Workshop agenda

Joint CAMI-M3 workshop on metagenomic software validation

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Workshop Day 1 (Sunday, May 7th) – 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) – 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 McHardy, Mihai Pop)

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