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. I'm also hoping to touch the (Python!) code.

Prior to working on Galaxy I ran the 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. From 2007 through 2012 I telecommuted from the Phillips and Cresko Labs in the Institute of Ecology and Evolution (IE2) at the University of Oregon. (That was the first time I got to stay in the same office while changing employers!) Since 2013 I have telecommuted from the Toomey Lab in the Department of Geological Sciences, also at the University of Oregon.

Details

E-mail clements AT galaxyproject DOT org
ORCID ID orcid.org/0000-0002-9970-6657

Background

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

Prior to working on Galaxy, and for NESCent and http://gmod.org/wiki/|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

Organizer

2010's

2000's

Presentations, Tutorials, Workshops, Demos and Posters

2016

Date Topic/Event Venue/Location Links
August 9-10 Introduction to Galaxy Workflows Workflows Workshop, Distributed Slides
August 1-4 Integrating Ontological and Genomic Analysis with Galaxy Workshop ICBO 2016, Corvallis, Oregon, United States Tutorial, Slides
July 21 Introduction to Galaxy Cornell University, Ithaca, New York, United States Slides
July 19-20 Introduction to Galaxy University of Rochester, Rochester, New York, United States Slides
July 13-17 An Introduction to Using Galaxy for Genetic Data Analysis The Allied Genetics Conference 2016 (TAGC), Orlando, Florida, United States Slides, Tutorial
April 20 Galaxy Update BUG, Oregon State University, Corvallis, Oregon, United States
February 20-23 (SW4) The Galaxy Platform for Multi-Omic Data Analysis and Informatics ABRF 2016, Fort Lauderdale, Florida, United States
January 21, 22 Introduction to Galaxy Workshop Icahn School of Medicine at Mt. Sinai, New York, New York, United States Slides
January 13 Galaxy Community Update Plant and Animal Genome XXIV (PAG 2016), San Diego, California, United States Slides
January 12 Galaxy for SNP and Variant Data Analysis Plant and Animal Genome XXIV (PAG 2016), San Diego, California, United States Slides

2015

Date Topic/Event Venue/Location Links
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

2014

Date Topic/Event Venue/Location Links
December 12 Introduction to Galaxy Workshop Virginia State University, Petersburg, Virginia, United States Slides
October 21 Galaxy: Accessible and Reproducible Data Analysis for Bench Scientists Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States Slides
July 28 - August 1 Workshop: DNA Sequence Bioinformatics Analysis with the Galaxy Platform University of São Paulo (USP), São Paulo, Brazil Slides
June 30 - July 2 P26: Galaxy Training Network 2014 Galaxy Community Conference (GCC2014), Baltimore, Maryland, United States Poster
May 13 Galaxy Workshop Institute of Genetics and Molecular Medicine (IGMM), Edinburgh, UK Sides
May 12 Galaxy Workshop University of Edinburgh, Edinburgh, UK Galaxy Sides, Edinburgh Genomics Sides
Galaxy Project Update 5th Edinburgh Bioinformatics Meeting, University of Edinburgh, Edinburgh, UK Sides
May 9 Introduction to Galaxy Workshop The Genome Analysis Centre (TGAC), Norwich, United Kingdom Slides
May 6-7 Scaling Galaxy for Big Data NGS Data after the Gold Rush, TGAC, Norwich, United Kingdom Slides
March 7 Galaxy Workshop University of Georgia, Athens, Georgia, United States Slides
February 26-28 GMOD Malaysia 2014 Kuala Lumpur, Malaysia Slides
January 16-17 Galaxy Project Update 2014 GMOD Meeting, San Diego, California, United States Slides
January 11-15 Galaxy for NGS Data Analysis: A Hands-on Computer Demo
with Anushka Brownley
Plant and Animal Genome XXII (PAG 2014), San Diego, California, United States Slides
Galaxy Cloudman: A Gentle Introduction to Data Analysis on the Cloud
Part of the GMOD Workshop
Slides

2013

Date Topic/Event Venue/Location Links
October 21-25 NGS Data Analysis and Galaxy Workshop
University of Cape Town
2013 South Africa Galaxy Workshop Tour Slides
October 14-18 NGS Data Analysis and Galaxy Workshop
University of Pretoria
2013 South Africa Galaxy Workshop Tour Slides
July 18-23 Introduction to Galaxy Workshop
National Institute of Environmental Health Sciences (NIEHS)
2013 Research Triangle Workshop Tour, North Carolina, United States Slides
Introduction to Galaxy Workshop
University of North Carolina, Chapel Hill
Slides
Galaxy Installation Tutorial
Introduction to Galaxy Workshop
North Carolina State University
Slides
June 20-22 W1: Next-generation sequencing data analysis with GenomeSpace and Galaxy FGED Conference, Seattle, Washington Slides
April 29 - May 2 Introduction to Galaxy Workshops Washington University in St. Louis Slides
Saint Louis University Slides
University of Missouri Columbia Slides
April 12 Transparent, accessible, reproducible analysis with Galaxy The Genome Analysis Centre, Norwich, United Kingdom Slides
April 11 Introduction to Galaxy Workshop Slides
April 7-10 GO Galaxy Workshop, with Chris Mungall Biocuration 2013, Cambridge, United Kingdom Galaxy Intro slides, GO Galaxy Slides
April 5-6 Galaxy Project Update 2013 GMOD Meeting, Cambridge, United Kingdom, immediately prior to Biocuration 2013 Slides
Community Building and Support Slides
Installing Galaxy on the Cloud Workshop Tutorial
March 5 Galaxy for Biologists Caltech, Pasadena, California, United States Slides
March 2-5 Accessible, Transparent and Reproducible Analysis With Galaxy, part of Galaxy for Core Facilities, part of ABRF 2013
Palm Springs, California, United States
SW1 Workshop slides, W6 Workshop slides
Febrary 4 & 5 Introduction to Galaxy Workshop, with Mo Heydarian Johns Hopkins University, Baltimore, Maryland, United States Slides

2012

2011

2010

2009

2008

2007 and Before