Tutiorial. February 15, 2021.
- GWAS Analysis with Galaxy on the Analysis Visualization Integrated Lab-space (AnVIL), ASHG 2020, Online, United States. Tutorial (only open to ASHG members).October 27, 2020.
- Galaxy for Immunological and Infectious Disease Research, NIAID Webinar, Online, United States. Slides. September 4, 2029.
- Webinar: Using the new Galaxy-SRA Connection, Online, United States. Slides, Video. June 24.
- Galaxy Project: Enabling an active global research community, SGCI Webinar Series, Online, North America. Slides, Video. May 13 2020.
- Using the Galaxy Training Network tutorial library for bioinformatics training programs, ABRF 2020 pre-conference workshop, Palm Springs, California, United States. Poster. March 2, 2020.
- Single Cell RNA-Seq and Visualization Using the Galaxy Workbench, ABRF 2020 pre-conference workshop, Palm Springs, California, United States. February 29, 2021.
- The Path from Galaxy Team to Galaxy Community, NCI ITCR Training and Outreach Working Group, Online, United States. Slides, February 13, 2020.
- Introduction to Galaxy and the Galaxy Ecosystem, Plant and Animal Genome XXVIII, San Diego, California, United States. Slides. January 14, 2020.
- Galaxy Demo: Genomic Selection and Genome Wide Association Study (GWAS) Analysis with Excellence in Breeding Tools, Plant and Animal Genome XXVIII, San Diego, California, United States. History. January 14, 2020.
- Galaxy: A Global Platform & Community for Life Science Data Integration & Analysis, Plant and Animal Genome XXVIII, San Diego, California, United States. Poster. January 13, 2020
(Before 2020, my formatting here is a bit chaotic.)
- Galaxy for Genomics-enabled Breeding, GOBii Project, Monthly meeting, Online, Global. Slides, Video. December 16, 2019
- Genomic data science with the Galaxy workbench, 2019 SACNAS, Honolulu, Hawai'i, United States. October 30, 2019.
- Reproducible Genomic Data Analysis with the Galaxy Workbench, AISES 2019, Milwaukee, Wisconsin, United States. October 11, 2019.
- Plenary Panel: Effective Checklists for Developers and Researchers to Gather Requirements for Science Gateways, Gateways 2019, San Diego, California, United States. September 24, 2019
- Building a regional Galaxy Community and Platform, InCoB 2019, Jakarta, Indonesia. September 12, 2019
- Workshop : An introduction to the Galaxy platform for computational biology – with real-world hands-on demonstration, InCoB 2019, Jakarta, Indonesia. September 11, 2019.
- Use Galaxy, Right Now!, GCC2019, Freiburg, Germany. Slides. July 4, 2021.
- Galaxy Publication Library, GCC2019, Freiburg, Germany. Slides. July 4, 2019.
- Recent Developments in Galaxy, CGRB Spring Conference 2019, Oregon State University, Corvallis, Oregon, United States. Slides. April 19, 2019.
2018 & 2017
Are coming, the next time I need to do a biosketch.
- Introduction to Galaxy Workflows, Workflows Workshop, Distributed. Slides. August 9-10, 2016.
- Integrating Ontological and Genomic Analysis with Galaxy Workshop, ICBO 2016, Corvallis, Oregon, United States. Tutorial, Slides. August 1-4, 2016.
- Introduction to Galaxy, Cornell University, Ithaca, New York, United States. Slides. July 21, 2016.
- Introduction to Galaxy, University of Rochester, Rochester, New York, United States. Slides. July 19-20, 2016
- An Introduction to Using Galaxy for Genetic Data Analysis, The Allied Genetics Conference 2016 (TAGC), Orlando, Florida, United States. Slides, Tutorial. July 13-17, 2016.
- Galaxy Update, BUG, Oregon State University, Corvallis, Oregon, United States. April 20 , 2016.
- (SW4) The Galaxy Platform for Multi-Omic Data Analysis and Informatics, ABRF 2016, Fort Lauderdale, Florida, United States. February 20-23, 2016.
- Introduction to Galaxy Workshop, Icahn School of Medicine at Mt. Sinai, New York, New York, United States. Slides. January 21, 22, 2016.
- Galaxy Community Update, Plant and Animal Genome XXIV (PAG 2016), San Diego, California, United States. Slides. January 13, 2016.
- Galaxy for SNP and Variant Data Analysis, Plant and Animal Genome XXIV (PAG 2016), San Diego, California, United States. Slides. January 12, 2016.
|September 17-18||Utilizing the Galaxy Analysis Framework at Core Facilities||Western Association of Core Directors (WACD) Annual Meeting, Portland, Oregon, United States||Slides, Slides with notes|
|June 11-12||Introduction to Galaxy: RNA-seq and ChIP-seq data analysis Workshop||University of Cambridge, Cambridge, United Kingdom||Slides|
|June 8-9|| Introduction to Galaxy Workshop
Workshop is full, but there is a waiting list
|University of Glasgow, Glasgow, United Kingdom||Slides|
|June 6||WS02: NGS Variant Analysis with Galaxy||ESHG 2015, Glasgow, United Kingdom||Slides|
|February 27||Introduction to Galaxy||Northwestern University, Chicago, Illinois, United States||Slides|
|January 10-14||Galaxy for SNP and Variant Data Analysis||Plant and Animal Genome XXIII (PAG2014), San Diego, California, United States||Slides|
- 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 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, 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.
- 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.
- 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.
2000s and Before
- 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 2008, 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 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).