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1. Facilitating Bioinformatics Reproducibility

Author

Keefe, Christopher R., Dillon, Matthew R., Herman, Chloe, Jewell, Mary, Wood, Colin V., Bolyen, Evan, and Caporaso, J. Gregory

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving many different tools. Additionally many biologists aren't trained in how to effectively record their bioinformatics analysis steps to ensure reproducibility, so critical information is often missing. Software tools used in bioinformatics can automate provenance tracking of the results they generate, removing most barriers to bioinformatics reproducibility. Here we present an implementation of that idea, Provenance Replay, a tool for generating new executable code from results generated with the QIIME 2 bioinformatics platform, and discuss considerations for bioinformatics developers who wish to implement similar functionality in their software., Comment: 5 pages, 2 figures

Published
2023

2. Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.

Author

Dillon, Matthew R, Bolyen, Evan, Adamov, Anja, Belk, Aeriel, Borsom, Emily, Burcham, Zachary, Debelius, Justine W, Deel, Heather, Emmons, Alex, Estaki, Mehrbod, Herman, Chloe, Keefe, Christopher R, Morton, Jamie T, Oliveira, Renato RM, Sanchez, Andrew, Simard, Anthony, Vázquez-Baeza, Yoshiki, Ziemski, Michal, Miwa, Hazuki E, Kerere, Terry A, Coote, Carline, Bonneau, Richard, Knight, Rob, Oliveira, Guilherme, Gopalasingam, Piraveen, Kaehler, Benjamin D, Cope, Emily K, Metcalf, Jessica L, Robeson Ii, Michael S, Bokulich, Nicholas A, and Caporaso, J Gregory

Subjects
Humans, Computational Biology, Feedback, Microbiota, COVID-19, SARS-CoV-2, Bioinformatics, Mathematical Sciences, Biological Sciences, Information and Computing Sciences
Abstract

In October of 2020, in response to the Coronavirus Disease 2019 (COVID-19) pandemic, our team hosted our first fully online workshop teaching the QIIME 2 microbiome bioinformatics platform. We had 75 enrolled participants who joined from at least 25 different countries on 6 continents, and we had 22 instructors on 4 continents. In the 5-day workshop, participants worked hands-on with a cloud-based shared compute cluster that we deployed for this course. The event was well received, and participants provided feedback and suggestions in a postworkshop questionnaire. In January of 2021, we followed this workshop with a second fully online workshop, incorporating lessons from the first. Here, we present details on the technology and protocols that we used to run these workshops, focusing on the first workshop and then introducing changes made for the second workshop. We discuss what worked well, what didn't work well, and what we plan to do differently in future workshops.

Published
2021

3. QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

Author

Estaki, Mehrbod, Jiang, Lingjing, Bokulich, Nicholas A, McDonald, Daniel, González, Antonio, Kosciolek, Tomasz, Martino, Cameron, Zhu, Qiyun, Birmingham, Amanda, Vázquez‐Baeza, Yoshiki, Dillon, Matthew R, Bolyen, Evan, Caporaso, J Gregory, and Knight, Rob

Subjects
Networking and Information Technology R&D (NITRD), Generic health relevance, Biodiversity, Databases as Topic, Linear Models, Microbiota, Phylogeny, Software, QIIME 2, Qiita, bioinformatics, metagenomics, microbiome, Bioinformatics
Abstract

QIIME 2 is a completely re-engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open-source web-based platform, to re-use available data for meta-analysis. The following basic protocol describes how to install QIIME 2 on a single computer and analyze microbiome sequence data, from processing of raw DNA sequence reads through generating publishable interactive figures. These interactive figures allow readers of a study to interact with data with the same ease as its authors, advancing microbiome science transparency and reproducibility. We also show how plug-ins developed by the community to add analysis capabilities can be installed and used with QIIME 2, enhancing various aspects of microbiome analyses-e.g., improving taxonomic classification accuracy. Finally, we illustrate how users can perform meta-analyses combining different datasets using readily available public data through Qiita. In this tutorial, we analyze a subset of the Early Childhood Antibiotics and the Microbiome (ECAM) study, which tracked the microbiome composition and development of 43 infants in the United States from birth to 2 years of age, identifying microbiome associations with antibiotic exposure, delivery mode, and diet. For more information about QIIME 2, see https://qiime2.org. To troubleshoot or ask questions about QIIME 2 and microbiome analysis, join the active community at https://forum.qiime2.org. © 2020 The Authors. Basic Protocol: Using QIIME 2 with microbiome data Support Protocol: Further microbiome analyses.

Published
2020

5. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Author

Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J., Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G. I., Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Morton, Jamie T., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Orchanian, Stephanie B., Pearson, Talima, Peoples, Samuel L., Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, II, Michael S., Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R., Swafford, Austin D., Thompson, Luke R., Torres, Pedro J., Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J., Ul-Hasan, Sabah, van der Hooft, Justin J. J., Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H. D., Willis, Amy D., Xu, Zhenjiang Zech, Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, and Caporaso, J. Gregory

Published
2019
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6. Predicting neurodegenerative disease using the unique gut microbiota composition of transgenic mice modeling amyloid‐β plaques and neurofibrillary tangles

Author

Borsom, Emily M, primary, Conn, Kathryn A, additional, Keefe, Christopher R, additional, Hirsch, Allyson H, additional, Orsini, Gabrielle M, additional, Jaramillo, Sierra A, additional, Testo, George, additional, Avila, Melanie Palma, additional, Bolyen, Evan K, additional, Dillon, Matthew R, additional, Lee, Keehoon, additional, Caporaso, J. Gregory, additional, and Cope, Emily K, additional

Published
2022
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7. Influence of fecal microbiota transplantation on gut microbiota composition in transgenic mice modeling amyloid‐β plaques and neurofibrillary tangles

Author

Borsom, Emily M, primary, Keefe, Christopher R, additional, Hirsch, Allyson H, additional, Conn, Kathryn A, additional, Orsini, Gabrielle M, additional, Jaramillo, Sierra A, additional, Bolyen, Evan K, additional, Dillon, Matthew R, additional, Lee, Keehoon, additional, Caporaso, J. Gregory, additional, and Cope, Emily K, additional

Published
2022
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8. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Author

Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J., Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G. I., Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Morton, Jamie T., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Orchanian, Stephanie B., Pearson, Talima, Peoples, Samuel L., Petras, Daniel, Preuss, Mary Lai, Pruesse, Elmar, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, II, Michael S., Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, Song, Se Jin, Spear, John R., Swafford, Austin D., Thompson, Luke R., Torres, Pedro J., Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J., Ul-Hasan, Sabah, van der Hooft, Justin J. J., Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H. D., Willis, Amy D., Xu, Zhenjiang Zech, Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, and Caporaso, J. Gregory

Published
2019
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10. QIIME 2

Author

Caporaso, J Gregory and Dillon, Matthew R

Abstract

QIIME 2 is a platform for microbiome bioinformatics that serves researchers around the world. Microbiomes are communities of microorganisms that are ubiquitous in our bodies and on our planet. Advances in DNA sequencing and bioinformatics technologies in the past few decades have provided a new lens into the microbial world, and developing our understanding of microbiomes promises to improve diverse aspects of human health, assist with environmental sustainability and feeding of 8 billion people, and maybe even save us from a post-antibiotic world. The QIIME project has existed for just over 10 years, and has been cited in nearly 20,000 microbiome research studies. QIIME 2 succeeded QIIME 1 on Jan 1 2018. QIIME 2 is a plugin-based platform that enables reproducible microbiome research through different interface types.

Published
2020
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11. Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity

Author

Bolyen, Evan, primary, Dillon, Matthew R., additional, Bokulich, Nicholas A., additional, Ladner, Jason T., additional, Larsen, Brendan B., additional, Hepp, Crystal M., additional, Lemmer, Darrin, additional, Sahl, Jason W., additional, Sanchez, Andrew, additional, Holdgraf, Chris, additional, Sewell, Chris, additional, Choudhury, Aakash G., additional, Stachurski, John, additional, McKay, Matthew, additional, Simard, Anthony, additional, Engelthaler, David M., additional, Worobey, Michael, additional, Keim, Paul, additional, and Caporaso, J. Gregory, additional

Published
2020
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13. Microbiotyping the Sinonasal Microbiome

Author

Bassiouni, Ahmed, primary, Paramasivan, Sathish, additional, Shiffer, Arron, additional, Dillon, Matthew R., additional, Cope, Emily K., additional, Cooksley, Clare, additional, Ramezanpour, Mahnaz, additional, Moraitis, Sophia, additional, Ali, Mohammad Javed, additional, Bleier, Benjamin S., additional, Callejas, Claudio, additional, Cornet, Marjolein E., additional, Douglas, Richard G., additional, Dutra, Daniel, additional, Georgalas, Christos, additional, Harvey, Richard J., additional, Hwang, Peter H., additional, Luong, Amber U., additional, Schlosser, Rodney J., additional, Tantilipikorn, Pongsakorn, additional, Tewfik, Marc A., additional, Vreugde, Sarah, additional, Wormald, Peter-John, additional, Caporaso, J. Gregory, additional, and Psaltis, Alkis J., additional

Published
2020
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14. The international sinonasal microbiome study: A multicentre, multinational characterization of sinonasal bacterial ecology

Author

Paramasivan, Sathish, primary, Bassiouni, Ahmed, additional, Shiffer, Arron, additional, Dillon, Matthew R., additional, Cope, Emily K., additional, Cooksley, Clare, additional, Ramezanpour, Mahnaz, additional, Moraitis, Sophia, additional, Ali, Mohammad Javed, additional, Bleier, Benjamin, additional, Callejas, Claudio, additional, Cornet, Marjolein E., additional, Douglas, Richard G., additional, Dutra, Daniel, additional, Georgalas, Christos, additional, Harvey, Richard J., additional, Hwang, Peter H., additional, Luong, Amber U., additional, Schlosser, Rodney J., additional, Tantilipikorn, Pongsakorn, additional, Tewfik, Marc A., additional, Vreugde, Sarah, additional, Wormald, Peter‐John, additional, Caporaso, J. Gregory, additional, and Psaltis, Alkis J., additional

Published
2020
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15. Enabling Reproducible Microbiome Science through Decentralized Provenance Tracking in QIIME 2

Author

Naimey, Ahmad Turan, Keefe, Christopher, Bolyen, Evan, Dillon, Matthew R, and J Gregory Caporaso

Abstract

We demonstrate the ways in which automatic, integrated, decentralized provenance tracking in QIIME 2, a leading microbiome bioinformatics platform, enables reproducible microbiome science. We use sample data from a recent study of arid soil microbiomes (Significant Impacts of Increasing Aridity on the Arid Soil Microbiome; Neilson et al, 2017[2]), to illustrate specific analyses that QIIME 2 supports, and to frame our discussion of the QIIME 2 platform. QIIME 2 actions yield as outputs Artifacts integrating the requested data or visualization with comprehensive data provenance that describes the computational history of that data or visualization, including all methods and parameters involved in its creation. This approach gives users, reviewers, and readers powerful tools for understanding, reproducing, and extending studies. The benefits this approach provides to both the researcher and the scientific community are significant, and provide a useful model for research software developers across disciplines.

Published
2019
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16. Developing a QIIME 2 plugin: a simple annotation for robust tools

Author

Keefe, Christopher, Bolyen, Evan, Dillon, Matthew R, and J. Gregory Caporaso

Abstract

Research software development plays a critical role in microbiome science, but many biologists lack formal training in software development. As such, computational methods for microbiome analysis vary widely in readability, maintainability, error prevention, accessibility to users, and level of user support. Even computationally advanced biologists may not be able to prioritize the development of complex software architecture and support infrastructure, when that development time comes at the expense of other important research goals. Here we present an overview of plugin development for QIIME 23, an open-source microbiome bioinformatics platform designed to support and provide value to developers of computational methods. Developed under a “plugin” model, QIIME 2 provides valuable architecture for type-checking, error reporting, data access, communication between disparate methods within a computational pipeline, and convenient visualization of computational results. We present techniques for richly annotating new or existing computational methods to allow users to access them via diverse pre-built user interfaces, while ensuring accurate method citation and provenance tracking. Finally, we discuss platform infrastructure for the dissemination and support of third-party computational methods. In so doing, we provide an introduction, and resources for further study, to developers of computational methods which might benefit from existing architecture. For many computational microbiome scientists, these plugins will improve their return on time invested, and encouraging meaningful collaboration with others in the field.

Published
2019
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17. Microbiotyping the sinonasal microbiome

Author

Bassiouni, Ahmed, primary, Paramasivan, Sathish, additional, Shiffer, Arron, additional, Dillon, Matthew R, additional, Cope, Emily K, additional, Cooksley, Clare, additional, Ali, Mohammad Javed, additional, Bleier, Benjamin, additional, Callejas, Claudio, additional, Cornet, Marjolein E, additional, Douglas, Richard G, additional, Dutra, Daniel, additional, Georgalas, Christos, additional, Harvey, Richard J, additional, Hwang, Peter H, additional, Luong, Amber U, additional, Schlosser, Rodney J, additional, Tantilipikorn, Pongsakorn, additional, Tewfik, Marc A, additional, Vreugde, Sarah, additional, Wormald, Peter-John, additional, Caporaso, J Gregory, additional, and Psaltis, Alkis J, additional

Published
2019
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18. The international sinonasal microbiome study (ISMS): a multi-centre, multi-national collaboration characterising the microbial ecology of the sinonasal cavity

Author

Paramasivan, Sathish, primary, Bassiouni, Ahmed, additional, Shiffer, Arron, additional, Dillon, Matthew R, additional, Cope, Emily K, additional, Cooksley, Clare, additional, Ali, Mohammad Javed, additional, Bleier, Benjamin, additional, Callejas, Claudio, additional, Cornet, Marjolein E, additional, Douglas, Richard G, additional, Dutra, Daniel, additional, Georgalas, Christos, additional, Harvey, Richard J, additional, Hwang, Peter H, additional, Luong, Amber U, additional, Schlosser, Rodney J, additional, Tantilipikorn, Pongsakorn, additional, Tewfik, Marc A, additional, Vreugde, Sarah, additional, Wormald, Peter-John, additional, Caporaso, J Gregory, additional, and Psaltis, Alkis J, additional

Published
2019
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19. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

Author

Bolyen, Evan, primary, Rideout, Jai Ram, additional, Dillon, Matthew R, additional, Bokulich, Nicholas A, additional, Abnet, Christian, additional, Al-Ghalith, Gabriel A, additional, Alexander, Harriet, additional, Alm, Eric J, additional, Arumugam, Manimozhiyan, additional, Asnicar, Francesco, additional, Bai, Yang, additional, Bisanz, Jordan E, additional, Bittinger, Kyle, additional, Brejnrod, Asker, additional, Brislawn, Colin J, additional, Brown, C Titus, additional, Callahan, Benjamin J, additional, Caraballo-Rodríguez, Andrés Mauricio, additional, Chase, John, additional, Cope, Emily, additional, Da Silva, Ricardo, additional, Dorrestein, Pieter C, additional, Douglas, Gavin M, additional, Durall, Daniel M, additional, Duvallet, Claire, additional, Edwardson, Christian F, additional, Ernst, Madeleine, additional, Estaki, Mehrbod, additional, Fouquier, Jennifer, additional, Gauglitz, Julia M, additional, Gibson, Deanna L, additional, Gonzalez, Antonio, additional, Gorlick, Kestrel, additional, Guo, Jiarong, additional, Hillmann, Benjamin, additional, Holmes, Susan, additional, Holste, Hannes, additional, Huttenhower, Curtis, additional, Huttley, Gavin, additional, Janssen, Stefan, additional, Jarmusch, Alan K, additional, Jiang, Lingjing, additional, Kaehler, Benjamin, additional, Kang, Kyo Bin, additional, Keefe, Christopher R, additional, Keim, Paul, additional, Kelley, Scott T, additional, Knights, Dan, additional, Koester, Irina, additional, Kosciolek, Tomasz, additional, Kreps, Jorden, additional, Langille, Morgan GI, additional, Lee, Joslynn, additional, Ley, Ruth, additional, Liu, Yong-Xin, additional, Loftfield, Erikka, additional, Lozupone, Catherine, additional, Maher, Massoud, additional, Marotz, Clarisse, additional, Martin, Bryan D, additional, McDonald, Daniel, additional, McIver, Lauren J, additional, Melnik, Alexey V, additional, Metcalf, Jessica L, additional, Morgan, Sydney C, additional, Morton, Jamie, additional, Naimey, Ahmad Turan, additional, Navas-Molina, Jose A, additional, Nothias, Louis Felix, additional, Orchanian, Stephanie B, additional, Pearson, Talima, additional, Peoples, Samuel L, additional, Petras, Daniel, additional, Preuss, Mary Lai, additional, Pruesse, Elmar, additional, Rasmussen, Lasse Buur, additional, Rivers, Adam, additional, Robeson, II, Michael S, additional, Rosenthal, Patrick, additional, Segata, Nicola, additional, Shaffer, Michael, additional, Shiffer, Arron, additional, Sinha, Rashmi, additional, Song, Se Jin, additional, Spear, John R, additional, Swafford, Austin D, additional, Thompson, Luke R, additional, Torres, Pedro J, additional, Trinh, Pauline, additional, Tripathi, Anupriya, additional, Turnbaugh, Peter J, additional, Ul-Hasan, Sabah, additional, van der Hooft, Justin JJ, additional, Vargas, Fernando, additional, Vázquez-Baeza, Yoshiki, additional, Vogtmann, Emily, additional, von Hippel, Max, additional, Walters, William, additional, Wan, Yunhu, additional, Wang, Mingxun, additional, Warren, Jonathan, additional, Weber, Kyle C, additional, Williamson, Chase HD, additional, Willis, Amy D, additional, Xu, Zhenjiang Zech, additional, Zaneveld, Jesse R, additional, Zhang, Yilong, additional, Zhu, Qiyun, additional, Knight, Rob, additional, and Caporaso, J Gregory, additional

Published
2018
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