Nov. 14, 2019
Even as NAU associate professor Greg Caporaso and his team were putting the final touches on their QIIME 2 paper, published earlier this year, he was already planning several major enhancements to this open source and free bioinformatics software that enables scientists to perform microbiome analysis from increasingly large amounts of DNA sequencing and other data.
Caporaso submitted a proposal to the Chan Zuckerberg Initiative’s (CZI) new Essential Open Source Software for Science funding program, which, according to its website, was launched “to provide one-year grants to support software maintenance, growth, development and community engagement for critical open source tools.”
Today, Caporaso was awarded a $150,000 grant by CZI for the one-year project, with an opportunity to reapply for renewal for a second year.
“This project is directly aimed at building a more diverse community of users and developers by making it easier for microbiome scientists and software developers around the world to learn and contribute to QIIME 2,” Caporaso said. “We’re very excited about the new functionality that this grant will enable and honored to be selected for funding in the first round of this new program.”
“Open source software is more than just writing code,” CZI Head of Science Cori Bargmann said in a news release. “It includes improving documentation, addressing usability, managing projects and building community. Giving scientists access to high-quality tools and technologies helps them do their work more efficiently and accelerates the process of discovery. We’re thrilled to support the open source software that scientists use each day as part of our commitment to supporting more open, inclusive science.”
Caporaso’s proposal to CZI requested funding to achieve two goals: expand the functionality of the QIIME 2 Library, a web platform for sharing community-developed QIIME 2 plugins and documentation, and co-convene a QIIME 2 user and developer workshop in Latin America in collaboration with CABANA, a capacity strengthening project for bioinformatics in Latin America.
Goal 1: QIIME 2 library
Sharing a plugin on the QIIME 2 Library requires regular maintenance on the part of its developer. After uploading their plugin and associated documentation, the developer must manually update both when new versions are released. This results in plugins becoming outdated in the library. After completion of this goal, plugin developers will tell the QIIME 2 Library where to find plugin source code once, and the QIIME 2 Library will periodically check for and integrate new releases.
“We’ll also automate the testing of plugins and their documentation in the QIIME 2 Library, which will allow us to alert developers if there is a problem with their code,” Caporaso said. “Automating testing is also good for users, who will be able to confirm that the code they’d like to use has been tested and works as expected, and to ensure that a plugin’s usage documentation is up-to-date and working correctly.
The QIIME 2 Library also will assist with discovery of plugins, benefiting users by helping them find the latest tools that may be relevant for their microbiome analysis and benefiting developers by helping them disseminate their methods.
Goal 2: QIIME 2 user and developer workshop
Caporaso’s second goal is to co-convene a five-day workshop for both QIIME 2 users and developers to facilitate networking across these communities. Members of the QIIME 2 team have already led more than 25 user-focused workshops for QIIME 2 users all over the world, including two workshops at the National Institutes for Health as well as a workshop for 40 students in Copenhagen, Denmark, but have only held one workshop that was entirely dedicated to developers.
“There is great enthusiasm among the QIIME 2 developer community for a second developer workshop, and we would like to make this an opportunity for third-party developers to interact directly with QIIME 2 users since those interactions have been extremely helpful for our core development team. We would also like to host this workshop in a developing country to help build bioinformatics capacity around the world and foster diverse user and developer communities,” Caporaso said. “This will help to advance our goal for QIIME 2 of cultivating a diverse and inclusive community of scientists, software engineers, statisticians, educators, students and other microbiome stakeholders who are openly sharing methods, data and knowledge to advance microbiome research.”
The team will work with Guilherme Oliveira at the Vale Institute of Technology in Brazil and his team to plan, coordinate, host and teach the workshop.
“We very much look forward to working with Dr. Caporaso and his team to host this workshop. This will be an excellent opportunity to bring our teams together to advance bioinformatics education and microbiome science across the Americas,” Oliveira said.
The paper describing the QIIME 1 platform, published in 2010, has been cited in more than 17,000 academic papers, making it one of the most often-cited scholarly works by an NAU author.
Caporaso is director of the Center for Applied Microbiome Science in NAU’s Pathogen and Microbiome Institute. NAU research software engineers Evan Bolyen, Matthew Dillon and Jai Ram Rideout performed the primary development of QIIME 2, along with research assistant professor Nicholas Bokulich. Additional NAU collaborators include faculty researchers Paul Keim, Emily Cope and Tal Pearson; research staff Charles HD Williamson; and students John Chase, Jorden Kreps, Chris Keefe, Ahmad Turan Naimey, Arron Shiffer, Anthony Simard, and David Rodriguez.
Founded by Dr. Priscilla Chan and Mark Zuckerberg in 2015, the Chan Zuckerberg Initiative is a new kind of philanthropy that’s leveraging technology to help solve some of the world’s toughest challenges from eradicating disease to improving education to reforming the criminal justice system. Across three core Initiative focus areas of science, education and justice and opportunity, the organization is pairing engineering with grantmaking, impact investing and policy and advocacy work to help build an inclusive, just and healthy future for everyone. Learn more at chanzuckerberg.com.
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