{"id":1507,"date":"2019-12-16T14:09:18","date_gmt":"2019-12-16T21:09:18","guid":{"rendered":"https:\/\/nau.edu\/undergraduate-research\/?page_id=1507"},"modified":"2022-05-27T09:58:05","modified_gmt":"2022-05-27T16:58:05","slug":"designing-software","status":"publish","type":"page","link":"https:\/\/in.nau.edu\/office-undergraduate-research\/student-research-stories\/designing-software\/","title":{"rendered":"Allen Clarke: Designing software for microbiologists and geneticists"},"content":{"rendered":"\n
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Student spotlight<\/h3>\n <\/div>\n
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Allen Clarke<\/p>\n

Major<\/strong>: Computer Science, Mathematics<\/p>\n

Mentor<\/strong>: Dawn Birdsell<\/p>\n<\/div>\n <\/div>\n <\/div>\n<\/div>\n<\/div>\n\n

Designing software for microbiologists and geneticists<\/h1>\n

\"AllenAllen Clarke, <\/strong>a Computer Science<\/a> and Mathematics<\/a> double major, has been sharpening his software development abilities at NAU\u2019s Pathogen and Microbiome Institute<\/a> (PMI). He is leveraging his programming expertise to create tools that help PMI researchers complete their cutting-edge work on gene sequencing.<\/p>\n

\u201cAn analogy I’ve heard a lot is they’re building the plane while it’s taking off,\u201d he said. \u201cThe researchers kind of know where they’re going, but they don’t yet have all the pieces they need to get there.\u201d<\/p>\n

Clarke is helping to put those pieces together. His aspiration is to become a software developer, a profession that connects his interests in web development and database management.<\/p>\n

Clarke\u2019s current project at PMI focuses heavily on both interests. He is expanding his knowledge of database management by ensuring the security of researchers\u2019 data; he is also preparing PMI\u2019s Google Sheets database to accommodate potentially extensive data sets. His software development skills are in high demand. The work is never truly done, as researchers routinely introduce new elements to the system.<\/p>\n

Clarke explained PMI researchers use 10x gene sequencing on pathogens. Although in the past they may have identified only one feature barcode to use when sequencing data, many now identify four feature barcodes because of advanced DNA sequencing, and databases need to accommodate the added complexity. The use of additional\u00a0feature barcodes enables geneticists to get longer DNA reads out of sequencers designed to handle shorter DNA reads.<\/p>\n

Because of this project, Clarke has also been exposed to three different programming languages\u2014essential to his dream career as a software developer. \u201cI’ve been doing a lot of back-end work in one language, Go,\u201d he said. \u201cI also have been doing some front-end work with Google Sheets in JavaScript and developed some websites in HTML.\u201d<\/p>\n

When he began working at PMI, Clarke felt overwhelmed by everything he needed to learn and concerned that he wasn\u2019t up to the task of working at a research facility. Public speaking was also an uncomfortable prospect. He credits PMI associate director Dawn Birdsell\u2019s <\/strong>mentorship for helping him to overcome these challenges. Birdsell routinely helps student researchers develop presentations for the university\u2019s Undergraduate Symposium<\/a>. At last year\u2019s event, Clarke had advanced so much he earned second place in the competition\u2019s research category.<\/p>\n

Clarke is impressed with the opportunities he\u2019s been given at NAU.<\/p>\n

\u201cThe fact that there are so many undergrad research opportunities relative to the number of undergraduates here blows my mind,\u201d he said. \u201cI\u2019m thankful I can look back at the work I completed at PMI and say I contributed to something meaningful.\u201d<\/p>\n

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Designing software for microbiologists and geneticists Allen Clarke, a Computer Science and Mathematics double major, has been sharpening his software development abilities at NAU\u2019s Pathogen and Microbiome Institute (PMI). He is leveraging his programming expertise to create tools that help PMI researchers complete their cutting-edge work on gene sequencing. \u201cAn analogy I’ve heard a lot […]<\/p>\n","protected":false},"author":14,"featured_media":0,"parent":15,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_relevanssi_hide_post":"","_relevanssi_hide_content":"","_relevanssi_pin_for_all":"","_relevanssi_pin_keywords":"","_relevanssi_unpin_keywords":"","_relevanssi_related_keywords":"","_relevanssi_related_include_ids":"","_relevanssi_related_exclude_ids":"","_relevanssi_related_no_append":"","_relevanssi_related_not_related":"","_relevanssi_related_posts":"","_relevanssi_noindex_reason":"","_oasis_is_in_workflow":0,"_oasis_original":0,"_oasis_task_priority":"","ring_central_script_selection":"","footnotes":""},"class_list":["post-1507","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/in.nau.edu\/office-undergraduate-research\/wp-json\/wp\/v2\/pages\/1507","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/in.nau.edu\/office-undergraduate-research\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/in.nau.edu\/office-undergraduate-research\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/in.nau.edu\/office-undergraduate-research\/wp-json\/wp\/v2\/users\/14"}],"replies":[{"embeddable":true,"href":"https:\/\/in.nau.edu\/office-undergraduate-research\/wp-json\/wp\/v2\/comments?post=1507"}],"version-history":[{"count":2,"href":"https:\/\/in.nau.edu\/office-undergraduate-research\/wp-json\/wp\/v2\/pages\/1507\/revisions"}],"predecessor-version":[{"id":1510,"href":"https:\/\/in.nau.edu\/office-undergraduate-research\/wp-json\/wp\/v2\/pages\/1507\/revisions\/1510"}],"up":[{"embeddable":true,"href":"https:\/\/in.nau.edu\/office-undergraduate-research\/wp-json\/wp\/v2\/pages\/15"}],"wp:attachment":[{"href":"https:\/\/in.nau.edu\/office-undergraduate-research\/wp-json\/wp\/v2\/media?parent=1507"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}