{"id":1775,"date":"2012-01-19T20:06:25","date_gmt":"2012-01-19T20:06:25","guid":{"rendered":"http:\/\/www.joswassink.nl\/insight\/?p=1775"},"modified":"2012-01-19T20:06:25","modified_gmt":"2012-01-19T20:06:25","slug":"genomes-flashing-through-lightpaths","status":"publish","type":"post","link":"https:\/\/www.joswassink.nl\/insight\/?p=1775","title":{"rendered":"Genomes flashing through lightpaths"},"content":{"rendered":"<div id=\"attachment_1777\" style=\"width: 310px\" class=\"wp-caption alignright\"><a rel=\"attachment wp-att-1777\" href=\"http:\/\/www.joswassink.nl\/insight\/?attachment_id=1777\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1777\" class=\"size-thumbnail wp-image-1777\" title=\"scfiber_optic_illuminated_548x343\" src=\"http:\/\/www.joswassink.nl\/insight\/wp-content\/uploads\/scfiber_optic_illuminated_548x343-300x187.jpg\" alt=\"\" width=\"300\" height=\"187\" \/><\/a><p id=\"caption-attachment-1777\" class=\"wp-caption-text\">Optic fibre, Photo: Gary Sholl<\/p><\/div>\n<p><strong>The idea to connect the TU with genomic centres via dedicated glass  fibres won first prize at last year\u2019s Surfnet \u2018Enlighten Your Research  3\u2019 competition.<\/strong><\/p>\n<p>\u201cNow we\u2019ve got a ten gigabit per second connection for each  university, which serves the transport of scientific data but also  students reading news sites. Consequently, you\u2019re never sure what  capacity is available,\u201d Jan Bot (MSc &#8211; EEMCS) explains, regarding the  need for dedicated glass fibre connections, called lightpaths, for the  exchange of genomic data.<!--more--><\/p>\n<p>His proposal, titled \u2018Next generation  networking for next generation sequencing\u2019, was awarded first prize at  the \u2018Enlighten Your Research 3\u2019 (EYR3) competition, organized by  Surfnet, the academic internet provider, on 7 December 2011. Bot\u2019s  proposal entails a network of lightpaths between the TU and several  other institutes: AMC, University of Groningen, Hubrecht laboratory,  LUMC, VU Amsterdam, Wageningen University, Beijing Genomic s Institute  in Hong Kong and Complete Genomics in California. The last two  connections are specialized sequencing companies. \u201cBlood in, bits out,\u201d  Bot says.<\/p>\n<p>Bioinformatics means data, lots of data, although less then particle  physics. A human genome with 23,000 genes in the current industry  standard measures about 300 gigabyte. It takes a single sequencing  machine a few days to sequence all the DNA fragments, after which a  computer needs about a week to stitch the entire genome together. In  practice, these tasks are sped up by parallel processing or by using  supercomputers. Up until now, however, research samples are flown to  sequencing plants, and then couriers like FedEx or UPS bring the hard  disks back. Sending the data by internet or via a cloud is not powerful  enough, nor is it secure.<\/p>\n<p>Bot expects the genomic optical network  to be operational within a year, after which the exchange of  bioinformatics data will be both easier and more secure, since a light  path is essentially one continuous fibre without side-branches.<\/p>\n<p>EYR3\u2019s  second prize was also awarded to a TU Delft project led by Dr Henri  Vrooman (Erasmus MC). He proposed connecting Leiden and Groningen  medical centres to the SARA supercomputer and the TU visualization group  as an infrastructure for comparing MRI images from population studies.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The idea to connect the TU with genomic centres via dedicated glass fibres won first prize at last year\u2019s Surfnet \u2018Enlighten Your Research 3\u2019 competition.<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3,6],"tags":[63,244,261,322],"class_list":["post-1775","post","type-post","status-publish","format-standard","hentry","category-articles","category-delta","tag-bio-informatics","tag-jan-bot","tag-lightpath","tag-optic-fibre"],"_links":{"self":[{"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/posts\/1775","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1775"}],"version-history":[{"count":0,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=\/wp\/v2\/posts\/1775\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1775"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1775"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.joswassink.nl\/insight\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1775"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}