CAMI + M3 Workshop May 7-8 2017, Washington D.C.

We ​enthusiastically ​​invite ​​you ​​to ​​attend ​​you ​a ​​joint ​​CAMI ​​(Critical ​​Assessment ​​of ​​Metagenomic ​​Interpretation) ​​and ​​Spring ​2017 ​M3 ​​(Mid-Atlantic ​​Microbiome ​​Meetup) ​​workshop. ​The ​overarching ​theme ​of ​this ​workshop ​ ​will ​be ​assessment ​and ​standards ​for ​metagenome ​interpretation, ​with ​special ​focus ​on ​long ​reads ​and ​strain ​level ​evaluation. ​This ​joint ​workshop ​will ​take ​place ​on ​Sunday, ​May ​7th ​and ​Monday, ​May ​8th 2017 ​at ​the ​University ​of ​Maryland ​College ​Park, ​and ​will ​be ​preceded ​by ​a ​3-day ​CAMI2 ​hackathon ​taking ​place ​from ​Wednesday, ​May ​3rd ​through ​Friday ​May ​5th ​(hosted ​at ​CBCB, ​University ​of ​Maryland ​College ​Park).

  • CAMI Workshop: 11am-7pm, Sunday, May 7th (2203K, STAMP, University of Maryland College Park)
  • M3 Workshop: 9am-4pm, Monday, May 8th (Colony Ballroom, STAMP, University of Maryland College Park)

How to register for the CAMI+Spring 2017 M3 event:

  • Website:
  • Fees (includes lunch, coffee, snacks, and conference materials):
    • CAMI Workshop (Sunday, May 7th): $50
    • M3 Workshop (Monday, May 8th): $50



Workshop Day 1 (Sunday, May 7th 2017) – CAMI 2 Workshop  

10:30 to 11:00 Registration & Coffee (Juan Jimenez room 2208)

11:00 to 11:10 CAMI Welcome (STAMP, Charles Carrol room 2203)

  (Alice McHardy, Helmholtz Centre for Infection Research)

11:10 to 11:40 CAMI 1 recap and lessons learned

         (Alice McHardy, Helmholtz Centre for Infection Research; Alex Sczyrba, Bielefeld University)

11:40 to 12:40 Updates from Hackathon

11:40 to 12:00 “Emerging sequencing technologies” 

                           (Andreas Bremges, Helmholtz Centre for Infection Research)

 12:00 to 12:20 “Challenges in evaluating strain level resolution”

                           (Adrian Fritz, Helmholtz Centre for Infection Research)

 12:20 to 12:40 “Binning evaluation as part of analysis pipelines”

                            (Fernando Meyer, Helmholtz Centre for Infection Research)

12:40 to 13:25 Lunch (Juan Jimenez room 2208)

13:25 to 13:45 “Bioboxes overview and discussion”

   (Peter Belmann, Bielefeld University)

13:45 to 16:00 CAMI 2 kick-off

13:45 to 14:00 Short CAMI 2 roadmap

           (Alice McHardy)

14:00 to 14:45 CAMI 2 – discussing datasets

                  (Group discussion)

14:45 to 15:00 Coffee break

                         (Juan Jimenez room 2208)

15:00 to 16:00 CAMI 2 – discussing challenges and performance metrics

                         (Group discussion)

16:00 to 17:00 “Perspectives on prediction – keeping the goals in sight”  

    (CAMI Keynote, Fiona Brinkman, Simon Fraser University)

17:00 to 17:10 Break

17:10 to 17:30 “Supercomputing Resources for Open, Accessible, Reproducible Genomic Analysis”

                          (Phil Blood, Pittsburgh Supercomputing Center)

17:30 to 18:30 Activities with working groups

           (Alex Sczyrba)

18:30 to 20:30 Welcome reception and Poster session (Juan Jimenez room 2208)



Workshop Day 2 (Monday May 8th 2017) – M3 

8:30 to  9:00  Registration (STAMP, Colony Ballroom room 2203)

9:00 to  9:10  M3 Welcome

  (Todd Treangen, University of Maryland College Park)

9:10 to 10:10 “Identifying the micro from the peta: tales of big data in the micro world”  

  (M3 Keynote, Nikos Kyrpides, JGI)

10:10 to 10:20 Coffee break

10:20 to 10:50 “Standards for Microbiome and Metagenomic Measurements: Supporting the Commercial Translation of Microbiome Science”

     (Scott Jackson, NIST)

10:50 to 12:00 Lightning talk session

10:50 to 11:00 “Enhancing metagenomics classification in Kraken with unique k-mer counts”

                          (Florian Breitwieser, Johns Hopkins University)

11:00 to 11:10 “MinHash techniques for scalable compositional analyses”

                                  (Sergey Koren, NHGRI/NIH)

11:10 to 11:20 “Past, present and future of metaSPAdes metagenomic assembler”

                          (Sergey Nurk, Saint-Petersburg State University)

11:20 to 11:25 Q&A

11:25 to 11:35 “Democratizing shotgun metagenomics with leaderboard sequencing”

                         (John Sanders, University of California San Diego)

11:35 to 11:45 “Strain-Level Discrimination of Shiga Toxin-Producing Escherichia coli in the Spinach Microbiome”

                           (Susan Leonard, US FDA)

11:45 to 11:55 “Bacterial and viral interactions within the oral cavity of tobacco-users”

                          (Jess Chopyk, University of Maryland College Park)

11:55 to 12:00 Q&A

12:00 to 12:30 Lunch (provided)

12:30 to 15:00 M3 breakout session: Software tool workshop/hands-on-training

12:30 to 13:30 “Metagenome assembly and validation”

                            (Mihai Pop, Todd Treangen, University of Maryland College Park)

13:30 to 13:45 Break

13:45 to 15:00 “Phylogenetic methods for taxonomic profiling”

                           (Siavash Mirarab, University of California San Diego)

15:00 to 15:15 Afternoon coffee & Tea

15:15 to 15:45 “Challenges and recent approaches in viral metagenomics”

   (Thomas Rattei, University of Vienna)

15:45 to 16:00 CAMI-M3 Closing Comments

           (Alice McHardyMihai Pop)