Caporaso submitted a proposal to the Chan Zuckerberg Initiative<\/a>\u2019s (CZI)\nnew Essential Open Source Software for Science funding program, which,\naccording to its website, was launched \u201cto provide one-year grants to support\nsoftware maintenance, growth, development and community engagement for critical\nopen source tools.\u201d<\/p>\n\n\n\n Today, Caporaso was awarded a $150,000\ngrant by CZI for the one-year project, with an opportunity to reapply for\nrenewal for a second year. <\/p>\n\n\n\n \u201cThis project is directly aimed at\nbuilding a more diverse community of users and developers by making it easier\nfor microbiome scientists and software developers around the world to learn and\ncontribute to QIIME 2,\u201d Caporaso said. \u201cWe\u2019re very excited about the new\nfunctionality that this grant will enable and honored to be selected for\nfunding in the first round of this new program.\u201d<\/p>\n\n\n\n \u201cOpen source software is more\nthan just writing code,\u201d CZI Head of Science Cori Bargmann said in a news\nrelease. \u201cIt includes improving documentation, addressing usability, managing\nprojects and building community. Giving scientists access to high-quality tools\nand technologies helps them do their work more efficiently and accelerates the\nprocess of discovery. We\u2019re thrilled to support the open source software that\nscientists use each day as part of our commitment to supporting more open,\ninclusive science.\u201d<\/p>\n\n\n\n Caporaso\u2019s proposal to CZI requested\nfunding to achieve two goals: expand the functionality of the QIIME 2 Library,\na web platform for sharing community-developed QIIME 2 plugins and\ndocumentation, and co-convene a QIIME 2 user and developer workshop in Latin\nAmerica in collaboration with CABANA<\/a>, a capacity strengthening project for bioinformatics\nin Latin America.<\/p>\n\n\n\n <\/strong>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 This results in plugins becoming outdated in the library.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. <\/p>\n\n\n\n \u201cWe\u2019ll 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,\u201d Caporaso said. \u201cAutomating testing is also good for users, who will be able to confirm that the code they\u2019d like to use has been tested and works as expected, and to ensure that a plugin\u2019s usage documentation is up-to-date and working correctly.<\/p>\n\n\n\n The QIIME 2 Library also will assist\nwith discovery of plugins, benefiting users by helping them find the latest\ntools that may be relevant for their microbiome analysis and benefiting\ndevelopers by helping them disseminate their methods.<\/p>\n\n\n\n <\/strong>Caporaso\u2019s 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<\/a> 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.<\/p>\n\n\n\n \u201cThere is great enthusiasm among the\nQIIME 2 developer community for a second developer workshop, and we would like\nto make this an opportunity for third-party developers to interact directly\nwith QIIME 2 users since those interactions have been extremely helpful for our\ncore development team. We would also like to host this workshop in a developing\ncountry to help build bioinformatics capacity around the world and foster\ndiverse user and developer communities,\u201d Caporaso said. \u201cThis will help to\nadvance our goal for QIIME 2 of cultivating a diverse and inclusive community\nof scientists, software engineers, statisticians, educators, students and other\nmicrobiome stakeholders who are openly sharing methods, data and knowledge to\nadvance microbiome research.\u201d<\/p>\n\n\n\n The team will work with Guilherme\nOliveira at the Vale Institute of Technology in Brazil and his team to plan,\ncoordinate, host and teach the workshop. <\/p>\n\n\n\n \u201cWe very much look forward to working\nwith Dr. Caporaso and his team to host this workshop. This will be an excellent\nopportunity to bring our teams together to advance bioinformatics education and\nmicrobiome science across the Americas,\u201d Oliveira said.<\/p>\n\n\n\n The paper describing the QIIME 1\nplatform, published in 2010, has been cited in more than 17,000 academic\npapers, making it one of the most often-cited scholarly works by an NAU author.\n<\/p>\n\n\n\n Caporaso is director of the Center for\nApplied Microbiome Science in NAU\u2019s Pathogen and\nMicrobiome Institute<\/a>. NAU research software engineers Evan Bolyen<\/strong>, Matthew Dillon <\/strong>and Jai Ram\nRideout <\/strong>performed the primary development of QIIME 2, along with research\nassistant professor Nicholas Bokulich<\/strong>.\nAdditional NAU collaborators include faculty researchers Paul Keim<\/strong>, Emily Cope<\/strong>\nand Tal Pearson;<\/strong> research staff Charles HD Williamson<\/strong>; and students John Chase<\/strong>, Jorden Kreps,<\/strong> Chris<\/strong> Keefe<\/strong>, Ahmad Turan Naimey<\/strong>, Arron\nShiffer, Anthony Simard, and David Rodriguez<\/strong>.<\/p>\n\n\n\n Founded by Dr. Priscilla Chan and Mark Zuckerberg in 2015, the Chan Zuckerberg Initiative is a new kind of philanthropy that\u2019s leveraging technology to help solve some of the world\u2019s 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<\/a>.<\/p>\n\n\n\nGoal 1: QIIME 2 library<\/strong><\/h4>\n\n\n\n
Goal 2: QIIME 2 user and developer workshop<\/strong><\/h4>\n\n\n\n
About CZI<\/strong><\/h4>\n\n\n\n
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