{"id":2114,"date":"2018-12-24T15:00:59","date_gmt":"2018-12-24T03:00:59","guid":{"rendered":"https:\/\/www.funk.co.nz\/blog\/?p=2114"},"modified":"2021-04-19T12:42:52","modified_gmt":"2021-04-19T00:42:52","slug":"aminosee-dna-visualisation","status":"publish","type":"post","link":"https:\/\/www.funk.co.nz\/blog\/visuals\/aminosee-dna-visualisation","title":{"rendered":"Introducing AminoSee DNA Visualisation"},"content":{"rendered":"<p>Press release for my newly released genomics software visualisation project \"<a href=\"\/aminosee\/\"><strong>AminoSee<\/strong><\/a>\". Send <strong><a href=\"https:\/\/www.funk.co.nz\/pdf\/AminoSee_WhitePaper_09Jan2019.pdf\">this PDF<\/a><\/strong> to your local scientist!<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-large wp-image-3394\" src=\"https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2021\/04\/aminosee-screenshot-900x470.png\" alt=\"DNA Viewer\" width=\"900\" height=\"470\" srcset=\"https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2021\/04\/aminosee-screenshot-900x470.png 900w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2021\/04\/aminosee-screenshot-600x313.png 600w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2021\/04\/aminosee-screenshot-650x340.png 650w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2021\/04\/aminosee-screenshot-768x401.png 768w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2021\/04\/aminosee-screenshot.png 1537w\" sizes=\"auto, (max-width: 900px) 100vw, 900px\" \/><\/p>\n<p><a href=\"\/pdf\/AminoSee_WhitePaper_09Jan2019.pdf\"><img decoding=\"async\" class=\"wp-image-2132 size-medium\" src=\"https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/one-shot-650x517.png\" alt=\"The goal: Visually represent an entire genome graphically ...in one shot\" width=\"99%\" height=\"auto\" srcset=\"https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/one-shot-650x517.png 650w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/one-shot-600x477.png 600w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/one-shot-768x610.png 768w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/one-shot-900x715.png 900w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/one-shot.png 1359w\" sizes=\"(max-width: 650px) 100vw, 650px\" \/><\/a><\/p>\n<p><iframe class=\"iframe\" src=\"https:\/\/www.youtube.com\/embed\/QerMTQs2bDs\" allowfullscreen=\"allowfullscreen\"><\/iframe><\/p>\n<p>FOR IMMEDIATE RELEASE: Monday 24 December 2018<br \/>\nSection: International \/ Science \/ Infotech<br \/>\nSuggested Headline 1: NZ Musician Invents DNA Viewer<br \/>\nSuggested Headline 2: Free DNA Software For Christmas<\/p>\n<p><strong>A kiwi drummer has today gifted the public an open-source license to his innovative new computer software that is able to render an image from a digital file of any DNA or RNA data file.<\/strong><\/p>\n<p>Tom Atkinson, the drummer for Dam Native, Breaks Co-op, SJD, The Triptonites and many other groups turned out the software - which he has called the AminoSeeNoEvil DNA Viewer - in a sudden burst of creativity over the past 6 weeks after it came to him in a sudden realisation late one evening.<\/p>\n<p>\u00e2\u20ac\u0153My fingers just kept going at the keyboard like crazy. I just really wanted to see it in the end. Without anyone to help or slow me down, and realising the significance of the idea, I went all in. Glad I got it done before the end of the year, now it\u00e2\u20ac\u2122s time to get this to some scientists\u00e2\u20ac\u009d -Tom.<\/p>\n<p>It creates full colour images and was designed to enable inter-species comparisons between humans and primates; to understand the role of the regulatory \u00e2\u20ac\u0153non-coding\u00e2\u20ac\u009d junk DNA; as a thought experiment and exercise in processing enormous datasets; but most of all just purely out of curiosity and to inspire youth to get into science.<\/p>\n<p>An experimental 3D mode enables visitors to <strong><a href=\"http:\/\/aminosee.funk.nz\/\">http:\/\/aminosee.funk.nz\/<\/a><\/strong> to interactively fly through the DNA using the keyboard and mouse for a closer look! This even works on modern mobiles, but a desktop computer running macOS, Windows, or Linux is suggested. You can currently browse though his renderings of a handful of organisms such a human, primates, Octopus, Eucalyptus, Cannabis, Alligator, and the Brown Kiwi, with more coming soon.<\/p>\n<p>It is available now on popular github.com collaboration site, released under the same software license as the Linux free operating system, sometimes called a \u00e2\u20ac\u0153copy-left\u00e2\u20ac\u009d license, a play on the word \u00e2\u20ac\u0153copyright\u00e2\u20ac\u009d. This allows anyone to make copies, provide download mirrors, and even charge a fee to install or include in a bigger package with the requirement that the enhancements are provided back to the community also in source code format.<\/p>\n<p>This allows commercial grade enhancements that will yield improvements to the free product, while benefiting all. For example, this is what enables IBM to sell for profit it\u00e2\u20ac\u2122s Redhat Linux system, with the improvements to the underlying kernel given back to the wider community for all to use.<\/p>\n<p>The software is now being sent to universities and genomics researchers worldwide, hoping to gain some feedback and suggestions on the final colours for each amino acid.<\/p>\n<p>Strapline: \u00e2\u20ac\u0153I can see it now - I can AminoSee it!\u00e2\u20ac\u009d<\/p>\n<p><a href=\"https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/chrY_Pan_Clint_PR.png\" rel=\"http:\/\/www.funk.co.nz\/aminosee\/output\/Chimp_Clint_chrY\/images\/Chimp_Clint_chrY.gbk.aminosee_HILBERT_m7_c7.3_Reference.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-2125\" src=\"https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/chrY_Pan_Clint_PR-650x650.png\" alt=\"Chromosome Y from &quot;Clint&quot; the Chimpanzee\" width=\"720\" height=\"720\" srcset=\"https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/chrY_Pan_Clint_PR-650x650.png 650w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/chrY_Pan_Clint_PR-300x300.png 300w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/chrY_Pan_Clint_PR-100x100.png 100w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/chrY_Pan_Clint_PR-600x600.png 600w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/chrY_Pan_Clint_PR-150x150.png 150w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/chrY_Pan_Clint_PR-768x768.png 768w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/chrY_Pan_Clint_PR-900x900.png 900w, https:\/\/www.funk.co.nz\/blog\/wp-content\/uploads\/2018\/12\/chrY_Pan_Clint_PR.png 1024w\" sizes=\"auto, (max-width: 720px) 100vw, 720px\" \/><\/a><\/p>\n<p>Official site:<br \/>\n<a href=\"http:\/\/aminosee.funk.nz\/\">http:\/\/aminosee.funk.nz\/<\/a> (Demo site with 3D viewer demo, and 2D reports)<br \/>\nAuthor: Tom Atkinson &lt;tom@funk.co.nz&gt;<br \/>\n<a href=\"http:\/\/www.funk.co.nz\/aminosee\/output\/Chimp_Clint_chrY\/images\/Chimp_Clint_chrY.gbk.aminosee_HILBERT_m7_c7.3_Reference.png\">http:\/\/www.funk.co.nz\/aminosee\/output\/Chimp_Clint_chrY\/images\/Chimp_Clint_chrY.gbk.aminosee_HILBERT_m7_c7.3_Reference.png<\/a> (reference image of Chimpanzee Y chromosome shows ~7.3 amino acids per pixel)<br \/>\n<a href=\"https:\/\/www.funk.co.nz\/pdf\/AminoSee_WhitePaper_09Jan2019.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/www.funk.co.nz\/pdf\/AminoSee_WhitePaper_09Jan2019.pdf<\/a> (press release PDF with images)<\/p>\n<p><video controls=\"controls\" width=\"99%\" height=\"240\"><source src=\"https:\/\/www.funk.co.nz\/aminosee\/gource.mp4\" type=\"video\/mp4\" \/>Your browser does not support the video tag.<\/video><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Press release for my newly released genomics software visualisation project &#8220;AminoSee&#8221;. Send this PDF to your local scientist! FOR IMMEDIATE RELEASE: Monday 24 December 2018 Section: International \/ Science \/ Infotech Suggested Headline 1: NZ Musician Invents DNA Viewer Suggested Headline 2: Free DNA Software For Christmas A kiwi drummer has today gifted the public [&hellip;]<\/p>\n","protected":false},"author":3,"featured_media":2135,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[49,36,33],"tags":[54,77,48],"class_list":["post-2114","post","type-post","status-publish","format-standard","hentry","category-news","category-science","category-visuals","tag-fractals","tag-genomics","tag-webgl"],"_links":{"self":[{"href":"https:\/\/www.funk.co.nz\/blog\/wp-json\/wp\/v2\/posts\/2114","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.funk.co.nz\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.funk.co.nz\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.funk.co.nz\/blog\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.funk.co.nz\/blog\/wp-json\/wp\/v2\/comments?post=2114"}],"version-history":[{"count":0,"href":"https:\/\/www.funk.co.nz\/blog\/wp-json\/wp\/v2\/posts\/2114\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.funk.co.nz\/blog\/wp-json\/wp\/v2\/media\/2135"}],"wp:attachment":[{"href":"https:\/\/www.funk.co.nz\/blog\/wp-json\/wp\/v2\/media?parent=2114"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.funk.co.nz\/blog\/wp-json\/wp\/v2\/categories?post=2114"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.funk.co.nz\/blog\/wp-json\/wp\/v2\/tags?post=2114"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}