I’m extremely excited to announce that QIIME 2 is now funded by the National Cancer Institute through the Informatics Technology for Cancer Research program! This five-year project, entitled Advancing our Understanding of Cancer and the Human Microbiome with QIIME 2, provides stable support for our core development team so we can keep building and supporting QIIME 2 for you. It will also enable many new features for QIIME 2 that stand to improve your microbiome research projects.
For folks interested in the details, I provide some information below on what’s to come. But first, I want to thank the entire QIIME 2 community for your support. This grant, and QIIME 2 as a whole, would not be possible without our development and support teams, our third party developers, and our user community. I look forward to continuing to work together to advance microbiome research and improve human health, environmental health and sustainability, and all of the incredible projects that folks are now using QIIME 2 for which we never could have imagined when we got started.
Thank you, thank you, thank you, as always, for your interest in and support of QIIME!
Now, onto the details…
In an analysis I performed in May of 2019, I estimated that nearly 20% of the articles citing QIIME were focused on cancer research. This was surprising given that the QIIME development team has spent no specific effort in reaching out to the cancer research community until very recently! This funding allows us to specifically improve many aspects of QIIME 2 to better support this substantial fraction of our user community. And of course, many of those improvements will also benefit researchers working in other areas.
This grant, a collaboration between my lab at Northern Arizona University and Rob Knight’s lab at UCSD, is divided into three specific aims. In our first aim, we will increase the accessibility of the QIIME 2 platform and cancer microbiome data to the cancer research community. To achieve this aim we’ll soon provide full access to QIIME 2 through Galaxy, we’ll develop support for accessing QIIME 2 functionality directly through R, we’ll develop a cancer microbiome data resource through Qiita, and we’ll create a new cancer-focused QIIME 2 user workshop series. We’ll also be working with the NCI Cloud Resources teams to integrate QIIME 2 into those platforms - this will be extremely powerful for cancer microbiome research as it will provide a platform containing the software, hardware, data, and educational content for microbiome multi-omics in an environment that supports other tools and data for cancer research, such as GATK and TCGA.
Our second aim is focused on making QIIME 2 a microbiome mutli-omics bioinformatics platform. This will include working directly with our third-party developer community to build plugins supporting microbiome metabolomics, metatranscriptomics, shotgun metagenomics, and metaproteomics, as well as plugins supporting integrated multi-omics analysis of these data. We’re extremely interested in collaborating with teams already developing tools in these areas - our goal is not to compete on these bioinformatics tools, but rather join forces to improve the microbiome multi-omics software space. Toward that end, we’ll also initiate a new microbiome multi-omics bioinformatics developers’ conference where we can share new tools and ideas, collaboratively develop software, and work together to expand and improve microbiome multi-omics research software. Paired with many new features coming to the QIIME 2 Library funded by the Chan–Zuckerberg Initiative, we hope to create an environment where users can discover and learn to use reliable new microbiome multi-omics tools that benefits both users and developers.
In our third aim, we will further facilitate reproducible microbiome multi-omics bioinformatics by expanding our support for automated methods tracking and reporting, and developing new tools to assist with data archiving. This will include the development of functionality for provenance replay (i.e., the ability to generate executable workflows from an existing artifact or visualization’s data provenance), support for viewing of data provenance diagrams in more interfaces of QIIME 2 including export of provenance diagrams in publication-quality vector graphics formats, allowing users viewing data provenance to opt in to automated workflow bug detection (a feature that will let you know if some software or reference data that was used in your workflow has been flagged as problematic), and the development of new plugins to help users submit their data and metadata to long-term archival repositories.
So, lots of cool stuff to come over the next few years! As we progress with these projects, we’ll regularly be reaching out to users and developers for feedback. We’re now working on shifting our workshops to online events, and I expect that we’ll continue that trend into the future to improve access to QIIME 2 to folks all over the world. I hope to see you (virtually, or in person again when it’s safe) at one of our user or developer events!
Stay safe and healthy out there, and please remember to take care of yourselves and others!