AAI Course in Big Data Analysis in Immunology

  This course is now closed.

September 6-9, 2017
Johns Hopkins University Montgomery County Campus
Rockville, MD

With the vast amount of immunological data available, immunology research has entered the big data era. The challenge for immunologists is to transition from working with data, to obtaining knowledge that can be used to generate data-driven hypotheses. Knowledge discovery relies on both the availability of accurate and well-organized data, and proper analysis.

The AAI Course in Big Data Analysis in Immunology will provide hands-on training in specialized analysis of large immunological datasets. Topics covered include, but are not limited to: reproducibility, introduction to programming (Linux and R), high-throughput flow cytometry data analysis, RNA sequencing data analysis, downstream analysis, biological data repositories (ImmPort, Immune Epitope Database and Analysis Resource), and biological networks.

This course is taught by experienced bioinformatics experts and is suitable for participants with an intermediate or advanced understanding of the principles of immunology; laboratory experience helpful. Previous experience using Linux or R programming is helpful, but is not required.

Course attendees will need to bring their own laptops, with R Studio installed (free online). Immunological datasets will be provided for analysis during the course. Because this course offers hands-on training, space is limited to 40 attendees.

The Course in Big Data Analysis in Immunology is sponsored by The American Association of Immunologists, the largest and most prestigious association in the world for professional scientists engaged in basic and clinical immunological research.

Notice: While AAI has rented facilities from the Johns Hopkins University, AAI and any programs operated by it are not related to or affiliated with the Johns Hopkins University in any way.  AAI is an entirely separate legal entity with no connection to the Johns Hopkins University, aside from the temporary use of facility for the specified program.


Course Instructors:

R. Burke Squires, M.S.


Maarten Leerkes, Ph.D.


Ryan Dale, M.S., Ph.D.

Wednesday, September 6, 2017

  1. What are the command line, Linux, and the Bash shell?
    • Motivation
    • Installing and using the Bash shell
    • Getting to the command line
  2. Navigation, working with files, and project organization
  3. Shell scripting and Unix utilities

  *Lunch break from 12:00 to 1:00 PM (on your own)

Thursday, September 7, 2017

  1. Introduction to flow cytometry
    • Flow cytometry hardware innovation
    • The challenges of manual gating
    • The need for automation
  2. Automated flow cytometry solutions
    • Flow cytometry analysis standards
    • FlowCAP competitions
    • Review of existing automated flow cytometry tools
  3. An automated flow cytometry analysis workflow
    • Preprocessing, QA / QC and normalization
    • Automated gating
    • Cluster labeling
    • Feature extraction
    • Biological interpretations

  *Lunch break from 12:00 to 1:00 PM (on your own)

  *Coffee and tea will be served at the beginning of the morning and afternoon sessions.

Friday, September 8, 2017

  1. Introduction to RNA-Seq
    • Aspects of RNA-Seq
    • From next generation sequencing to RNA-Seq
  2. Basics of statistical analysis of RNA-Seq data
  3. RNA-Seq gene expression data analysis pipeline: methods, tools and issues
    • Data and bam file import
    • QA/QC
    • Alignment
    • Quantification and normalization
    • Differential expression analysis
  4. Visualizations
  5. Biological interpretation

  *Lunch break from 12:00 to 1:00 PM (on your own)

  *Coffee and tea will be served at the beginning of the morning and afternoon sessions.

Saturday, September 9, 2017

  1. Introduction to downstream analysis
    • Important considerations for downstream analysis
    • RNA-Seq data analysis in the context of biological networks
  2. Survey of downstream analysis tools
    • Pathway analysis, GSEA, MSigDB, DAVID, GO gene ontology, KEGG, Reactome
  3. A simple downstream analysis workflow

  *Lunch break from 12:00 to 1:00 PM (on your own)

  1. Immunological data standards
  2. Immunological data repositories
  1. Biological networks
    • Introduction to biological networks
  2. A simple biological network workflow
    • Genomic classification to identify underlying structure for classification
    • Construction of co-expression network
    • Identification of co-expression modules
    • Relation of co-expression modules to sample traits
    • Exploration of individual genes within co-expression module

  *Coffee and tea will be served at the beginning of the morning and afternoon sessions.

Registration fees include access to the course, printed course book, and hospitality events as listed in the schedule.


Member $1,400
Nonmember $1,800


Registration has closed. The course is full.

Registrants staying in the AAI room block at Hilton Garden Inn will receive complimentary shuttle service between the hotel and Johns Hopkins University Montgomery County Campus/Shady Grove Metro, and complimentary breakfast buffet each day.

Refund Policy

Refund requests will be accepted until July 28, 2017. Any registrant wishing to obtain a refund must submit a written request along with his/her confirmation number by July 28, 2017. Please send to meetings@aai.org.

A $100 non-refundable processing fee will be deducted from all refunds.

After July 28, 2017, no refunds will be issued.

Homewood Suites by Hilton Rockville

Homewood Suites by Hilton Rockville –Gaithersburg
14975 Shady Grove Road
Rockville, MD 20850

A block of rooms is available for Big Data attendees at the discounted rate of $165 plus 15% tax.

Hotel amenities included in your exclusive room rate:

  • Full, hot breakfast buffet each morning
  • Complimentary shuttle services within a 3-mile radius (including JHU – Montgomery County Campus and Shady Grove Metro)
  • Complimentary evening reception (Monday-Thursday 5-7 PM)
  • Indoor pool and fitness center

The AAI preferred room rate will be available until August 16, 2017, or until the group block is sold out, whichever comes first.

Housing Reservations now open!

Book a Room

Attendees must make their own hotel reservations. To book a room by telephone please call +1-240.507.1900 and reference the Group Code: AAI.

Course Location

Parking at Johns Hopkins University Montgomery County Campus

  • Free parking is available at Johns Hopkins University Montgomery County Campus in the lots on Broschart Road. All non-designated spaces are available for student and visitor use.

Child Policy

  • Child care services are not provided by AAI. We regret that children are not permitted entrance to the course, the pre-function and registration area, or any activities held in conjunction with the course. We suggest that you contact your hotel for referrals if you require baby-sitting services.

Disability & Special Services Information

  • If you have a disability or special need that may have an impact on your participation or attendance at the course, please contact the AAI Meeting Office at (301) 634-7399 or email meetings@aai.org. AAI cannot ensure the availability of appropriate accommodations without prior notification of need. All service animals must be accompanied by appropriate medical and veterinary documentation.

This link to the Visa Wizard is a guide to help foreign citizens understand which visa category might be appropriate for their travel to the United States: http://travel.state.gov/content/visas/english/general/visa-wizard.html.

For Attendees from Non-Participating Visa Waiver Program Countries:

To apply for a visa, please visit https://travel.state.gov/content/visas/en.html.

Visas should be applied for as early as possible and well in advance of the meeting (at least three months before the visa is needed). Information about visa wait times can be found at https://travel.state.gov/content/visas/en.html.

Be advised that you need to apply for Business Visitor Visa (B-1). The AAI Immunology Courses are comparable to a scientific meeting or workshop and will not qualify attendees for student visa status. You will be asked to name the meeting ("AAI Introductory Course in Immunology" or "AAI Advanced Course in Immunology") and explain the purpose of your visit.

NOTE: Registration refunds will not be issued after the refund deadline for any reason, including the inability to obtain a visa.

For Attendees from Participating Visa Waiver Program Countries:

In order to travel without a visa on the Visa Waiver Program, you must have authorization through the Electronic System for Travel Authorization (ESTA) prior to boarding a U.S. bound air or sea carrier. For detailed information about the Visa Waiver Program, visit https://travel.state.gov/content/visas/en/visit/visa-waiver-program.html.

Requesting an Invitation Letter

For security purposes, letters of invitation will be sent only to individuals who are registered for a course. Once your registration is complete, please contact meetings@aai.org to request a personalized letter of invitation.

© The American Association of Immunologists, Inc.
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Phone: (301) 634-7178 | Fax: (301) 634-7887