{"id":1285,"date":"2021-03-17T17:30:45","date_gmt":"2021-03-17T17:30:45","guid":{"rendered":"http:\/\/protobiology.org\/wp3\/?p=1285"},"modified":"2025-08-26T21:25:14","modified_gmt":"2025-08-26T21:25:14","slug":"toolbox","status":"publish","type":"post","link":"http:\/\/protobiology.org\/wp3\/2021\/03\/17\/toolbox\/","title":{"rendered":"Toolbox"},"content":{"rendered":"<p><a class=\"bookmark\" name=\"toolbox\"><\/a><\/p>\n<h1>Synthetic cell tools developed by our lab<\/h1>\n<p>We have developed a toolbox of computational resources, custom devices and protocols for engineering synthetic cells.\u00a0<\/p>\n<table style=\"height: 202px; width: 75%; border-collapse: separate;\" cellpadding=\"10\">\n<tbody>\n<tr>\n<td style=\"width: 40%; background-color: #f5f5f5; border: 1px solid #000000;\">\n<p><a href=\"http:\/\/protobiology.org\/tools-liposome.php\" rel=\"noopener noreferrer\"> Liposome calculation tools<br \/>\n<\/a><a href=\"http:\/\/protobiology.org\/tools-liposome.php\" rel=\"noopener noreferrer\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter wp-image-1342\" src=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com1_-117x150.png\" alt=\"prototyping biology\" width=\"70\" height=\"90\" srcset=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com1_-117x150.png 117w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com1_-156x200.png 156w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com1_-800x1024.png 800w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com1_-768x983.png 768w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com1_-1200x1536.png 1200w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com1_-1599x2048.png 1599w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com1_.png 2000w\" sizes=\"auto, (max-width: 70px) 100vw, 70px\" \/><\/a><\/p>\n<\/td>\n<td style=\"width: 20%; border-color: #ffffff; background-color: #ffffff; border-width: 1px;\">\n<p>&nbsp;<\/p>\n<\/td>\n<td style=\"width: 40%; background-color: #f5f5f5; border: 1px solid #000000;\">\n<p><a href=\"http:\/\/trumpet.bio\" target=\"_blank\" rel=\"noopener noreferrer\">Trumpet: biocomputing platform.<br \/>\n<\/a><a href=\"http:\/\/trumpet.bio\" target=\"_blank\" rel=\"noopener noreferrer\"><img loading=\"lazy\" decoding=\"async\" class=\"alignleft wp-image-1340 size-thumbnail\" src=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/trumpet-logo-4-150x98.png\" alt=\"prototyping biology\" width=\"150\" height=\"98\" srcset=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/trumpet-logo-4-150x98.png 150w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/trumpet-logo-4-200x130.png 200w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/trumpet-logo-4-1024x666.png 1024w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/trumpet-logo-4-768x500.png 768w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/trumpet-logo-4.png 1360w\" sizes=\"auto, (max-width: 150px) 100vw, 150px\" \/><\/a><\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>&nbsp;<\/p>\n<table style=\"height: 202px; width: 75%; border-collapse: separate;\" cellpadding=\"10\">\n<tbody>\n<tr>\n<td style=\"width: 40%; background-color: #f5f5f5; border: 1px solid #000000;\">\n<p><a href=\"http:\/\/liposome.tech\" target=\"_blank\" rel=\"noopener noreferrer\">Liposome formation apparatus<br \/>\n<\/a><a href=\"http:\/\/liposome.tech\" target=\"_blank\" rel=\"noopener noreferrer\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter wp-image-1392 size-thumbnail\" src=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/ezgif.com-gif-maker-2-115x150.gif\" alt=\"prototyping biology\" width=\"115\" height=\"150\" srcset=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/ezgif.com-gif-maker-2-115x150.gif 115w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/ezgif.com-gif-maker-2-153x200.gif 153w\" sizes=\"auto, (max-width: 115px) 100vw, 115px\" \/><\/a><\/p>\n<\/td>\n<td style=\"width: 20%; border-color: #ffffff; background-color: #ffffff; border-width: 1px;\">\n<p>&nbsp;<\/p>\n<\/td>\n<td style=\"width: 40%; background-color: #f5f5f5; border: 1px solid #000000;\">\n<p><a href=\"https:\/\/www.akabycells.org\" target=\"_blank\" rel=\"noopener noreferrer\">Akaby strain<br \/>\n<\/a><a href=\"https:\/\/www.akabycells.org\" target=\"_blank\" rel=\"noopener noreferrer\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter wp-image-1485\" src=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com_-1-150x150.png\" alt=\"prototyping biology\" width=\"110\" height=\"110\" srcset=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com_-1-150x150.png 150w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com_-1-200x200.png 200w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com_-1-100x100.png 100w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/pngwing.com_-1.png 512w\" sizes=\"auto, (max-width: 110px) 100vw, 110px\" \/><\/a><\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>&nbsp;<\/p>\n<table style=\"height: 202px; width: 75%; border-collapse: separate;\" cellpadding=\"10\">\n<tbody>\n<tr>\n<td style=\"width: 40%; background-color: #f5f5f5; border: 1px solid #000000;\">\n<p><a href=\"https:\/\/trnafoundry.info\" target=\"_blank\" rel=\"noopener noreferrer\">tRNA Foundry<br \/>\n<\/a><a href=\"https:\/\/trnafoundry.info\" target=\"_blank\" rel=\"noopener noreferrer\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter wp-image-1997 size-thumbnail\" src=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/trnafoundrylogo-150x120.jpg\" alt=\"prototyping biology\" width=\"150\" height=\"120\" srcset=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/trnafoundrylogo-150x120.jpg 150w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/trnafoundrylogo-200x160.jpg 200w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/trnafoundrylogo-768x613.jpg 768w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/trnafoundrylogo.jpg 771w\" sizes=\"auto, (max-width: 150px) 100vw, 150px\" \/><\/a><\/p>\n<\/td>\n<td style=\"width: 20%; border-color: #ffffff; background-color: #ffffff; border-width: 1px;\">\n<p>&nbsp;<\/p>\n<\/td>\n<td style=\"width: 40%; background-color: #f5f5f5; border: 1px solid #000000;\">\n<p><a href=\"https:\/\/cyanoconstruct.com\/\" target=\"_blank\" rel=\"noopener noreferrer\">CyanoConstruct<br \/>\n<\/a><a href=\"https:\/\/cyanoconstruct.com\/\" target=\"_blank\" rel=\"noopener noreferrer\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter wp-image-1998 size-thumbnail\" src=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/cyanoconstruct-93x150.png\" alt=\"prototyping biology\" width=\"93\" height=\"150\" srcset=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/cyanoconstruct-93x150.png 93w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/cyanoconstruct-124x200.png 124w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/cyanoconstruct-637x1024.png 637w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/cyanoconstruct-768x1234.png 768w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/cyanoconstruct.png 832w\" sizes=\"auto, (max-width: 93px) 100vw, 93px\" \/><\/a><\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>&nbsp;<\/p>\n<p>Addgene deposits from out lab (plasmids and bacteria strains):<br \/>\n<a href=\"https:\/\/www.addgene.org\/Kate_Adamala\/\" target=\"_blank\" rel=\"noopener\">www.addgene.org\/Kate_Adamala\/<\/a><\/p>\n<p>&nbsp;<\/p>\n<hr \/>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignright wp-image-1328\" src=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/1gears-cell5-1-200x200.jpg\" alt=\"prototyping biology\" width=\"99\" height=\"99\" srcset=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/1gears-cell5-1-200x200.jpg 200w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/1gears-cell5-1-150x150.jpg 150w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/1gears-cell5-1-768x768.jpg 768w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/1gears-cell5-1-100x100.jpg 100w, http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/1gears-cell5-1.jpg 861w\" sizes=\"auto, (max-width: 99px) 100vw, 99px\" \/><\/p>\n<p><em>Coming soon:<\/em><\/p>\n<p>Cellulator<\/p>\n<p>&nbsp;<\/p>\n<p>Tools are free to use; <a href=\"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/\" target=\"_blank\" rel=\"noopener noreferrer\">CC BY-NC-SA 4.0<\/a>.<br \/>\n<img loading=\"lazy\" decoding=\"async\" class=\"alignleft wp-image-1368 size-full\" src=\"http:\/\/protobiology.org\/wp3\/wp-content\/uploads\/2021\/03\/88x31.png\" alt=\"prototyping biology\" width=\"88\" height=\"31\" \/><\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Synthetic cell tools developed by our lab We have developed a toolbox of computational resources, custom devices and protocols for engineering synthetic cells.\u00a0 Liposome calculation tools &nbsp; Trumpet: biocomputing platform. &nbsp; Liposome formation apparatus &nbsp; Akaby strain &nbsp; tRNA Foundry &nbsp; CyanoConstruct &nbsp; Addgene deposits from out lab (plasmids and bacteria strains): www.addgene.org\/Kate_Adamala\/ &nbsp; Coming &hellip; <\/p>\n<p class=\"link-more\"><a href=\"http:\/\/protobiology.org\/wp3\/2021\/03\/17\/toolbox\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Toolbox&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[11],"tags":[],"class_list":["post-1285","post","type-post","status-publish","format-standard","hentry","category-static"],"_links":{"self":[{"href":"http:\/\/protobiology.org\/wp3\/wp-json\/wp\/v2\/posts\/1285","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/protobiology.org\/wp3\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/protobiology.org\/wp3\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/protobiology.org\/wp3\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/protobiology.org\/wp3\/wp-json\/wp\/v2\/comments?post=1285"}],"version-history":[{"count":66,"href":"http:\/\/protobiology.org\/wp3\/wp-json\/wp\/v2\/posts\/1285\/revisions"}],"predecessor-version":[{"id":2021,"href":"http:\/\/protobiology.org\/wp3\/wp-json\/wp\/v2\/posts\/1285\/revisions\/2021"}],"wp:attachment":[{"href":"http:\/\/protobiology.org\/wp3\/wp-json\/wp\/v2\/media?parent=1285"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/protobiology.org\/wp3\/wp-json\/wp\/v2\/categories?post=1285"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/protobiology.org\/wp3\/wp-json\/wp\/v2\/tags?post=1285"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}