{"data":{"labs":[{"nid":"9580499","body":"We've already given you all some motivation<\/a> for the overall aim of redesigning a ribosome. I won't repeat the hype here, but in brief: we want to change an incredibly complex part of synthetic biology using the unique capabilities of Eterna players.In this challenge, try to stabilize the different components of the ribosome. There are three rRNA molecules: the 5S, 16S, and 23S. While we were interested in the 5S for the pilot challenge, the components that seem like they are the most challenging and interesting to design are the big ones -- the 16S and 23S. Since we have eight successful alternative 5S designs already, we can perhaps focus our efforts (and our experiments) on the harder puzzles.This first round will run until midnight Eastern time on 2\/1, at which point the 20 best 16S and 20 best 23S designs will be synthesized and evaluated using an in vitro assay at Northwestern.This ribosome pilot test is made possible due to experimental technologies developed and carried out by collaborators at Northwestern University (Antje Kruger, Michael Jewett), a new Linearfold folding engine developed by collaborators at Oregon State University (Liang Huang and his group), and special support for ribosome computational modeling by Andy Watkins.","title":"Ribosome Challenge Round 1","status":"1","created":"30 Oct, 2019","founder_uid":"57675","founder":"Omei","founder_picture":"sites\/default\/files\/pictures\/picture-57675.png","proposed_date":null,"synth_date":null,"num_synth":"40","affiliation":"Stanford University","selection":null,"cover_image":"https:\/\/s3.amazonaws.com\/eterna\/labs\/news_blog_images\/Simple+colored+ribosome+1.png","cloud_round":null,"puzzles":[{"round":1,"puzzles":[9622912,9630307,9695203,9691430,9696643,9696707,9698727,9699092,9698990,9699101,9699122,9700182,9700204,9701507,9701755,9701766,9701773,9701776,9701785],"playable":true}],"restart":false},{"nid":"9215705","body":"This project introduces an entirely new kind of lab challenge for Eterna players. By designing variations of a naturally occurring RNA-based assembly -- the ribosome --, we'll be taking part in a project to create new variants with a widely expanded array of uses. For more context of this challenge, read Andy Watkins' recent news post<\/a>.\r\n\r\nThe E Coli bacteria's ribosome contains three distinct strands of RNA, which are named 5S, 16S and 23S. The 5S has 120 bases -- in the same ballpark as our past lab puzzles. However, the 16S rRNA contains 1534 bases and the 23S has 2845. Working with RNAs of these lengths presents a number of challenges.\r\n\r\nIn this warm-up project, we have broken up the full 16S and 23S sequences into multiple pieces as part of a \"divide and conquer\" strategy. For each of these nine smaller puzzles, try to 1) lower the the Natural\/Target delta, with 2) a minimal number of mutations. These are competing goals, and we don't know what the optimal trade-off is. So please submit designs with a wide range of mutation counts, while trying to find the lowest energy delta for that number of mutations.\r\n\r\nBeing a warm-up project, there are no synthesis slots allocated directly to this project. The designs that will be synthesized and tested will be chosen from a second project (to be published soon) that has just three puzzles -- one for each of the full ribosomal RNA pieces.\r\n\r\nThis ribosome pilot test is made possible due to experimental technologies developed by collaborators at Northwestern University (Anne d'Aquino, Michael Jewett), a new Linearfold folding engine developed by collaborators at Oregon State University (Liang Huang and his group), and special support for ribosome computational modeling by Andy Watkins through the Center for Genetically Encoded Materials.","title":"Ribosome Pilot Challenge Warm-up","status":"1","created":"29 Jan, 2019","founder_uid":"57675","founder":"Omei","founder_picture":"sites\/default\/files\/pictures\/picture-57675.png","proposed_date":null,"synth_date":null,"num_synth":"0","affiliation":"Northwestern University, Oregon State University, Stanford University, Center for Genetically Encoded Materials","selection":null,"cover_image":"https:\/\/s3.amazonaws.com\/eterna\/labs\/news_blog_images\/Simple+colored+ribosome+1.png","cloud_round":"118","puzzles":[{"round":1,"puzzles":["9218290","9169766","9170775","9171664","9148855","9173653","9164548","9178580","9026448",9240080,9244083,9243585,9245552],"playable":false}],"restart":false}],"num_labs":"2","num_slots":"40"},"memcache":true}