{"id":16530,"date":"2012-07-21T12:43:58","date_gmt":"2012-07-21T10:43:58","guid":{"rendered":"https:\/\/mamchenkov.net\/wordpress\/?p=16530"},"modified":"2012-07-21T12:45:19","modified_gmt":"2012-07-21T10:45:19","slug":"software-emulates-a-living-organism","status":"publish","type":"post","link":"https:\/\/mamchenkov.net\/wordpress\/2012\/07\/21\/software-emulates-a-living-organism\/","title":{"rendered":"Software emulates a living organism"},"content":{"rendered":"<!-- google_ad_section_start -->\n<p><a href=\"http:\/\/www.nytimes.com\/2012\/07\/21\/science\/in-a-first-an-entire-organism-is-simulated-by-software.html\">The New York Times<\/a> covers the story of the first ever living organism simulation in software.<\/p>\n<blockquote><p>Scientists at Stanford University and the J. Craig Venter Institute have developed the first software simulation of an entire organism, a humble single-cell bacterium that lives in the human genital and respiratory tracts.<\/p>\n<p>The scientists and other experts said the work was a giant step toward developing computerized laboratories that could carry out many thousands of experiments much faster than is possible now, helping scientists penetrate the mysteries of diseases like cancer and Alzheimer\u2019s.<\/p>\n<p>[&#8230;]<\/p>\n<p>The simulation of the complete life cycle of the pathogen, Mycoplasma genitalium, was presented on Friday in the journal Cell. The scientists called it a \u201cfirst draft\u201d but added that the effort was the first time an entire organism had been modeled in such detail \u2014 in this case, all of its 525 genes.<\/p>\n<p>The simulation, which runs on a cluster of 128 computers, models the complete life span of the cell at the molecular level, charting the interactions of 28 categories of molecules \u2014 including DNA, RNA, proteins and small molecules known as metabolites, which are generated by cell processes.<\/p><\/blockquote>\n<p>Super super cool!<\/p>\n<!-- google_ad_section_end -->\n","protected":false},"excerpt":{"rendered":"<!-- google_ad_section_start -->\n<p>The New York Times covers the story of the first ever living organism simulation in software. Scientists at Stanford University and the J. Craig Venter Institute have developed the first software simulation of an entire organism, a humble single-cell bacterium that lives in the human genital and respiratory tracts. The scientists and other experts said &hellip; <a href=\"https:\/\/mamchenkov.net\/wordpress\/2012\/07\/21\/software-emulates-a-living-organism\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Software emulates a living organism<\/span><\/a><\/p>\n<!-- google_ad_section_end -->\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"_links_to":"","_links_to_target":""},"categories":[1,62],"tags":[2985,1336,351,655],"keyring_services":[],"class_list":["post-16530","post","type-post","status-publish","format-standard","hentry","category-general","category-technology","tag-biology","tag-inspiration","tag-medicine","tag-science"],"aioseo_notices":[],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack-related-posts":[{"id":41,"url":"https:\/\/mamchenkov.net\/wordpress\/2002\/04\/17\/funny-day\/","url_meta":{"origin":16530,"position":0},"title":"Funny day","author":"Leonid Mamchenkov","date":"April 17, 2002","format":false,"excerpt":"First of all, my collegue and me were playing with Domain Policies and push installations on Win2k again. Luckily, we can afford full testing environment with simulation domain, etc. It's nice to know that renaming of default domain policy removes all software SAP Web Application server gave us a strange\u2026","rel":"","context":"In &quot;All&quot;","block_context":{"text":"All","link":"https:\/\/mamchenkov.net\/wordpress\/category\/general\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":16540,"url":"https:\/\/mamchenkov.net\/wordpress\/2012\/07\/22\/weekly-digest-2012-07-22\/","url_meta":{"origin":16530,"position":1},"title":"Weekly digest &#8211; 2012-07-22","author":"Leonid Mamchenkov","date":"July 22, 2012","format":false,"excerpt":"Tribute to MS Outlook http:\/\/t.co\/XjIhglhJ # Stash - privately hosted Git repositories http:\/\/t.co\/Ms8Y0ZVR # Requiem For A Digg http:\/\/t.co\/SBiUFv8w # The Most Important Tech Company You've Never Heard Of http:\/\/t.co\/KEvwjBJP # This is What Snake Venom Does to Blood! http:\/\/t.co\/Z6HRcelU # New note : \u041a\u0430\u043a \u0432\u044b\u0433\u043b\u044f\u0434\u044f\u0442 \u043a\u0440\u044f\u043a\u043e\u0437\u044f\u0431\u0440\u044b? http:\/\/t.co\/TYM79cYA # New\u2026","rel":"","context":"In &quot;All&quot;","block_context":{"text":"All","link":"https:\/\/mamchenkov.net\/wordpress\/category\/general\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":26095,"url":"https:\/\/mamchenkov.net\/wordpress\/2016\/05\/04\/jimmy-kimmel-scientists-climate-change\/","url_meta":{"origin":16530,"position":2},"title":"Jimmy Kimmel and Scientists on Climate Change","author":"Leonid Mamchenkov","date":"May 4, 2016","format":"video","excerpt":"https:\/\/www.youtube.com\/watch?v=9UCdFbyL8y0","rel":"","context":"In &quot;All&quot;","block_context":{"text":"All","link":"https:\/\/mamchenkov.net\/wordpress\/category\/general\/"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/img.youtube.com\/vi\/9UCdFbyL8y0\/0.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":11007,"url":"https:\/\/mamchenkov.net\/wordpress\/2008\/01\/05\/black-people-in-science-and-innovation\/","url_meta":{"origin":16530,"position":3},"title":"Black people in science and innovation","author":"Leonid Mamchenkov","date":"January 5, 2008","format":false,"excerpt":"It's been a few times already that I heard the argument that \"black people made no contribution to computer science\".\u00c2\u00a0 I've also heard a few alternative versions, which were less or more specific, varying from \"African blacks\" and \"no innovations\", to \"black women\" and \"no contribution to science\". Depending on\u2026","rel":"","context":"In &quot;All&quot;","block_context":{"text":"All","link":"https:\/\/mamchenkov.net\/wordpress\/category\/general\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":7560,"url":"https:\/\/mamchenkov.net\/wordpress\/2004\/06\/09\/p800-updates\/","url_meta":{"origin":16530,"position":4},"title":"P800 updates","author":"Leonid Mamchenkov","date":"June 9, 2004","format":false,"excerpt":"It has been a long time since I checked the SonyEricsson P800 scene. Meanwhile there were plenty software updates and a lot more media content published. I've spent a good deal of today downloading all sorts of sounds and pictures, testing new software products and updating the old ones. Out\u2026","rel":"","context":"In &quot;All&quot;","block_context":{"text":"All","link":"https:\/\/mamchenkov.net\/wordpress\/category\/general\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":28111,"url":"https:\/\/mamchenkov.net\/wordpress\/2017\/10\/17\/the-sudden-death-and-eternal-life-of-solaris\/","url_meta":{"origin":16530,"position":5},"title":"The sudden death and eternal life of Solaris","author":"Leonid Mamchenkov","date":"October 17, 2017","format":false,"excerpt":"Bryan Cantrill wrote this blog post on the death of Solaris.\u00a0 Here's a bit like the most about it, which talks about the proprietary software vs. Open Source: Assuming that this is indeed the end of Solaris (and it certainly looks that way), it offers a time for reflection. 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