IGEM 2009 Project - Revision history

MaCampbell at 18:20, 27 August 2009

2009-08-27T18:20:37Z

MaCampbell at 18:19, 27 August 2009

2009-08-27T18:19:56Z

Olhoshing at 16:02, 15 August 2009

2009-08-15T16:02:03Z

Olhoshing at 11:38, 15 August 2009

2009-08-15T11:38:00Z

Olhoshing at 11:36, 15 August 2009

2009-08-15T11:36:10Z

MaCampbell at 14:38, 23 July 2009

2009-07-23T14:38:36Z

MaCampbell at 14:37, 23 July 2009

2009-07-23T14:37:20Z

Letaylor at 21:30, 17 July 2009

2009-07-17T21:30:47Z

Letaylor at 21:30, 17 July 2009

2009-07-17T21:30:26Z

Letaylor at 21:23, 17 July 2009

2009-07-17T21:23:59Z

@@ Line 5: / Line 5: @@
 *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:
+Examples:<br>
-(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') AND (a' OR b') AND (a OR b)  is a 2-variable, '''2-SAT problem''' with 3 clauses using 4 literals.<br>
-(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
+(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>
-The question of interest for a SAT problem is whether or not there exists an input that makes the overall logical expression true.
+#The question of interest for a SAT problem is whether or not there exists an input that makes the overall logical expression true.
+#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.

← Older revision		Revision as of 18:19, 27 August 2009
Line 1:		Line 1:
		+	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
		+
		+	The question of interest for a SAT problem is whether or not there exists an input that makes the overall logical expression true.
		+
		+	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:		Biology Based:
	#[[Which reporters are we going to use?]]		#[[Which reporters are we going to use?]]

@@ Line 26: / Line 26: @@
 | 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||  Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') ||  100% match 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-9 || Pro3||  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-9 || Pro6 ||  Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS ('''100% match''') || No 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-9 || Arg2 ||  Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') || 100% match 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

@@ Line 26: / Line 26: @@
 | 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||  Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') ||  '''100% match 5mer+Tet resistance''' screening pLacRBS ligations
+| Romina Clemente|| CUAGU || UUACUAGAC-9 || 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||  Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') || '''100% match 5mer+Tet resistance''' screening pLacRBS ligations
+| Shamita Punjabi|| CCACU || CUAGUGGAC-9 || 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 ||  Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS ('''100% match''') || No 5mer+Tet resistance
 |-
-| Alyndria Thompson|| CGGUC || UUGACCGAC-9 || Arg2 ||  Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') || '''100% match 5mer+Tet resistance''' screening pLacRBS ligations
+| Alyndria Thompson|| CGGUC || UUGACCGAC-9 || 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

@@ Line 13: / Line 13: @@
 '''Team Progress Table'''
-{| border="1" cellpadding="2"
+{| style="text-align:center" border="1" cellpadding="2"
 !width="120"|Student Name
 !width="30"|5mer Codon
@@ Line 22: / Line 22: @@
 !width="150"|5mer+Drug resistance Status
 |-
-| Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || '''100% match''', sequencing pBAD ligation  || '''100% match 5mer+RFP''', verifying pLacRBS ligation || zero 5mer+Tet resistance
+| 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 || '''100% match''', sequencing pBAD ligation  || '''100% match 5mer+RFP''', verifying pLacRBS ligation || zero 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-9 || Leu4|| '''100% match''', sequencing pBAD ligation || '''100% match 5mer+RFP''', verifying pLacRBS ligation ||  '''100% match 5mer+Tet resistance''' screening pLacRBS ligations
+| Romina Clemente|| CUAGU || UUACUAGAC-9 || Leu4||  Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') ||  '''100% match 5mer+Tet resistance''' screening pLacRBS ligations
 |-
-| Shamita Punjabi|| CCACU || CUAGUGGAC-9 || Pro3|| '''100% match''', sequencing pBAD ligation || '''100% match 5mer+RFP''', verifying pLacRBS ligation || '''100% match 5mer+Tet resistance''' screening pLacRBS ligations
+| Shamita Punjabi|| CCACU || CUAGUGGAC-9 || Pro3||  Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') || '''100% match 5mer+Tet resistance''' screening pLacRBS ligations
 |-
-| Leland Taylor || CCCUC || CUGAGGGUC-9 || Pro6 || '''100% match''', sequencing pBAD ligation || '''100% match 5mer+RFP''', verifying pLacRBS ligation || zero 5mer+Tet resistance
+| Leland Taylor || CCCUC || CUGAGGGUC-9 || Pro6 ||  Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS ('''100% match''') || No 5mer+Tet resistance
 |-
-| Alyndria Thompson|| CGGUC || UUGACCGAC-9 || Arg2 || '''100% match''', sequencing pBAD ligation || '''100% match 5mer+RFP''', verifying pLacRBS ligation || '''100% match 5mer+Tet resistance''' screening pLacRBS ligations
+| Alyndria Thompson|| CGGUC || UUGACCGAC-9 || Arg2 ||  Ligated to pBad ('''100% match''') || 'Ligated to pLac-RBS, and that to pBad-tRNA ('''100% match''') || '''100% match 5mer+Tet resistance''' screening pLacRBS ligations
 |-
-| Clif Davis|| 5mer codon || Anticodon Sequence || Leu3|| tRNA Status || 5mer+RFP Status || 2 5mer+CAT sequenced-99% Match with a Conservative Mutation
+| 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
+| 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
 |-
 |}

@@ Line 24: / Line 24: @@
 | Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || '''2 verified clones''' , both ligated with pBad  || 2 5mer+RFPs sequencing || 5 5mer+Tets sequencing
 |-
-| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || '''1 verified clone''' , both ligated with pBad  || 1 5mer+RFPs sequencing || 0 5mer+Tets
+| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || '''1 verified clone''' , both ligated with pBad  || 1 5mer+RFPs 100% match || 0 5mer+Tets
 |-
 | Romina Clemente|| CUAGU || UUACUAGAC-9 || Leu4|| '''1 clone 100% match''', putting pBAD upstream || 9 5mer+RFPs sequencing || 5 5mer+Tets sequencing

@@ Line 24: / Line 24: @@
 | Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || '''2 verified clones''' , both ligated with pBad  || 2 5mer+RFPs sequencing || 5 5mer+Tets sequencing
 |-
-| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || '''1 verified clone''' , both ligated with pBad  || 2 5mer+RFPs sequencing || 5 5mer+Tets sequencing
+| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || '''1 verified clone''' , both ligated with pBad  || 1 5mer+RFPs sequencing || 0 5mer+Tets
 |-
 | Romina Clemente|| CUAGU || UUACUAGAC-9 || Leu4|| '''1 clone 100% match''', putting pBAD upstream || 9 5mer+RFPs sequencing || 5 5mer+Tets sequencing
@@ Line 30: / Line 30: @@
 | Shamita Punjabi|| CCACU || CUAGUGGAC-9 || Pro3|| 2 clones being resequenced || 6 5mer+RFPs sequencing || 5 5mer+Tets sequencing
 |-
-| Leland Taylor || CCCUC || CUGAGGGUC-9 || Pro6 || '''1 clone 100% match''', putting pBAD upstream || 7 5mer+RFPs sequencing || 7 5mer+Tets sequencing
+| Leland Taylor || CCCUC || CUGAGGGUC-9 || Pro6 || '''1 clone 100% match''', putting pBAD upstream || 4 5mers+RFP 100% match || 0 5mer+Tets
 |-
 | Alyndria Thompson|| CGGUC || UUGACCGAC-9 || Arg2 || '''4 clones 100%match''', pBad is upstream clone || '''3 clones matched''' to Nco1 -  5mer+RFPs sequencing || '''2 clones matche'''d to BamH1 - 5mer+Tets sequencing