{"data":{"labs":[{"nid":"9630307","body":"TBD","title":"E. coli Ribosome 23S rRNA, Round 1","created":"01 Dec, 2019","founder_uid":"57675","founder":"Omei","field_puzzle_synthesis_winner_nid":"386950","num_synth":"20","affiliation":null,"selection":null,"cover_image":null,"num_synthesized":0,"winners":[]},{"nid":"3293294","body":"The Reproducibilty Test Lab is a series of cloud labs that will be synthesized with each synthesis round. The idea is to run a controlled set of RNA designs over multiple synthesis rounds and compare the SHAPE results between identical designs over time.\r\n\r\nThe objectives for this series are:\r\n\r\n * Provide a consistent measure of the reproducibility of the cloud lab synthesis results, for long term quality control,\r\n * Determine how much of the variation in synthesis results is captured by the error estimates reported for each synthesized base,\r\nThe Reproducibilty Test Lab is a series of cloud labs that will be synthesized with each synthesis round. The idea is to run a controlled set of RNA designs over multiple synthesis rounds and compare the SHAPE results between identical designs over time.The objectives for this series are: * Provide a consistent measure of the reproducibility of the cloud lab synthesis results, for long term quality control, * Determine how much of the variation in synthesis results is captured by the error estimates reported for each synthesized base, * Provide some guidance as to where the synthesis process might be improved, in order to increase reproducibility, and * Give those analyzing the synthesis data a better understanding of the variation to expect when comparing data from different synthesis rounds.\r\n\r\n*** 9\/26\/13 *** This got into the Active labs tab by mistake. I can't fix this myself; a developer will have to do that. But if you do have a sequence you want to suggest for the Reproducibility Lab, contact me (through the forum thread, the wiki page, or PM) directly. -- Omei","title":"Reproducibility Lab 1","created":"03 Sep, 2013","founder_uid":"57675","founder":"Omei","field_puzzle_synthesis_winner_nid":"12441","num_synth":"40","affiliation":"Eterna players","selection":null,"cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1378244610.png","num_synthesized":0,"winners":[]},{"nid":"3282859","body":"This is part of the codon riboswitch project -- another sequence that should switch when it binds histidine. [I originally posted the incorrect sequences -- thanks to brourd for catching this mistake.]","title":"Codon riboswitch [histidine]","created":"31 Aug, 2013","founder_uid":"20","founder":"rhiju","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"63","affiliation":"Rhiju Das, Stanford University","selection":null,"cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1377980114.jpg","num_synthesized":0,"winners":[]},{"nid":"3281145","body":"generate the golden standard data for CE auto assign.","title":"EteRNA R43 the Backwards C","created":"31 Aug, 2013","founder_uid":"25782","founder":"Hanjoo Kim","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"10","affiliation":"Hanjoo Kim (ACL, SNU)","selection":null,"cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1377924921.png","num_synthesized":0,"winners":[]},{"nid":"3281090","body":"generate golden standard for CE auto assigning data.\r\n","title":"EteRNA R45-46 FMN Aptamer with Single Binding Site","created":"31 Aug, 2013","founder_uid":"25782","founder":"Hanjoo Kim","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"28","affiliation":"Hanjoo Kim (ACL, SNU)","selection":null,"cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1377924439.png","num_synthesized":0,"winners":[]},{"nid":"3280580","body":"A version of the tristable RNA that will be more robust to barcode hairpin interferences. This mutate-and-map will push forward our understanding of multi-stable RNAs.","title":"M-stable","created":"31 Aug, 2013","founder_uid":"168","founder":"tsuname","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"41","affiliation":"Pablo Cordero, Stanford University","selection":null,"cover_image":null,"num_synthesized":0,"winners":[]},{"nid":"3280522","body":"An RNA with multiple structures predicted to be in almost equivalent portions in the ensemble. This mutate-and-map experiment will provide further insights in multi-stable RNAs.","title":"Un-stable","created":"31 Aug, 2013","founder_uid":"168","founder":"tsuname","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"46","affiliation":"Pablo Cordero, Stanford University","selection":null,"cover_image":null,"num_synthesized":0,"winners":[]},{"nid":"3280395","body":"Correcting barcode interference issues from the last MedLoop mutate-and-map run.","title":"MedLoop resurrected","created":"31 Aug, 2013","founder_uid":"168","founder":"tsuname","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"61","affiliation":"Pablo Cordero, Stanford University","selection":null,"cover_image":null,"num_synthesized":0,"winners":[]},{"nid":"3280109","body":"The mutate-and-map of the class I ligase, the first of several types of synthetic ribozymes produced by in vitro evolution and selection techniques and an important predecessor to the RNA replicase. What design principles can we extract from the ensemble of this molecule?","title":"Class I ligase","created":"31 Aug, 2013","founder_uid":"168","founder":"tsuname","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"91","affiliation":"Pablo Cordero, Stanford University","selection":null,"cover_image":null,"num_synthesized":0,"winners":[]},{"nid":"3279019","body":"This is part of the codon riboswitch project -- another sequence that should switch when it binds arginine.","title":"Codon riboswitch [arginine]","created":"30 Aug, 2013","founder_uid":"20","founder":"rhiju","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"59","affiliation":"Rhiju Das, Stanford University","selection":null,"cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1377885363.jpg","num_synthesized":0,"winners":[]},{"nid":"3278916","body":"This project tests an idea related to the origin of life, the so-called sterochemical hypothesis, and is described here: http:\/\/eterna.stanford.edu\/web\/lab\/3230283\/. I am rerunning the sequences to check for reproducibility and the effects of different barcode hairpins.","title":"Codon riboswitch [repeat of tryptophan]","created":"30 Aug, 2013","founder_uid":"20","founder":"rhiju","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"47","affiliation":"Rhiju Das, Stanford University","selection":null,"cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1377884446.jpg","num_synthesized":0,"winners":[]},{"nid":"3276955","body":"The goal is to design RNA sequences with multiple hairpins that fold correctly - i.e., 2 or 3 repeats of ms2 hairpins. In principle, each hairpin could also misfold with an adjacent hairpin, so in some sequences I include unique extensions of each stem loop. I need to find out what is the minimum length stem loop extension that will allow multiple hairpin repeats to fold correctly.","title":"Repeat hairpins v1","created":"29 Aug, 2013","founder_uid":"122003","founder":"jzalatan","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"17","affiliation":"jzalatan (Lim Lab)","selection":null,"cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1377815490.png","num_synthesized":0,"winners":[]},{"nid":"3272963","body":"sgRNA +48","title":"sgRNA48","created":"28 Aug, 2013","founder_uid":"106748","founder":"japas","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"63","affiliation":"Brian Alford (Das Lab)","selection":null,"cover_image":null,"num_synthesized":0,"winners":[]},{"nid":"3272880","body":"structure of the +67 sgRNA","title":"sgRNA67","created":"28 Aug, 2013","founder_uid":"106748","founder":"japas","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"82","affiliation":"Brian Alford (Das Lab)","selection":null,"cover_image":null,"num_synthesized":0,"winners":[]},{"nid":"3272795","body":"structure of the +89 sgRNA with no guide sequence","title":"sgRNA89_NGS","created":"28 Aug, 2013","founder_uid":"106748","founder":"japas","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"84","affiliation":"Brian Alford (Das Lab)","selection":null,"cover_image":null,"num_synthesized":0,"winners":[]},{"nid":"3272718","body":"structure of tracrRNA alone","title":"tracrRNA","created":"28 Aug, 2013","founder_uid":"106748","founder":"japas","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"76","affiliation":"Brian Alford (Das Lab)","selection":null,"cover_image":null,"num_synthesized":0,"winners":[]},{"nid":"3272668","body":"structure of crRNA alone","title":"crRNA","created":"28 Aug, 2013","founder_uid":"106748","founder":"japas","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"43","affiliation":"Brian Alford (Das Lab)","selection":null,"cover_image":null,"num_synthesized":0,"winners":[]},{"nid":"3230283","body":"This project tests an idea related to the origin of life, the so-called sterochemical hypothesis. I've hypothesized that there were switch-like molecules that converted amino acid signals to nucleic acid signals as an intermediate step in the development of the genetic code.\r\nThis is a designed of an RNA that responds to an amino acid (tryptophan) and changes its conformation to display a nucleic acid sequence; we've characterized its reponse to tryptophan in my lab but would like to get mutate\/map data to confirm its structure(s).\r\n","title":"A codon riboswitch","created":"10 Aug, 2013","founder_uid":"20","founder":"rhiju","field_puzzle_synthesis_winner_nid":"12441","num_synth":"47","affiliation":"Rhiju Das, Stanford University Biochemistry & Physics","selection":null,"cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1376176266.jpg","num_synthesized":0,"winners":[]},{"nid":"3230242","body":"This is a quick pilot scan looking for unusual conformations of a classic model system in RNA folding. Tandem G\/A pairs and A\/G pairs can form a number of conformations, some of which are pretty wacky. We want to see how the flanking base pairs toggle the structure and whether Eterna's SHAPE data can detect these switches! Pilot sequences have 4 hairpins, each containing some variant of the motif. In the names below, W, S, and K refer to A\/U, G\/C, and G\/U flanking pairs, respectively.\r\nMore info: http:\/\/www.rcsb.org\/pdb\/explore\/explore.do?structureId=2LX1\r\n","title":"Testing for crazy conformations of tandem G\/A and A\/G pairs","created":"10 Aug, 2013","founder_uid":"20","founder":"rhiju","field_puzzle_synthesis_winner_nid":"12441","num_synth":"18","affiliation":"Rhiju Das, Stanford University Biochemistry & Physics","selection":null,"cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1376175279.jpg","num_synthesized":0,"winners":[]},{"nid":"3230216","body":"Our lab has recently been focusing on understanding the stability and structure of G\/G mismatches -- famous in Eterna as boosted 1 by 1 loops. These mismatches can actually form two conformations in solution (see graphic) and predicting which one is more stable is an unsolved problem. We think Rosetta can solve it now. We also recently discovered (partly by mining Eterna data) that SHAPE distinguishes which conformation is dominant. This projects will test our predictions and set a foundation for a cool puzzle where we will challenge players to stabilize one of the conformations!","title":"Testing 3D structure prediction of G\/G mismatches (boosts!)","created":"10 Aug, 2013","founder_uid":"20","founder":"rhiju","field_puzzle_synthesis_winner_nid":"12441","num_synth":"16","affiliation":"Rhiju Das, Stanford University Biochemistry & Physics","selection":null,"cover_image":"\/sites\/default\/files\/cloud_lab_pictures\/picture-1376174976.png","num_synthesized":0,"winners":[]},{"nid":"3215320","body":"Now, here is a structure players have not had the chance to play with before. A five stem multibranch loop, with all stacks being adjacent to one another, being classified as 0-0-0-0-0 in terms of the number of unpaired bases. A bulge has been inserted into one stack as a marker to determine that the stem definitely has one unpaired nucleotide compared to the rest of the chemical footprint, which I expect to feature a high amount of protection from the SHAPE probe.","title":"Five Adjacent Stem Multibranch Loop","created":"06 Aug, 2013","founder_uid":"24263","founder":"Brourd","field_puzzle_synthesis_winner_nid":"2389702","num_synth":"60","affiliation":null,"selection":"user_vote","cover_image":null,"num_synthesized":60,"winners":[{"title":"Star Fisher","id":"3251730","puznid":"3215320","name":"garydfisher","uid":"57654","picture":"","SHAPE":"6, 0.0866, 0.0865, 0.0432, 0.0072, 0.0504, 0.1795, 0.2362, 0.0858, 0.0214, 0.0643, 0.1283, -0.0214, 0.0854, 0.2129, 0.9559, 0.2408, 0.4577, 0.0624, 0.0416, 0.083, 0.0829, 0.1242, -0.0028, 0.1032, 0.0413, 0.0824, -0.0427, 0.0206, 0.2054, 0.1844, 0.0819, 0.4293, 0.3907, 0.2149, 0.2676, 0.2467, 0.0799, 0.3974, 0.7046, 0.2743, 0.1564, 0.094, 0.0585, 0.1168, 0.3872, 0.0387, 0.0193, 0.0347, -0.0039, 0.0579, 0.1115, 0.4782, 0.7002, 0.7157, 0.391, 0.1301, 0.2593, 0.1478, 0.0369, 0.0554, 0.0369, 0.2299, 0.2961, 0.0731, 0.0183, 0.0589, -0.3154, 0.0288, 0.0668, 0.1393, 0.6306, 0.4477, 0.4272, 0.0356, 0.1884, 0.0177, 0.0532, 0.1415, 0.1059, 0.3813, 0.5937, 0.3348, 0.2244, 0.1129, 0.0955, 0.1715, 0.1028, 0.7956, 0.9264, 0.2827, 0.083, 0.0244, 0.3139, 0.0241, 0.0989, 0.4748, 1.2683, 0.2277, 1.0003, 0.2414","synthesis-score":"99"},{"title":"Mr. Clean's Brother","id":"3236135","puznid":"3215320","name":"Zanna","uid":"87216","picture":"sites\/default\/files\/pictures\/picture-87216.jpg","SHAPE":"6, 0.0926, 0.1095, 0.4504, 0.2369, 0.4232, 0.1054, 0.1328, 0.0302, 0.0052, 0.0226, 0.1054, 0.0973, 0.0246, 0.2505, 0.9434, 0.323, 0.4691, 0.1585, 0.0627, 0.2114, 0.12, 0.1817, 0.1767, 0.0811, 0.0358, 0.1, 0.05, 0.0095, 0.0517, 0.082, 0.1815, 0.1787, 0.2208, 0.3217, 0.4948, 0.2316, 0.1314, 0.2586, 0.4309, 0.2283, 0.0897, 0.0926, 0.0532, 0.1725, 0.3561, 0.2543, 0.0697, 0.1257, 0.2826, 0.0884, 0.3366, 0.3393, 0.9529, 0.6383, 0.7658, 0.1205, 0.0414, 0.044, 0.067, 0.0822, 0.0397, 0.1286, 0.0946, 0.0888, 0.0916, 0.0817, 0.2579, 0.0825, 0.0657, 0.1276, 0.5637, 0.3768, 0.1698, 0.2027, 0.1077, 0.0108, 0.0558, 0.0532, 0.0286, 0.1398, 0.1264, 0.0448, 0.0854, 0.0918, 0.1055, 0.0757, 0.1184, 0.9037, 0.4586, 0.0933, 0.0554, 0.0356, 0.0399, 0.0574, 0.0592, 0.0946, 0.4467, 0.0998, 0.1678, 0.0741","synthesis-score":"98"},{"title":"Mr. Clean's Cousins","id":"3236149","puznid":"3215320","name":"Zanna","uid":"87216","picture":"sites\/default\/files\/pictures\/picture-87216.jpg","SHAPE":"6, 0.0809, 0.232, 0.6288, 0.4123, 0.355, 0.0982, 0.146, 0.1187, 0.0125, 0.0624, 0.0223, 0.0933, 0.0839, 0.2848, 0.7787, 0.4309, 0.422, 0.2156, 0.0723, 0.1942, 0.1219, 0.2052, 0.1848, 0.1191, 0.0298, 0.0951, 0.0119, 0.0066, 0.0376, 0.0583, 0.1441, 0.2166, 0.0719, 0.2228, 0.4891, 0.4685, 0.1128, 0.1924, 0.474, 0.2039, 0.1265, 0.0789, 0.1216, 0.1136, 0.4124, 0.2617, 0.0581, 0.1394, 0.1752, 0.0475, 0.339, 0.2607, 0.8621, 0.6826, 0.7981, 0.0553, 0.0579, 0.0209, 0.0481, 0.064, 0.032, 0.1325, 0.0797, 0.0897, 0.0578, 0.1103, 0.2721, 0.1014, 0.0857, 0.1671, 0.4997, 0.3351, 0.222, 0.1948, 0.0934, 0.0403, 0.0556, 0.0436, 0.0359, 0.145, 0.0869, 0.0613, 0.0705, 0.1508, 0.0966, 0.0609, 0.1712, 0.7841, 0.9528, 0.2314, 0.1524, 0.0331, 0.054, 0.1567, 0.0463, 0.2098, 0.6721, 0.2188, 0.1321, 0.1319","synthesis-score":"98"},{"title":"JR_5Adj_Rnd1_Sub2","id":"3236789","puznid":"3215320","name":"JR","uid":"42833","picture":"sites\/default\/files\/pictures\/picture-42833.png","SHAPE":"6, 0.0135, 0.0134, 0.0537, 0.0134, 0.0403, 0.194, 0.3196, 0.1462, 0.0266, 0.0299, 0.1821, 0.1256, 0.0659, 0.3175, 0.155, 0.1091, 0.2888, 0.1497, 0.038, 0.0714, 0.251, 0.1935, 0.304, 0.1889, 0.2362, 0.1897, 0.0439, 0.0502, 0.1838, 0.0602, 0.0696, 0.249, 0.1439, 0.1945, 0.2251, 0.1186, 0.0769, 0.1102, 0.659, 0.0729, 0.0431, 0.0509, 0.013, 0.1939, 0.3804, 0.1055, 0.0639, 0.0699, 0.0948, 0.0425, 0.103, 0.5159, 0.2115, 0.2837, 0.2604, 0.101, 0.1428, 0.0198, 0.073, 0.0503, 0.0561, 0.1047, 0.1295, 0.0911, 0.0249, 0.0235, 0.0235, 0.0489, 0.0972, 0.3027, 0.1661, 0.2007, 0.1462, 0.0983, 0.1483, 0.0519, 0.0253, 0.0788, 0.027, 0.3862, 0.2403, 0.1176, 0.0795, 0.0681, 0.0567, 0.034, 0.0622, 0.5616, 0.4576, 0.1781, 0.0501, 0.0389, 0.0201, 0.1387, 0.061, 0.1328, 0.5171, 0.0918, 0.2162, 0.1798","synthesis-score":"98"},{"title":"Five SS - Brourd - Lab 'Five Adjacent Stem Multibranch Loop' R1 - Sub 3 (G-C ++)","id":"3236816","puznid":"3215320","name":"Brourd","uid":"24263","picture":"sites\/default\/files\/pictures\/picture-24263.png","SHAPE":"6, -0.0449, 0.0458, 0, -0.0907, -0.0448, 0.0687, 0.2963, 0.1365, -0.045, 0, -0.0896, 0, 0.0454, 0.1359, 0.4501, 0.4028, 0.4006, 0.1333, 0.0444, 0, 0.0887, 0.0443, 0.2649, 0.1322, 0, 0.044, 0.1319, 0.0878, -0.0462, 0.0877, 0.0876, 0.2182, 1.1596, 0.5117, 0.466, 0.1269, 0.0423, 0.2947, 1.1597, 0.0414, 0.1652, 0.0825, 0.0824, 0.0823, 0.0411, 0.1027, 0.0616, 0.082, 0.0819, 0, 0.0818, 0.0817, 0.768, 0.2015, 0.1207, 0, 0.0804, 0, 0, 0.0803, 0.2002, 0.1996, 0.0694, 0.1127, 0.1917, 0.1451, 0.1806, 0.1014, 0.1273, 0.3262, 0.6337, 0.6472, 0.5391, 0.1521, -0.0137, 0.1138, 0.0758, 0.0757, 0.2264, 0.338, 0.075, 0.075, 0.1869, 0.0374, 0.1863, 0.0592, 0.2594, 0.5151, 0.8004, 0.3085, 0.1805, 0.0721, 0.036, -0.0533, 0.1438, 0.4998, 2.4485, 1.1537, 0.5389, 0.7994","synthesis-score":"98"},{"title":"Mat - Five stem loop - D3","id":"3248010","puznid":"3215320","name":"mat747","uid":"267","picture":"sites\/default\/files\/pictures\/picture-267.jpg","SHAPE":"6, 0.0587, 0.0659, 0.0659, 0.0585, 0.0738, 0.0645, 0.2684, 0.1481, 0.0151, 0.029, 0.1308, -0.0133, 0.0722, 0.161, 0.9135, 0.3775, 0.4641, 0.0492, 0.0492, 0.0107, 0.0456, 0.0245, 0.8348, 0.1037, 0.0484, 0.1449, 0.1101, 0.0137, 0.055, 0.0513, 0.1336, 0.3242, 0.9343, 0.6302, 0.3887, 0.0619, 0.0756, 0.1223, 1.4053, 0.2003, 0.071, 0.1215, 0.0579, 0.167, 0.1538, 0.0566, 0.0118, 0.032, 0.0756, -0.0074, 0.0447, 0.1354, 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