Difference between revisions of "IGEM 2009 Project"

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Vocabulary:
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*A '''variable''' is simply a letter of the alphabet (e.g. A) that comes in two types called literals -- a and a'.  Note:  Alternative notations could be A and a, or (a) and (not a).
 +
*A '''clause''' is made up of two or more literals with the logical operator OR between (e.g.  (a OR b') is a clause.) 
 +
*A '''SAT problem''' in conjunctive normal form is comprised of two or more clauses with the logical operator AND between.  The number of literals in each clause is the value of k in our use of k-SAT to describe a problem. 
 +
*An '''input''' is an assignment of one of the corresponding literals to each of the variables.  For example, (a, b' c') is one of eight possible inputs in a 3-variable problem.
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 +
Examples:<br>
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(a OR b') AND (a' OR b') AND (a OR b)  is a 2-variable, '''2-SAT problem''' with 3 clauses using 4 literals.<br>
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(a OR b OR c) AND (a' OR b OR d) AND (a OR b' OR d') is a 4-variable, '''3-SAT problem''' with 3 clauses using 7 literals. <br>
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#The question of interest for a SAT problem is whether or not there exists an input that makes the overall logical expression true.
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#The question of interest for a MAX SAT problem is to determine the maximum number of clauses satisfied when considered over the set of all possible inputs.
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 +
 
Biology Based:
 
Biology Based:
 
#[[Which reporters are we going to use?]]
 
#[[Which reporters are we going to use?]]
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[http://gcat.davidson.edu/GcatWiki/images/2/2c/Stop_Codons_in_LCs.doc Using Stop Codons to Truncate Translation]<br>
 
[http://gcat.davidson.edu/GcatWiki/images/2/2c/Stop_Codons_in_LCs.doc Using Stop Codons to Truncate Translation]<br>
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[http://gcat.davidson.edu/GcatWiki/images/8/81/D5merSequences.doc Davidson ATG+5mer BioBrick Sequences]
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[http://gcat.davidson.edu/GcatWiki/images/8/81/D5merSequences.doc Davidson ATG+5mer BioBrick Sequences]<br>
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[http://gcat.davidson.edu/GcatWiki/images/4/47/FML_CODING_SEQUENCE_2.doc Frameshift Mutation Leader PCR primers]<br>
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[http://gcat.davidson.edu/GcatWiki/images/4/47/FML_CODING_SEQUENCE_2.doc Frameshift Mutation Leader PCR primers]
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[http://www.staff.uni-bayreuth.de/~btc914/search/index.html Align E. coli tRNA sequences]<br>
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[http://media.pearsoncmg.com/bc/bc_campbell_genomics_2/medialib/jmol/trna/index.html Compare 2 tRNA structures]<br>
  
 
'''Team Progress Table'''
 
'''Team Progress Table'''
  
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{| border="1" cellpadding="2"
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{| style="text-align:center" border="1" cellpadding="2"
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!width="200"|Student Name
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!width="120"|Student Name
 
!width="30"|5mer Codon
 
!width="30"|5mer Codon
 
!width="40"|Anticodon Sequence
 
!width="40"|Anticodon Sequence
 
!width="40"| [http://gcat.davidson.edu/GcatWiki/index.php/What_naming_system_are_we_going_to_use_for_the_suppressor_tRNAs%3F Codon Short Name]
 
!width="40"| [http://gcat.davidson.edu/GcatWiki/index.php/What_naming_system_are_we_going_to_use_for_the_suppressor_tRNAs%3F Codon Short Name]
 
!width="150"|tRNA Status
 
!width="150"|tRNA Status
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!width="150"|5mer+RFP Status
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!width="150"|5mer+XFP Status
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!width="150"|5mer+Tet Resistance Status
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!width="150"|5mer+Drug resistance Status
 
|-  
 
|-  
−
| Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || 4 clones being sequenced || Amplifying 5mer+RFP || Amplifying 5mer+Tet
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| Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || Ligated to pBad ('''100% match''')  || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') || No 5mer+Tet resistance
 
|-   
 
|-   
−
| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || 3 clones being sequenced || Amplifying 5mer+RFP || Amplifying 5mer+Tet
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| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || Ligated to pBad ('''100% match''')  || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') || No 5mer+Tet resistance
 
|-   
 
|-   
−
| Romina Clemente|| CUAGU || UUACUAGAC-9 || Leu4|| 1 clone being sequenced || Gel purifying 5mer+RFP || Gel purifying 5mer+Tet Resistance
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| Romina Clemente|| CUAGU || UUACUAGAC || Leu4|| Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') || 100% match 5mer+Tet resistance
 
|-   
 
|-   
−
| Shamita Punjabi|| CCACU || CUAGUGGAC-9 || Pro3|| 3 clones being sequenced || Cleaning/Concentrating 5mer+ RFP || Cleaning+Conc 5mer +Tet  
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| Shamita Punjabi|| CCACU || CUAGUGGAC || Pro3|| Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') || 100% match 5mer+Tet resistance
 
|-   
 
|-   
−
| Leland Taylor || CCCUC || CUGAGGGUC-9 || Pro6 || 2 clones being sequenced || Transformed 5mer+RFP || Transformed 5mer+Tet
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| Leland Taylor || CCCUC || CUGAGGGUC || Pro6 || Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS ('''100% match''') || No 5mer+Tet resistance
 
|-   
 
|-   
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| Alyndria Thompson|| CGGUC || UUGACCGAC-9 || Arg2 || 5 clones being sequenced || Transformed || Transformed
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| Alyndria Thompson|| CGGUC || UUGACCGAC || Arg2 || Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') || 100% match 5mer+Tet resistance
 
|-   
 
|-   
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| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
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| Clif Davis|| 5mer codon || Anticodon Sequence || Leu3|| '''100% match''' || 5mer+GFP Status || 2 5mer+CAT sequenced-99% Match with a Conservative Mutation
 
|-   
 
|-   
−
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
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| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| '''100% match''' || 5mer+GFP Status || 5mer+CAT Resistance Status
 
|-   
 
|-   
−
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
+
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| '''100% match''' || 5mer+GFP Status || 5mer+CAT Resistance Status
 
|-   
 
|-   
−
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
+
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| '''100% match''' || 5mer+GFP Status || 5mer+CAT Resistance Status
 
|-   
 
|-   
−
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
+
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| '''100% match''' || 5mer+GFP Status || 5mer+CAT Resistance Status
 
|-   
 
|-   
−
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
+
| Student Name|| 5mer codon || Anticodon Sequence || Codon Short Name|| '''100% match''' || 5mer+GFP Status || 5mer+CAT Resistance Status
 
|-   
 
|-   
 
|}
 
|}

Latest revision as of 18:20, 27 August 2009

Vocabulary:

  • A variable is simply a letter of the alphabet (e.g. A) that comes in two types called literals -- a and a'. Note: Alternative notations could be A and a, or (a) and (not a).
  • A clause is made up of two or more literals with the logical operator OR between (e.g. (a OR b') is a clause.)
  • A SAT problem in conjunctive normal form is comprised of two or more clauses with the logical operator AND between. The number of literals in each clause is the value of k in our use of k-SAT to describe a problem.
  • An input is an assignment of one of the corresponding literals to each of the variables. For example, (a, b' c') is one of eight possible inputs in a 3-variable problem.

Examples:
(a OR b') AND (a' OR b') AND (a OR b) is a 2-variable, 2-SAT problem with 3 clauses using 4 literals.
(a OR b OR c) AND (a' OR b OR d) AND (a OR b' OR d') is a 4-variable, 3-SAT problem with 3 clauses using 7 literals.

  1. The question of interest for a SAT problem is whether or not there exists an input that makes the overall logical expression true.
  2. The question of interest for a MAX SAT problem is to determine the maximum number of clauses satisfied when considered over the set of all possible inputs.


Biology Based:

  1. Which reporters are we going to use?
  2. What naming system are we going to use for the suppressor tRNAs?
  3. How do you build the tRNA construct?
  4. How are we going to build the 5-mer BioBricks?

Using Stop Codons to Truncate Translation
Davidson ATG+5mer BioBrick Sequences
Frameshift Mutation Leader PCR primers
Align E. coli tRNA sequences
Compare 2 tRNA structures

Team Progress Table

Student Name 5mer Codon Anticodon Sequence Codon Short Name tRNA Status 5mer+XFP Status 5mer+Drug resistance Status
Olivia Ho-Shing CCAUC GUGAUCCAA-9 Pro4 Ligated to pBad (100% match) 'Ligated to pLac-RBS, and that to pBad-tRNA (100% match) No 5mer+Tet resistance
Olivia Ho-Shing CCAUC UUUGAUGGAG-10 Pro5 Ligated to pBad (100% match) 'Ligated to pLac-RBS, and that to pBad-tRNA (100% match) No 5mer+Tet resistance
Romina Clemente CUAGU UUACUAGAC Leu4 Ligated to pBad (100% match) 'Ligated to pLac-RBS, and that to pBad-tRNA (100% match) 100% match 5mer+Tet resistance
Shamita Punjabi CCACU CUAGUGGAC Pro3 Ligated to pBad (100% match) 'Ligated to pLac-RBS, and that to pBad-tRNA (100% match) 100% match 5mer+Tet resistance
Leland Taylor CCCUC CUGAGGGUC Pro6 Ligated to pBad (100% match) 'Ligated to pLac-RBS (100% match) No 5mer+Tet resistance
Alyndria Thompson CGGUC UUGACCGAC Arg2 Ligated to pBad (100% match) 'Ligated to pLac-RBS, and that to pBad-tRNA (100% match) 100% match 5mer+Tet resistance
Clif Davis 5mer codon Anticodon Sequence Leu3 100% match 5mer+GFP Status 2 5mer+CAT sequenced-99% Match with a Conservative Mutation
Student Name 5mer codon Anticodon Sequence Codon Short Name 100% match 5mer+GFP Status 5mer+CAT Resistance Status
Student Name 5mer codon Anticodon Sequence Codon Short Name 100% match 5mer+GFP Status 5mer+CAT Resistance Status
Student Name 5mer codon Anticodon Sequence Codon Short Name 100% match 5mer+GFP Status 5mer+CAT Resistance Status
Student Name 5mer codon Anticodon Sequence Codon Short Name 100% match 5mer+GFP Status 5mer+CAT Resistance Status
Student Name 5mer codon Anticodon Sequence Codon Short Name 100% match 5mer+GFP Status 5mer+CAT Resistance Status


Math Based: (Davidson) We have posted a Mathematica notebook on the Wiggio. Basically we are at a point where we can choose the number of variables, SAT number(2-SAT, 3-SAT, etc), and the number of clauses to use at a time and produce a table of inputs as the rows and clauses as the columns, with a 1 if the input satisfies the clause and a 0 if the input fails to satisfy the clause. In addition, we can produce a "Super Table," which lists all the SAT problems given the number of clauses in conjunctive normal form and displays how many of the clauses in a given problem each input satisfies. Feel free to view the posted Mathematica notebook; there are some instructions within the notebook itself. When you open it, there will be a window which asks about dynamic content; be sure to click "Enable Dynamic."

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