{"id":1744,"date":"2017-01-19T00:52:46","date_gmt":"2017-01-19T00:52:46","guid":{"rendered":"http:\/\/ladam.info\/?p=1744"},"modified":"2019-01-31T17:59:56","modified_gmt":"2019-01-31T17:59:56","slug":"lysd-language-for-yeast-spatiotemporal-development","status":"publish","type":"post","link":"https:\/\/ladam.info\/index.php\/2017\/01\/19\/lysd-language-for-yeast-spatiotemporal-development\/","title":{"rendered":"LYSD: Language for Yeast Spatiotemporal Development"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">LYSD is a language a created to <strong>specify a phenotype<\/strong>. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">It can be <strong>compiled down into a genetic designs<\/strong>, which ultimately can be automatically build into a lab (check out <a rel=\"noreferrer noopener\" aria-label=\"Aquarium (opens in a new tab)\" href=\"https:\/\/www.aquarium.bio\/\" target=\"_blank\">Aquarium<\/a> from the <a href=\"http:\/\/klavinslab.org\/\" target=\"_blank\" rel=\"noreferrer noopener\" aria-label=\"Klavins lab (opens in a new tab)\">Klavins lab<\/a>; I used it with a python API). <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">We could <strong>formally verify <\/strong>a programmed phenotype: microscopy images can be analysed and parsed against a LYSD program.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">It can be <strong>simulated using <\/strong><a href=\"https:\/\/ladam.info\/index.php\/2016\/01\/19\/gro-for-snowflake-yeast\/\"><strong>Gro<\/strong><\/a><strong>.<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Formally, LYSD is based on <strong>attribute graph grammars<\/strong>.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">I also used blockly (similar to Scratch) to let user program yeast microcolony in LYSD.<\/p>\n\n\n\n<figure class=\"wp-block-image\"><img data-recalc-dims=\"1\" decoding=\"async\" width=\"310\" height=\"396\" loading=\"lazy\" src=\"https:\/\/i0.wp.com\/ladam.info\/wp-content\/uploads\/2019\/01\/Screen-Shot-2016-12-02-at-1.30.48-PM.png?resize=310%2C396&#038;ssl=1\" alt=\"\" class=\"wp-image-1745\" srcset=\"https:\/\/i0.wp.com\/ladam.info\/wp-content\/uploads\/2019\/01\/Screen-Shot-2016-12-02-at-1.30.48-PM.png?w=310&amp;ssl=1 310w, https:\/\/i0.wp.com\/ladam.info\/wp-content\/uploads\/2019\/01\/Screen-Shot-2016-12-02-at-1.30.48-PM.png?resize=235%2C300&amp;ssl=1 235w\" sizes=\"auto, (max-width: 310px) 100vw, 310px\" \/><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>LYSD is a language a created to specify a phenotype. It can be compiled down into a genetic designs, which ultimately can be automatically build into a lab (check out Aquarium from the Klavins lab; I used it with a python API). We could formally verify a programmed phenotype: microscopy images can be analysed and&nbsp;&hellip;<\/p>\n","protected":false},"author":1,"featured_media":1746,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","om_disable_all_campaigns":false,"_monsterinsights_skip_tracking":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[260,257,254,279],"tags":[],"class_list":["post-1744","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-computational-biology","category-programming","category-synthetic-biology","category-yeast-spatiotemporal-development"],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"https:\/\/i0.wp.com\/ladam.info\/wp-content\/uploads\/2019\/01\/Screen-Shot-2016-07-21-at-10.35.07-PM.png?fit=427%2C427&ssl=1","_links":{"self":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1744","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/comments?post=1744"}],"version-history":[{"count":3,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1744\/revisions"}],"predecessor-version":[{"id":1770,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/posts\/1744\/revisions\/1770"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/media\/1746"}],"wp:attachment":[{"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/media?parent=1744"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/categories?post=1744"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ladam.info\/index.php\/wp-json\/wp\/v2\/tags?post=1744"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}