John Chilton

• Software developer on the Galaxy Project - a popular web-based platform for bioinformatics
• Lead development of workflow engine features and tool integration framework
• Contributed to multiple peer-reviewed publications on Galaxy infrastructure

• Built Web Services infrastructure enabling collaboration between University of Minnesota and Mayo Clinic (TROPIX project)
• Developed file and metadata store, analytical services, workflow engine, and Google Web Toolkit frontend
• Created secure distributed system for sharing clinical data with Groovy on Grails frontend
• Enabled secure job submissions to Windows clusters via ASP.NET Web Services (C#)
• Deployed and extended Galaxy, an open source Python framework for genomics research
• Developed complex Puppet infrastructure for deploying OpenStack cloud platform

• Involved in every stage of software life cycle for several successful projects
• TROPIX project collaboration with Mayo Clinic for bioinformatics research
• Built Web Services, workflow engines, and cloud deployment systems

• Grading, office hours, assignment design
• Leading discussions and lecturing in computer lab and classroom settings
• Taught groups ranging from 3 to 120 students

• Member of Multiple Autonomous Robotic Systems laboratory
• Worked on NASA grant to develop C++ application for mobile robot localization and mapping

• Investigated methods of promoting student learning in large college classes

• Developed program for statistical analysis of gene expression microarray data

• GPA: 4.00/4.00

• GPA: 3.99/4.00, Graduated with High Distinction
• Minors: Mathematics and Statistics

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

The Galaxy Community

Nucleic Acids Research • 2024-07 • DOI: 10.1093/nar/gkae410

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

Simon Bray, John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche, Martin Čech, Peter J.A. Cock, Björn Grüning, Anton Nekrutenko

Genome Research • 2023-02 • DOI: 10.1101/gr.276963.122

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

The Galaxy Community

Nucleic Acids Research • 2022-07 • DOI: 10.1093/nar/gkac247

GalaxyCloudRunner: enhancing scalable computing for Galaxy

Nuwan Goonasekera, Alexandru Mahmoud, John Chilton, Enis Afgan

Bioinformatics • 2021-01 • DOI: 10.1093/bioinformatics/btaa860

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

The Galaxy Community

PLOS Pathogens • 2020-08 • DOI: 10.1371/journal.ppat.1008643

Galaxy External Display Applications: closing a dataflow interoperability loop

Daniel Blankenberg, John Chilton, Nate Coraor

Nature Methods • 2020-02 • DOI: 10.1038/s41592-019-0727-x

Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges

Kyle Ellrott, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter, Bruce Hoff, James Eddy, John M. Chilton, Thomas Yu, Joshua M. Stuart, Julio Saez-Rodriguez, Gustavo Stolovitzky, Paul C. Boutros, Justin Guinney

Genome Biology • 2019-09 • DOI: 10.1186/s13059-019-1794-0

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

The Galaxy Community

Nucleic Acids Research • 2018-07 • DOI: 10.1093/nar/gky379

Community-Driven Data Analysis Training for Biology

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 Larivière, 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, James Taylor, Rolf Backofen, Anton Nekrutenko, Björn Grüning

Cell Systems • 2018-06 • DOI: 10.1016/j.cels.2018.05.012

Practical Computational Reproducibility in the Life Sciences

Björn Grüning, John Chilton, Johannes Köster, Ryan Dale, Nicola Soranzo, Marius van den Beek, Jeremy Goecks, Rolf Backofen, Anton Nekrutenko, James Taylor

Cell Systems • 2018-04 • DOI: 10.1016/j.cels.2018.03.014

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers

Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko

PLOS Computational Biology • 2017-05 • DOI: 10.1371/journal.pcbi.1005425

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

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, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, Jeremy Goecks

Nucleic Acids Research • 2016-07 • DOI: 10.1093/nar/gkw343

NCBI BLAST+ integrated into Galaxy

Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo

GigaScience • 2015-10 • DOI: 10.1186/s13742-015-0080-7

Multi-omic data analysis using Galaxy

Jorrit Boekel, John Chilton, Ira R Cooke, Peter L Horvatovich, Pratik D Jagtap, Lukas Kall, Janne Lehtio, Pieter Lukasse, Perry D Moerland, Timothy J Griffin

Nature Biotechnology • 2015-02 • DOI: 10.1038/nbt.3134

Community-driven development for computational biology at Sprints, Hackathons and Codefests

Steffen Möller, et al

BMC Bioinformatics • 2014-12 • DOI: 10.1186/1471-2105-15-S14-S7

Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory

Getiria Onsongo, Jesse Erdmann, Michael D Spears, John Chilton, Kenneth B Beckman, Adam Hauge, Sophia Yohe, Matthew Schomaker, Matthew Bower, Kevin A T Silverstein, Bharat Thyagarajan

BMC Research Notes • 2014-05 • DOI: 10.1186/1756-0500-7-314

CLIA-certified next-generation sequencing analysis in the cloud

The Whole Galaxy Team at MSI, Ying Zhang, Jesse Erdmann, John Chilton, Getiria Onsongo, Matthew Bower, Kenny Beckman, Bharat Thyagarajan, Kevin Silverstein, Anne-Francoise Lamblin

BMC Proceedings • 2012-08 • DOI: 10.1186/1753-6561-6-S6-P54

Workflow for analysis of high mass accuracy salivary dataset using MaxQuant and ProteinPilot search algorithm

Pratik Jagtap, Sricharan Bandhakavi, LeeAnn Higgins, Thomas McGowan, Rongxiao Sa, Matthew Stone, John Chilton, Edgar Arriaga, Sean Seymour, Tim Griffin

Proteomics • 2012-06

Minnesota Congenital Heart Network: Construction and Implementation of an Interoperable Standards-Based Information Model

Robert R. Freimuth, Michael Meiners, John Chilton, Jim Johnson, Benjamin Lynch, Genevieve Melton, Sheri Crow

AMIA 2010 Annual Symposium • 2010-10

LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments

Getiria Onsongo, Matthew Stone, Susan Van Riper, John Chilton, B. Wu, LeeAnn Higgins, T. Lund, John Carlis, Tim Griffin

Proteomics • 2010-08 • DOI: 10.1002/pmic.201000189

Rapidly Bringing Software to Biologists with Galaxy and Docker

John Chilton, Björn Grüning, Eric Rasche, the Galaxy Team

Biological Data Science, Cold Spring Harbor, NY • 2014-11

Building More Powerful Galaxy Workflows with Dataset Collections

John Chilton, the Galaxy Team

2014 Galaxy Community Conference, Baltimore, MD • 2014-07

Galaxy as an Extensible Job Execution Platform

John Chilton, the Galaxy Team

15th Annual Bioinformatics Open Source Conference, Boston, MA • 2013-07

Open Source Configuration of Bioinformatics Infrastructure

John Chilton, Pratik Jagtap, Benjamin Lynch, Brad Chapman, Timothy Griffin

14th Annual Bioinformatics Open Source Conference, Berlin, Germany • 2013-07

Innovative, Reproducible MS-based Proteomic Informatics in the Cloud for Emerging Applications with Galaxy-P and CloudBioLinux

John Chilton, James Johnson, Ebbing de Jong, Getiria Onsongo, Benjamin J. Lynch, Pratik D. Jagtap, Timothy J Griffin

2nd Mass Spectrometry Special Interest Group (MS-SIG), Berlin, Germany • 2013-07

Galaxy-P: Beyond Proteomics

John Chilton, James Johnson, Getiria Onsongo, Ebbing de Jong, Pratik Jagtap, Timothy Griffin

2013 Galaxy Community Conference, Oslo, Norway • 2013-07

Creating Cooperative Competition: Learning Games for the Classroom

Maria Gini, John Chilton, Murray Jensen

Academy of Distinguished Teachers Conference, Minneapolis, MN • 2007-04

Using the AIBOs in a CS1 Course

John Chilton, Maria Gini

AAAI Spring Symposium - Robots and Robot Venues, Palo Alto, CA • 2007-03

Learning Games: Creating Cooperative Competition

John Chilton, Maria Gini

Collaboration for the Advancement of College Teaching and Learning, Bloomington, MN • 2006-11

University of Minnesota

University of Minnesota

University of Minnesota

• Awarded to top three IT teaching assistants as voted by students

UMN Department of Computer Science and Engineering