Welcome to the QIIME 2 FAES January, 2022 workshop
Contents
Welcome to the QIIME 2 FAES January, 2022 workshop¶
We have a lot of exciting things planned for this week!
The new QIIME 2 Galaxy interface!
New tutorial data!
Core functionality and the latest plugins and tools!
Multi-interface QIIME 2 command examples!
Jupyter Book tutorial documentation!
Important!
Please review the QIIME 2 Community Code of Conduct . All workshop instructors agree to abide by these community expectations and we hope you will too.
Workshop links and protocols¶
We recommend reading the following before you arrive¶
These aren’t essential, but they’ll help get you ready for the workshop (listed in priority order).
Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant (Taur et al. [TCS+18])
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops (Dillon et al. [DBA+21])
Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients (Liao et al. [LTC+21])
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (Bolyen et al. [BRD+19])
q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data (Bokulich et al. [BDZ+18])
Thank you to our hosts¶
Thank you to our instruction team¶
Name |
Affiliation(s) |
|---|---|
Aeriel Belk |
Joint Institute for Food Safety and Applied Nutrition, United States Food and Drug Administration and the University of Maryland, USA |
Nicholas A. Bokulich |
Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zürich, Switzerland |
Evan Bolyen |
Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA |
Emily Borsom |
Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA |
J. Gregory Caporaso |
Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA |
Colin J. Brislawn |
Contamination Source Identification / Independent Investigator, USA |
Kalen Cantrell |
University of California San Diego, USA |
Justine Debelius |
Department of Epidemiology, Johns Hopkins School of Public Health, USA; Centre for Translational Microbiome Research, Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Sweden |
Matthew Dillon |
Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA |
Mehrbod Estaki |
International Microbiome Centre (IMC), University of Calgary |
Keegan Evans |
Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA |
Marcus Fedarko |
Department of Computer Science and Engineering, University of California San Diego, USA |
Lena Floerl |
Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zürich, Switzerland |
Elizabeth Gehret |
Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA |
Chloe Herman |
Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA |
Ben Kaehler |
School of Science, University of New South Wales, Canberra, Australia |
Chris Keefe |
Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA |
Lina Kim |
Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zürich, Switzerland |
Luca Lenzi |
Centre for Genomic Research, University of Liverpool, United Kingdom |
Chen Liao |
Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA |
Huang Lin |
Biostatistics and Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), USA |
Jeff Meilander |
Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA |
Michael S. Robeson II, Ph.D. |
Department of Biomedical Informatics, University of Arkansas for Medical Sciences, USA |
Anthony Simard |
Center for Applied Microbiome Sciences, Pathogen and Microbiome Institute, Northern Arizona University, USA |
Yoshiki Vazquez-Baeza |
BiomeSense, USA |
Thank you to our funders¶
The QIIME 2 project is funded in part by:
The National Cancer Institute:
Informatics Technology for Cancer Reserach (1U24CA248454-01) to JGC
The Partnership for Native American Cancer Prevention (U54CA143925 and U54CA143924) to JGC
Chan-Zuckerberg Initiative Essential Open Source Software for Science to JGC
Jupyter Book is funded by the Alfred P. Sloan to JGC Foundation.
The preparation and dissemination of the data used in this tutorial was funded in part by the National Institutes of Health (NIH) grants U01 AI124275, R01 AI137269 and U54 CA209975 to Joao B. Xavier.
QIIME 2 was initially developed with support from the National Science Foundation (1565100) to JGC.
QIIME 2 resources¶
@qiime2 on Twitter (project announcements)