{"id":825,"date":"2010-06-09T10:38:14","date_gmt":"2010-06-09T09:38:14","guid":{"rendered":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/?p=825"},"modified":"2010-06-09T12:51:49","modified_gmt":"2010-06-09T11:51:49","slug":"sort-open-science-at-genome-scale","status":"publish","type":"post","link":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/2010\/06\/sort-open-science-at-genome-scale\/","title":{"rendered":"SORT &#8211; Open Science at Genome Scale"},"content":{"rendered":"<p>Second session of the second day &#8211; Liz Lyon from UKOLN<\/p>\n<p>Open Science at Web-scale report &#8211; a consultative document, Liz says now <a href=\"http:\/\/writetoreply.org\/openscience\/\">available on writetoreply<\/a> (but I can&#8217;t find it) (thanks to Kevin Ashley, now got a link to this <a href=\"http:\/\/writetoreply.org\/openscience\/\">http:\/\/writetoreply.org\/openscience\/<\/a>)<\/p>\n<p>OK &#8211; Liz talking about the amount of data being generated by Genome sequencing machines &#8211; now into second generation of Genome sequencing, and the next generation is being worked on which will work at orders of magnitude larger volumes of data.<\/p>\n<p>This type of huge data production brings challenges. Need large-scale data storage that is:<\/p>\n<ul>\n<li>Cost effective<\/li>\n<li>Secure<\/li>\n<li>Robust and resilient<\/li>\n<li>Low entry barrier<\/li>\n<li>Has data-handling\/transfer\/analysis capability<\/li>\n<\/ul>\n<p>Looking at &#8216;cloud services&#8217; that could offer this &#8211; e.g. <a href=\"http:\/\/dx.doi.org\/10.1038\/nbt0110-13\">Nature Biotechnology 10.1038\/nbt0110-13<\/a> details use of cloud services in biotechnology.<\/p>\n<p>Starting to see data sets as new instruments for science.<\/p>\n<p>Cost of genome sequencing dropping, while number of sequenced genomes rises.<\/p>\n<p>Leroy Hood says &#8220;medicine is going to become an information science&#8221;. P4 medicine:<\/p>\n<ul>\n<li>Predictive<\/li>\n<li>Personalised<\/li>\n<li>Preventive<\/li>\n<li>Participatory<\/li>\n<\/ul>\n<p>Stephen Friend &#8211; chief exec of Sage Bionetworks &#8211; wants to develop open data repository (Sage Commons) to start to develop redictive models of disease &#8211; liver\/breast\/colon cancer, diabetes, obesity.<\/p>\n<p>Paraphrasing a quote Liz read out: To Cultural forces encourage sharing &#8211; the way people handle personal data will impact on how researchers deal with data and mean they have not choice to share.<\/p>\n<p>Need to think about ways to incentivise researchers to share data &#8211; through mechanisms that allow credit and attribution which will then mean researchers benefit from sharing data.<\/p>\n<p>Need to thing about:<\/p>\n<ul>\n<li>Scaleable data infrastructure<\/li>\n<li>Personal genomic &#8211; share your data?<\/li>\n<li>Transform 21st Century medicine\/bioscience<\/li>\n<li>Credit and attribution for data and models<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Second session of the second day &#8211; Liz Lyon from UKOLN Open Science at Web-scale report &#8211; a consultative document, Liz says now available on writetoreply (but I can&#8217;t find it) (thanks to Kevin Ashley, now got a link to this http:\/\/writetoreply.org\/openscience\/) OK &#8211; Liz talking about the amount of data being generated by Genome [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[46],"class_list":["post-825","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-sort2010"],"_links":{"self":[{"href":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/wp-json\/wp\/v2\/posts\/825","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/wp-json\/wp\/v2\/comments?post=825"}],"version-history":[{"count":3,"href":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/wp-json\/wp\/v2\/posts\/825\/revisions"}],"predecessor-version":[{"id":844,"href":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/wp-json\/wp\/v2\/posts\/825\/revisions\/844"}],"wp:attachment":[{"href":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/wp-json\/wp\/v2\/media?parent=825"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/wp-json\/wp\/v2\/categories?post=825"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.meanboyfriend.com\/overdue_ideas\/wp-json\/wp\/v2\/tags?post=825"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}