{"id":31277,"date":"2014-07-15T10:53:18","date_gmt":"2014-07-15T17:53:18","guid":{"rendered":"http:\/\/stage.headlessnauedu-b6hgdzckfdgxgzhe.westus-01.azurewebsites.net\/?p=31277"},"modified":"2014-07-28T11:29:29","modified_gmt":"2014-07-28T18:29:29","slug":"world-awash-data-projects-proliferate-nau-informaticist","status":"publish","type":"post","link":"https:\/\/in.nau.edu\/news\/world-awash-data-projects-proliferate-nau-informaticist\/","title":{"rendered":"In a world awash with data, projects proliferate for NAU informaticist"},"content":{"rendered":"

\"Greg<\/a>In a small, nondescript office on the Northern Arizona University campus, those keystrokes Greg Caporaso<\/strong> is fervently tapping into his laptop spell possibility.<\/p>\n

They could be a line of code for his interactive informatics textbook, or advice to a graduate student analyzing complex communities of DNA. Maybe he\u2019s posting his own microbial ecology research results to share with other scientists, or putting down a few thoughts about a potential link between the human gut microbiome and the severity of autism.<\/p>\n

As DNA sequencing churns out one rushing tributary of the exponentially growing river known as \u201cbig data,\u201d and as high performance computing delivers greater potential for discerning meaning from the torrent, those who combine computer science and biology occupy a world where there is no shortage of territory to explore.<\/p>\n

Informatics is no place for hunt and peck.<\/p>\n

The field broadly defines the infusion of computation into more familiar disciplines: biology was a forerunner, now joined by everything from geology and astronomy to business, virtual reality and even the arts.<\/p>\n

So much information is being generated in all these areas that dealing with it effectively has become a pursuit in its own right. The field is young enough that widely agreed-upon standards are still catching up with developments.<\/p>\n

\u201cFor more straightforward questions, we\u2019ve got pretty good protocols in place,\u201d said Caporaso, assistant professor of biological sciences at NAU. But especially in the realm of DNA sequencing, even the groundbreaking work that emerged less than a decade ago has already receded into history.<\/p>\n

\u201cIt\u2019s one problem to take a sequence and figure out what organism it belongs to and what its function is,\u201d Caporaso said. \u201cIt\u2019s a very different problem to do that with a hundred million sequences.\u201d<\/p>\n

Most of Caporaso\u2019s published work combines his knowledge of the human microbiome\u2014the trillions of microorganisms living in your gut\u2014with expertise in developing software to interpret DNA sequencing results. The research requires ever more powerful computing capacity, so the recent addition of \u201cmonsoon,\u201d the high-performance computing cluster at NAU, opens new research and educational opportunities to Caporaso and his students.<\/p>\n

One of Caporaso\u2019s graduate students has focused on building models of known DNA sequences to identify bacterial species through unknown sequences. \u201cHer project wouldn\u2019t have been possible without monsoon,\u201d Caporaso said.<\/p>\n

A post-doctoral student is preparing an endeavor so big \u201cit could tie the whole system up for a month or two,\u201d Caporaso said, although it won\u2019t\u2014multiple researchers on campus share the resource. \u201cEssentially, what she\u2019s doing is benchmarking some of the standard approaches for analyzing complex communities of DNA.\u201d<\/p>\n

Not only are such benchmarks desperately needed, Caporaso said, but the work extends ongoing microbiome research and sets up a major project just getting under way with collaborators at Arizona State University.<\/p>\n

\u201cA lot of the studies we do involve going out into the environment somewhere, which might be the soil or a swab of the human mouth, and looking at all the microbes that are present,\u201d Caporaso said. \u201cOne of the things we\u2019re really interested in comparing is the functional potential of the organisms that live in and on your body versus my body.\u201d<\/p>\n

Some of that potential may be disease. Funded with a tri-university grant from the Arizona Board of Regents, Carporaso\u2019s team, along with Rosa Krajmalnik-Brown and James Adams at ASU and Matthew Sullivan at the University of Arizona, will examine associations<\/a> between the microbiome and the severity of autism.<\/p>\n

\u201cThere\u2019s been some recent evidence, some of it published out of ASU, that microbes living in the gut may be producing chemicals than can affect the severity of the symptoms of autism,\u201d Caporaso said. \u201cAnd there also has been quite a bit of anecdotal evidence that altering that community of microbiomes with certain probiotics can reduce the severity of those symptoms.\u201d<\/p>\n

The project is still in the planning and discussion stage, leaving Caporaso time to give some additional attention to another regents-funded pursuit, this one directly related to his teaching. He has built an online, interactive textbook and used it in his undergraduate bioinformatics course\u2014cross-listed, of course, in biology and computer science.<\/p>\n

Caporaso recreated his slides and notes as an online, interactive tool that includes executable code. Students can learn about bioinformatics methods in the context of their implementation.<\/p>\n

\u201cIf we\u2019re going through the lecture and somebody has a question about how changing a parameter might change the result of an algorithm, I don\u2019t have to give a theoretical description because we\u2019ve all got the code right in front of us,\u201d Caporaso said. \u201cSo we end up working on it together.\u201d<\/p>\n

Caporaso hopes to find the funding to develop the project into a \u201cfully stand-alone, open source, completely free online bioinformatics textbook. It\u2019s not necessarily a research project like my others, but it\u2019s one of the projects that I\u2019m most excited about right now.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"

In a small, nondescript office on the Northern Arizona University campus, those keystrokes Greg Caporaso is fervently tapping into his laptop spell possibility. They could be a line of code for his interactive informatics textbook, or advice to a graduate student analyzing complex communities of DNA. Maybe he\u2019s posting his own microbial ecology research results…<\/a><\/p>\n","protected":false},"author":46,"featured_media":31432,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[11],"tags":[462,262,850,851,848,849,853,854,38,24,852],"class_list":["post-31277","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-research-academics","tag-autism","tag-bioinformatics","tag-dna-sequencing","tag-greg-caporaso","tag-high-performance-computing","tag-informatics","tag-james-adams","tag-matthew-sullivan","tag-nau","tag-northern-arizona-university","tag-rosa-krajmalnik-brown"],"acf":[],"_links":{"self":[{"href":"https:\/\/in.nau.edu\/news\/wp-json\/wp\/v2\/posts\/31277","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/in.nau.edu\/news\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/in.nau.edu\/news\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/in.nau.edu\/news\/wp-json\/wp\/v2\/users\/46"}],"replies":[{"embeddable":true,"href":"https:\/\/in.nau.edu\/news\/wp-json\/wp\/v2\/comments?post=31277"}],"version-history":[{"count":0,"href":"https:\/\/in.nau.edu\/news\/wp-json\/wp\/v2\/posts\/31277\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/in.nau.edu\/news\/wp-json\/wp\/v2\/media\/31432"}],"wp:attachment":[{"href":"https:\/\/in.nau.edu\/news\/wp-json\/wp\/v2\/media?parent=31277"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/in.nau.edu\/news\/wp-json\/wp\/v2\/categories?post=31277"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/in.nau.edu\/news\/wp-json\/wp\/v2\/tags?post=31277"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}