Topics » Microbiome Analysis in the Cloud

Human Microbiome Project

Training Workshop:
Microbiome Analysis in the Cloud

June 15-16, 2017

Application Deadline: May 15, 2017

This is an advanced interactive workshop from leaders in the field of microbiome analysis. It will provide hands-on training in accessing cloud-based Human Microbiome Project data and utilizing Docker-based workflows to perform metagenome shotgun and 16S sequence analysis. Open source tools (e.g., HUMAnN, Qiime, MetaViz) will be utilized for multiple types of analyses including metabolic profiling, phylogenetic profiling, assembly, annotation, and data visualization. Attendees will leave the workshop with practical experience using a freely available Docker image they can take home and share with others or apply to their own studies.

The workshop will cover two main types of microbiome studies: 16S analysis and whole metagenome shotgun analysis.

Presenters and Organizers*:

  • Owen White, University of Maryland School of Medicine
  • Mihai Pop, University of Maryland College Park
  • Rob Knight, University of California San Diego
  • Curtis Huttenhower, Harvard University
  • Greg Caporaso, Northern Arizona University
  • Nicola Segata, University of Trento, Italy
  • Hector Corrada Bravo, University of Maryland College Park

* Some presenters will be joining the workshop remotely

The workshop will cover two main types of microbiome studies: 16S analysis and whole metagenome shotgun analysis. Sessions will be a combination of lecture and hands-on exercises. All attendees will need to bring a laptop for use during the workshop. Lunch and continental breakfast will be provided both days. The preliminary schedule is:

Day 1: 9:00AM – 6:00PM

  • Introduction/Cloud computing systems 9:00 – 10:15
  • 16S analysis 10:30 – 12:30, 1:15 – 2:15
    • Qiime and Qiita
  • MetaViz visualization tool 2:15 – 3:15
  • Flash talks from developers on new areas of research 3:30 – 4:30
  • Reception/social hour 4:30 – 6:00

Day 2: 9:00AM – 4:30PM

  • Whole metagenome shotgun analysis
    • Profiling with HUMAnN2, MetaPhlAn, and StrainPhlAn 9:00 – 12:15
    • Assembly and Annotation 1:00 – 4:15
    • Conclusions and Wrap-Up 4:15 – 4:30

Target audience:
We hope to attract individuals who will maximize the impact of this workshop by returning home and passing on the knowledge gained during the training. For example, core and shared resource directors are in excellent positions to share information with the research communities they serve.  This workshop is intended for attendees with some experience in the utilization of common bioinformatic tools. Absolutely required is knowledge of how to operate comfortably in a Linux command-line environment. Some knowledge of scripting with python would be a plus, but is not required.

Application information:
To apply to attend this workshop, fill out the online application form. Applications will be reviewed, and applicants notified of acceptance decisions, on a continuing basis. Application deadline is May 15th. Space is limited to 50 attendees so apply early.

Travel subsidies:
Limited funds are available to provide travel subsidies for attendees. If you wish to apply for a travel subsidy, please indicate that on your application form.

About the data that will be used in the workshop:
The NIH Human Microbiome Project (HMP) has provided one of the broadest characterizations of the baseline human microbiome in existence, and it has served as a reference in studies of disease, microbial population diversity, biogeography, and molecular function. These data primarily come from six body sites sampled at up to three time points in a population of 265 individuals. All data have been made available as Amazon S3 public datasets ( as part of a project supported by NIH NIAID and the Common Fund. Datasets include whole metagenome shotgun and 16S sequence as well as downstream analysis products. More information about these data can be found here. It is important to note that although we will be using HMP data for the workshop, all of the tools used in the workshop are applicable to microbiome data from any source.

Date: June 15-16, 2017
Location: Institute for Genome Sciences, University of Maryland School of Medicine
801 W. Baltimore St., Baltimore, MD 21201, 1st floor

Cost: If accepted, cost to attend will be $300 (includes lunch and continental breakfast for two days as well as an evening reception), fee does NOT include lodging which attendees much arrange for separately.

Prerequisites to attend:
Experience operating on the command line in a Linux environment is mandatory for this workshop. Some experience with Python is a plus but is not required. All attendees must bring a laptop computer (not tablet) for use during the workshop. If you do not have a computer that you can bring, we have limited laptops available to borrow, but you must request this ahead of the workshop.

Travel Info

Driving Directions:
Directions can be found here. Parking is available for $9.00 per day in a garage at the corner of W. Baltimore and Poppleton, this is about 1 block from our building.

The closest airport is Baltimore Washington International Thurgood Marshall Airport (BWI). Other airports in the region (1 – 1.5 hours away) are Dulles and Reagan National.

Baltimore is served by Amtrak and MARC train service.

Local nearby hotels:

Instead of a room block, we are providing a list of nearby hotels that range in price and amenities so that attendees can choose a hotel suited to their needs.

Hampton Inn Baltimore Downtown Convention Center

Hilton Baltimore

Baltimore Marriott Inner Harbor at Camden Yards

Hyatt Regency Baltimore Inner Harbor

Sheraton Inner Harbor

Holiday Inn Baltimore Inner Harbor

Days Inn Baltimore Inner Harbor



We gratefully acknowledge the NIH for funding part of this workshop.