API for Server Data Queries/Server Queries: type=active projects

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Contents

Sample query

http://eterna.cmu.edu//get/?type=active_projects

Results

{
   "data":{
      "labs":[
         {
            "nid":"3381843",
            "body":"There are two ways to approach the problem I'm presenting this time.<br\/><br\/>The first is simply to try to solve the structure the way it is actually presented in the lab (see picture below), and get the best possible score. To those who will follow this path, I wish good luck. <br\/><br\/><img style=\"width: 400px;\"  src=\"http:\/\/eternawiki.org\/wiki\/images\/NF3_direct.png\"\/><br\/><i>(the color coding is simply blue\/yellow = paired\/unpaired)<\/i><br\/><br\/>The other path is (for my money) a little smarter. If you guys manage to create a so-called \"kissing hairpin\", which is another form of pseudoknot that we haven't played with until now, well, you may reach a 100 score, or very close, and given the outline below and our recent successes with pseudoknots, this seems to be easier.<br\/><br\/><img style=\"width: 400px;\" src=\"http:\/\/eternawiki.org\/wiki\/images\/NF3_kiss.png\" \/><br\/><br\/>Have fun! :)<br\/>",
            "title":"New Frontier 3",
            "status":"1",
            "created":"28 Sep, 2013",
            "founder_uid":"49507",
            "founder":"ElNando888",
            "founder_picture":"sites\/default\/files\/pictures\/picture-49507.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"60",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":"https:\/\/s3.amazonaws.com\/eterna\/puzzle_mid_thumbnails\/thumbnail3381843.png",
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3381842"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376361",
            "body":"As some of you may know, a handful of players have taken a keen interest in the analysis and discussion of Poly Adenine sequences. An important feature present in every run of protected Poly A is an exposed stretch of about 6 adenine residues on the 3' end. This project is meant to test several things.\r\n\r\n1. The stability of the poly A structure compared to the predicted MFE structure.\r\n\r\n2. The necessity of the 3' exposed adenine to not be participating in any interaction.\r\n\r\nHopefully, this project can shed a little light on the nature of the Poly A structure.\r\n\r\n30 slots are requested for synthesis.",
            "title":"Poly (A) Structure Analysis 1",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"30",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3363516"
                  ]
               }
            ],
            "restart":false
         },
         ...
      ],
      "num_labs":"23",
      "num_slots":"725"
   },
   "memcache":true
}

Notes

 

{
   "data":{
      "labs":[
         {
            "nid":"3381843",
            "body":"There are two ways to approach the problem I'm presenting this time.<br\/><br\/>The first is simply to try to solve the structure the way it is actually presented in the lab (see picture below), and get the best possible score. To those who will follow this path, I wish good luck. <br\/><br\/><img style=\"width: 400px;\"  src=\"http:\/\/eternawiki.org\/wiki\/images\/NF3_direct.png\"\/><br\/><i>(the color coding is simply blue\/yellow = paired\/unpaired)<\/i><br\/><br\/>The other path is (for my money) a little smarter. If you guys manage to create a so-called \"kissing hairpin\", which is another form of pseudoknot that we haven't played with until now, well, you may reach a 100 score, or very close, and given the outline below and our recent successes with pseudoknots, this seems to be easier.<br\/><br\/><img style=\"width: 400px;\" src=\"http:\/\/eternawiki.org\/wiki\/images\/NF3_kiss.png\" \/><br\/><br\/>Have fun! :)<br\/>",
            "title":"New Frontier 3",
            "status":"1",
            "created":"28 Sep, 2013",
            "founder_uid":"49507",
            "founder":"ElNando888",
            "founder_picture":"sites\/default\/files\/pictures\/picture-49507.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"60",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":"https:\/\/s3.amazonaws.com\/eterna\/puzzle_mid_thumbnails\/thumbnail3381843.png",
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3381842"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376361",
            "body":"As some of you may know, a handful of players have taken a keen interest in the analysis and discussion of Poly Adenine sequences. An important feature present in every run of protected Poly A is an exposed stretch of about 6 adenine residues on the 3' end. This project is meant to test several things.\r\n\r\n1. The stability of the poly A structure compared to the predicted MFE structure.\r\n\r\n2. The necessity of the 3' exposed adenine to not be participating in any interaction.\r\n\r\nHopefully, this project can shed a little light on the nature of the Poly A structure.\r\n\r\n30 slots are requested for synthesis.",
            "title":"Poly (A) Structure Analysis 1",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"30",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3363516"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376358",
            "body":"Ready for a new twist in lab puzzles?<br\/><br\/>

<\/br>
�������***�CURSES!�FOILED�AGAIN!�***<\/div>
When�I�proposed�this�lab,�there�was�no�UI�for�going�back�and�checking�or�editing�the�proposal.��I�didn't�find�out�until�just�now�that�the�bases�I�intended�to�lock,�in�order�to�block�the�obvious�AU�matches�from�forming�the�target�structure,�didn't�get�locked.��So�as�it�stands,�this�lab,�if�synthesized,�could�be�completely�pointless.

Here's�what�I�propose�in�order�to�make�something�useful�out�of�this.��There's�been�a�discussion�on�the�forum�about�how�to�augment�the�lab�submission\/voting�procedures�to�better�support�player�research�where�incentivizing�players�to�get�a�top�score�with�the�normal�scoring�procedure�is�actually�counter-productive.��Some�have�come�out�in�favor�of�simply�giving�the�lab�proposer�total�control�of�which�designs�get�synthesized.��I'm�not�totally�against�that,�but�I�think�it�could�lead�to�some�resentment�that�we've�so�successfully�avoided�on�Eterna.��I�think�it�would�be�better�if�we�could�use�some�combination�of�limited�administrative�power�and�players'�cooperation�to�achieve�just�as�good�results.

So�I�am�going�to�test�the�effectiveness�of�\"player�cooperation\"�by�asking�players�to�settle�on�one�design�(I�suggest�the�first�submitted�design,�Zanna's�\"Bender\")�to�vote�for�that�is�virtually�sure�to�get�you�a�top�score�for�your�best�vote.�Then,�don't�vote�for�any�other�design�that�relies�on�a�long�string�of�U's�to�achieve�the�target�SHAPE�with�the�long�string�of�locked�A's.�(After�all,�there's�nothing�in�it�for�you.)��Brourd's�first�submission,�for�example,�is�shooting�for�the�right�SHAPE�values�without�shooting�for�the�target�structure.��If�enough�players�heed�this�request,�there�will�be�little�incentive�to�even�submit�a�design�with�long�AU�strings,�and�most�of�the�designs�that�get�enough�votes�for�synthesis�will�actually�be�useful�from�a�research�perspective.

Thank�you.�--�Omei<\/i>

Now,�back�to�our�regular�sponsor.
<h5></h5><h5></h5><h5></h5><h5></h5></h5></h3><br\/><br\/>The target structure for this lab looks pretty boring.  The catch is that I have locked so many bases that you can't possibly get your sequence to fold into the target structure.  To get a good score (which should be quite possible), you'll have to confront the fact that the lab gets results that go beyond the energy model used in the game.<br\/><br\/>The scientific goal for this lab is to gather more data about how long strings of adenine somehow get protected from the SHAPE probe.  Back in round 1 of Cloud Lab 19 (Eli's Big Hairpin Loop), we learned that if a string has enough consecutive A's, the lab will score them \"blue\", as though they are bound, even if there are no complementary bases for them to pair with.  For round 2, most people had that figured out, and loops weren't left with long strings of A's.  This is actually the origin of the \"constraint\" that a lab sequence shouldn't have more than four consecutive A's.  The devs weren't sure whether the blue scores were real, or whether there was a problem with the experimental procedure.  But the data seems to be very real, and it suggests these poly-A strings could be of tremendous scientific and technological significance.<br\/><br\/>Your assignment, should you choose to accept it, is to predict how many consecutive A's (and where) it will take to get blue SHAPE data to match one half of the target's structure, and fill out the other half with two hairpins (or whatever else you can think of) to get the other half of the SHAPE data to match what the target structure implies.<br\/><br\/>There is already a bunch of discussion of poly-A results from past labs on the forums.  See <a href=\"https:\/\/getsatisfaction.com\/eternagame\/topics\/eixkksvt9lty3\">Long stretches of A\u2019s and metal ions - a love story?<\/a>, and I'll post some kind of compact summary of it when the lab goes live."</span>,
            "title":"Impossible Folding I",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"57675",
            "founder":"Omei",
            "founder_picture":"sites\/default\/files\/pictures\/picture-57675.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"40",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3340873"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376356",
            "body":"This frequency experiment a the continuation of Leontis\u2019 lab <a href=\"http:\/\/eterna.cmu.edu\/web\/lab\/3096140\/\">Intrinsically folded RNA<\/a><br\/><br\/>Instructions:<br\/>In this lab, I have locked the yellow bases at a particular interval. \n\nUPDATE: Originally I asked for following in this lab: \"Use either, blue, green or red bases at the unlocked spots in the string (63 bases) and use same color the whole way through.\"\n\nHowever after I proposed the lab, Omei and the forum discussion <a href=\"https:\/\/getsatisfaction.com\/eternagame\/topics\/is_there_a_position_dependent_bias_in_the_shape_data\">Is there a position-dependent bias in the SHAPE data?<\/a> brought to my attention that the DNA sequencing procedure used in the cloud labs starts to go bad if any 25 (or longer) sub-sequence of the design appears more than once in the full sequence.  This means you shouldn't fill in your entire design with the identical pattern, unless you are consciously doing it because you are curious about what the data processing will do with it.\n\n<br\/><br\/>Aim: This is part of an ongoing investigation to find out which bases draws special patterns in the SHAPE data. Already there are binding patterns emerging in the SHAPE data, in relation to the  frequency of a non-A base placed in a string of A\u2019s. We are several players taking interest in those.<br\/><br\/>Check out the discussion and ideas here:<br\/><br\/><a href=\"https:\/\/getsatisfaction.com\/eternagame\/topics\/eixkksvt9lty3\">Long stretches of A\u2019s and metal ions - a love story?<\/a><br\/>\n ",
            "title":"Intrinsical - Frequency 8",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"8627",
            "founder":"Eli Fisker",
            "founder_picture":"sites\/default\/files\/pictures\/picture-8627.jpg",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"60",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3337059"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376349",
            "body":"This frequency experiment a the continuation of Leontis\u2019 lab <a href=\"http:\/\/eterna.cmu.edu\/web\/lab\/3096140\/\">Intrinsically folded RNA<\/a><br\/><br\/>Instructions:<br\/>In this lab, I have locked the yellow bases at a particular interval. <br\/><br\/>UPDATE: Originally I asked for following in this lab: \"Use either, blue, green or red bases at the unlocked spots in the string (63 bases) and use same color the whole way through.\"<br\/><br\/>However after I proposed the lab, Omei and the forum discussion <a href=\"https:\/\/getsatisfaction.com\/eternagame\/topics\/is_there_a_position_dependent_bias_in_the_shape_data\">Is there a position-dependent bias in the SHAPE data?<\/a> brought to my attention that the DNA sequencing procedure used in the cloud labs starts to go bad if any 25 (or longer) sub-sequence of the design appears more than once in the full sequence.  This means you shouldn't fill in your entire design with the identical pattern, unless you are consciously doing it because you are curious about what the data processing will do with it.<br\/><br\/>Aim: This is part of an ongoing investigation to find out which bases draws special patterns in the SHAPE data. Already there are binding patterns emerging in the SHAPE data, in relation to the  frequency of a non-A base placed in a string of A\u2019s. We are several players taking interest in those.<br\/><br\/>Check out the discussion and ideas here:<br\/><br\/><a href=\"https:\/\/getsatisfaction.com\/eternagame\/topics\/eixkksvt9lty3\">Long stretches of A\u2019s and metal ions - a love story?<\/a><br\/><br\/><br\/>This lab is in honor of Nando who wish to check out CACA...<br\/><br\/><br\/><br\/><br\/>",
            "title":"Intrinsical - Frequency 1",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"8627",
            "founder":"Eli Fisker",
            "founder_picture":"sites\/default\/files\/pictures\/picture-8627.jpg",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"60",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3336922"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376343",
            "body":"My lab Big hairpin loop had 55 single nucleotides in the loop. Leontis lab Intrinsically folded RNA had 63 single bases in a row. (not counting the first 5 lead ones). In longer stretches of all A's, I see the color of SHAPE data and the bluish color beginning, change depending on length of the lines of A's. <br\/><br\/>So now I'm going to make a real big hairpin loop. I think the length of poly A's matter. <br\/><br\/>In this lab I expect the bluish pattern from the start of A's sequences to be longer, but also go weaker and more towards yellow in color, judging on what I see this far. <br\/><br\/>In this lab I have locked most of the loop nucleotides. In the control lab, I have left them unlocked, so you can test out what you think will be successfull patterns. <br\/><br\/>Omei proposed the idea that a coil might be happening in the RNA in long stretches of A's and this is why the loop appears to be binding up with itself. I find that interesting. <a href=\"https:\/\/getsatisfaction.com\/eternagame\/topics\/eixkksvt9lty3#reply_12910832\">Is this what happens?<\/a> <br\/><br\/>Read more about the ideas behind in this post. We are several players taking interest in this. <br\/><br\/> <a href=\"https:\/\/getsatisfaction.com\/eternagame\/topics\/eixkksvt9lty3#topic_5629966\">Long stretches of A\u2019s and metal ions - a love story?<\/a> <br\/><br\/>Welcome to join the investigation!<br\/><br\/>",
            "title":"Really big loop coil - Classic science toy",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"8627",
            "founder":"Eli Fisker",
            "founder_picture":"sites\/default\/files\/pictures\/picture-8627.jpg",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"40",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":"https:\/\/s3.amazonaws.com\/eterna\/cloud_lab_pictures\/picture-1379027081.png",
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3328967"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376328",
            "body":"In this project, the goal is to investigate the SHAPE profile of a structure where a sequence should have an almost equal chance to fold into two different conformations. In this case, it is a C-G pair with a single bulging residue. 25 slots are requested for synthesis.",
            "title":"SHAPE Profile - Most Likely Base Pair C\/G",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"25",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3292609"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376327",
            "body":"According to the results for Location Dependent Chemical Footprints Part 1, there was a most unexpected result.\r\n\r\n<img src=\"http:\/\/i.imgur.com\/xWZXUot.png\" alt=\"Puzzle creation challenge\" width=\"355\" height=\"329\">\r\n\r\nApparently, the entire helix was melted, even though there were 3 G-C pairs, and a GAAA tetraloop. According to the SHAPE reactivity data, every nucleotide except the cytosine residues in the CG\/CG quad are above 0.5, meaning the presence of the fold in the ensemble is questionably low. This challenge is proposed to determine if the result for this helix can be duplicated, and to investigate this lack of stability.\r\n\r\nThere are two parts to this project, flipping the A-U pair in the helix. \r\n\r\nIf results are duplicated, I hope to create a series of lab projects, to mutate pairs in the stem and tetraloop, to determine what can stabilize the helix.\r\n\r\n25 slots are requested for synthesis",
            "title":"Repeatability - Melted Helix Variation 2",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"25",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3284565"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376326",
            "body":"According to the results for Location Dependent Chemical Footprints Part 1, there was a most unexpected result.\r\n\r\n<img src=\"http:\/\/i.imgur.com\/xWZXUot.png\" alt=\"Puzzle creation challenge\" width=\"355\" height=\"329\">\r\n\r\nApparently, the entire helix was melted, even though there were 3 G-C pairs, and a GAAA tetraloop. According to the SHAPE reactivity data, every nucleotide except the cytosine residues in the CG\/CG quad are above 0.5, meaning the presence of the fold in the ensemble is questionably low. This challenge is proposed to determine if the result for this helix can be duplicated, and to investigate this lack of stability.\r\n\r\nThere are two parts to this project, flipping the A-U pair in the helix. \r\n\r\nIf results are duplicated, I hope to create a series of lab projects, to mutate pairs in the stem and tetraloop, to determine what can stabilize the helix.\r\n\r\n25 slots are requested for synthesis\r\n",
            "title":"Repeatability - Melted Helix Variation 1",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"25",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3284564"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376306",
            "body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying protected base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the A-A mismatch. Since the use of longer RNA molecules is brand new, and the stability of such a long helix is unknown, only 25 slots are requested for synthesis in this pilot run.",
            "title":"SHAPE Profile - A-A Mismatch - Pilot Run",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"25",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3263292"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376291",
            "body":"The majority of our puzzles all like the GAAA mismatch in Tetraloops but many solutions from nature have other configurations. Is this discrepancy due to a Eterna preference?\r\nTo test this, this series will synthesize various Tetraloop motifs to see if there is a distinct rank or synthesis preference.    \r\nThis series of labs will test various Tetraloop configurations. If one configuration\r\nis superior to any other, I would think that the synthesis results would show superior as well, creating a clear rank in synthesis results.\r\n \r\nFeel free to add to the series with your favorite Tetraloop pattern.   \r\n25 slots requested per proposed lab.",
            "title":"Tetraloop Competition Series - GAGA",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"42833",
            "founder":"JR",
            "founder_picture":"sites\/default\/files\/pictures\/picture-42833.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"25",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3252126"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376290",
            "body":"The majority of our puzzles all like the GAAA mismatch in Tetraloops but many solutions from nature have other configurations. Is this discrepancy due to a Eterna preference?\r\nTo test this, this series will synthesize various Tetraloop motifs to see if there is a distinct rank or synthesis preference.    \r\nThis series of labs will test various Tetraloop configurations. If one configuration\r\nis superior to any other, I would think that the synthesis results would show superior as well, creating a clear rank in synthesis results.\r\n \r\nFeel free to add to the series with your favorite Tetraloop pattern.   \r\n25 slots requested per proposed lab.",
            "title":"Tetraloop Competition Series - UACG",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"42833",
            "founder":"JR",
            "founder_picture":"sites\/default\/files\/pictures\/picture-42833.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"25",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3252125"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376289",
            "body":"The majority of our puzzles all like the GAAA mismatch in Tetraloops but many solutions from nature have other configurations. Is this discrepancy due to a Eterna preference?\r\nTo test this, this series will synthesize various Tetraloop motifs to see if there is a distinct rank or synthesis preference.    \r\nThis series of labs will test various Tetraloop configurations. If one configuration\r\nis superior to any other, I would think that the synthesis results would show superior as well, creating a clear rank in synthesis results.\r\n \r\nFeel free to add to the series with your favorite Tetraloop pattern.   \r\n25 slots requested per proposed lab.",
            "title":"Tetraloop Competition - UUCG",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"42833",
            "founder":"JR",
            "founder_picture":"sites\/default\/files\/pictures\/picture-42833.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"25",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3252115"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376288",
            "body":"The majority of our puzzles all like the GAAA mismatch in Tetraloops but many solutions from nature have other configurations. Is this discrepancy due to a Eterna preference?\r\nTo test this, this series will synthesize various Tetraloop motifs to see if there is a distinct rank or synthesis preference.    \r\nThis series of labs will test various Tetraloop configurations. If one configuration\r\nis superior to any other, I would think that the synthesis results would show superior as well, creating a clear rank in synthesis results.\r\n \r\nFeel free to add to the series with your favorite Tetraloop pattern.   \r\n25 slots requested per proposed lab.",
            "title":"Tetraloop Competition Series - GAAA",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"42833",
            "founder":"JR",
            "founder_picture":"sites\/default\/files\/pictures\/picture-42833.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"25",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3252114"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376286",
            "body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying stable base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the A-G mismatch, adjacent to various unstable secondary structures, including the open loop, a multiloop, two hairpin loops, and a single nucleotide bulge.\r\n\r\nFor this pilot run, the sequences for the loops and the pairs closing them are locked. In addition, there will be two parts to each project, with orientation for the closing base pairs differing with each. 20 Slots are requested for synthesis.",
            "title":"SHAPE Profile - A-G Mismatch - Pilot Run 2B",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"20",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3246489"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376285",
            "body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying stable base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the A-G mismatch, adjacent to various unstable secondary structures, including the open loop, a multiloop, two hairpin loops, and a single nucleotide bulge.\r\n\r\nFor this pilot run, the sequences for the loops and the pairs closing them are locked. In addition, there will be two parts to each project, with orientation for the closing base pairs differing with each. 20 Slots are requested for synthesis.",
            "title":"SHAPE Profile - A-G Mismatch - Pilot Run 2A",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"20",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3246488"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376274",
            "body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying stable base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the U-U mismatch, adjacent to various unstable secondary structures, including the open loop, a multiloop, two hairpin loops, and a single nucleotide bulge.<br<br>\r\nFor this pilot run, the sequences for the loops and the pairs closing them are locked. In addition, there will be two parts to each project, with orientation for the closing base pairs differing with each. 20 Slots are requested for synthesis.",
            "title":"SHAPE Profile - U-U Mismatch - Pilot Run 2B",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"20",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3244956"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376273",
            "body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying stable base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the U-U mismatch, adjacent to various unstable secondary structures, including the open loop, a multiloop, two hairpin loops, and a single nucleotide bulge.<br<br>\r\nFor this pilot run, the sequences for the loops and the pairs closing them are locked. In addition, there will be two parts to each project, with orientation for the closing base pairs differing with each. 20 Slots are requested for synthesis.",
            "title":"SHAPE Profile - U-U Mismatch - Pilot Run 2A",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"20",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3244953"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376269",
            "body":"It is well known, that multibranch loops are best closed with G-C pairs for stability. We even have a general rule that states they should be flipped a certain way. Now, this rule is not without merit, as it has been observed that the guanine on the 3' side of the base pair can be exposed when the pair is not flipped correctly. The goal of this lab project is to determine if having these G-C pairs oriented like this contributes to instability in the design overall, and to determine how often and under what conditions, a reactive 3' Guanine residue will occur. This is the second target structure in this lab challenge, with the length of the unpaired strands in the multibranch loop, decreased by 1 nucleotide each. 40 slots are requested for synthesis.",
            "title":"Reversed G-C Multibranch Loop Closing Base Pairs 2",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"40",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3242112"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376264",
            "body":"In RNA, interactions between any base can occur. In this series of lab projects, the goal is to investigate the SHAPE chemical footprint of these interactions, which can ultimately help with structure prediction and identifying protected base mismatches, for use in further experiments for determining the stability of these interactions. For this specific project, we will be testing the G-G mismatch. Since the use of longer RNA molecules is brand new, and the stability of such a long helix is unknown, only 25 slots are requested for synthesis in this pilot run.",
            "title":"SHAPE Profile - G-G Mismatch - Pilot Run",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"25",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3230979"
                  ]
               }
            ],
            "restart":false
         },
         {
            "nid":"3376244",
            "body":"For this project, an investigation into the stability of the various G-U\/G-U wobble base pair quads is being made. In this instance, we have a four base pair helix, connecting two multibranch loops. The two central base pairs of this four base pair stem, are a control for the fourth lab, with two locked A-U pairs, or a -0.9 kcal quad. This will be ran alongside 7 other projects, with 4 projects using G-U base pairs, and 4 projects using A-U base pairs as a control. 30 slots are requested for synthesis.",
            "title":"Wobble Quad Control 4",
            "status":"1",
            "created":"26 Sep, 2013",
            "founder_uid":"24263",
            "founder":"Brourd",
            "founder_picture":"sites\/default\/files\/pictures\/picture-24263.png",
            "proposed_date":null,
            "synth_date":null,
            "num_synth":"30",
            "affiliation":null,
            "selection":"user_vote",
            "cover_image":null,
            "cloud_round":"11",
            "puzzles":[
               {
                  "round":11,
                  "puzzles":[
                     "3213932"
                  ]
               }
            ],
            "restart":false
         }
      ],
      "num_labs":"23",
      "num_slots":"725"
   },
   "memcache":true
}

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