GcatWiki - User contributions [en]

IGEM 2009 Project

2009-06-18T16:21:20Z

Shsuresh:

Biology Based:
#[[Which reporters are we going to use?]]
#[[What naming system are we going to use for the suppressor tRNAs?]]
#[[How do you build the tRNA construct?]]
#[[How are we going to build the 5-mer BioBricks?]]

[http://gcat.davidson.edu/GcatWiki/images/2/2c/Stop_Codons_in_LCs.doc Using Stop Codons to Truncate Translation] 
[http://gcat.davidson.edu/GcatWiki/images/8/81/D5merSequences.doc Davidson ATG+5mer BioBrick Sequences]

[http://gcat.davidson.edu/GcatWiki/images/4/47/FML_CODING_SEQUENCE_2.doc Frameshift Mutation Leader PCR primers]

'''Team Progress Table'''

{| border="1" cellpadding="2"
!width="200"|Student Name
!width="30"|5mer Codon
!width="40"|Anticodon Sequence
!width="40"|Codon Short Name
!width="150"|tRNA Status
!width="150"|5mer+RFP Status
!width="150"|5mer+Tet Resistance Status
|-
| Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || x clones being sequenced || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || x clones being sequenced || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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."

IGEM 2009 Project

2009-06-18T14:21:44Z

Shsuresh:

Biology Based:
#[[Which reporters are we going to use?]]
#[[What naming system are we going to use for the suppressor tRNAs?]]
#[[How do you build the tRNA construct?]]
#[[How are we going to build the 5-mer BioBricks?]]

[http://gcat.davidson.edu/GcatWiki/images/2/2c/Stop_Codons_in_LCs.doc Using Stop Codons to Truncate Translation] 
[http://gcat.davidson.edu/GcatWiki/images/8/81/D5merSequences.doc Davidson ATG+5mer BioBrick Sequences]

[http://gcat.davidson.edu/GcatWiki/images/4/47/FML_CODING_SEQUENCE_2.doc Frameshift Mutation Leader PCR primers]

'''Team Progress Table'''

{| border="1" cellpadding="2"
!width="200"|Student Name
!width="30"|5mer Codon
!width="40"|Anticodon Sequence
!width="40"|Codon Short Name
!width="150"|tRNA Status
!width="150"|5mer+RFP Status
!width="150"|5mer+Tet Resistance Status
|-
| Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || x clones being sequenced || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || x clones being sequenced || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
|}

Math Based: 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."

IGEM 2009 Project

2009-06-18T14:21:29Z

Shsuresh:

Biology Based:
#[[Which reporters are we going to use?]]
#[[What naming system are we going to use for the suppressor tRNAs?]]
#[[How do you build the tRNA construct?]]
#[[How are we going to build the 5-mer BioBricks?]]

[http://gcat.davidson.edu/GcatWiki/images/2/2c/Stop_Codons_in_LCs.doc Using Stop Codons to Truncate Translation] 
[http://gcat.davidson.edu/GcatWiki/images/8/81/D5merSequences.doc Davidson ATG+5mer BioBrick Sequences]

[http://gcat.davidson.edu/GcatWiki/images/4/47/FML_CODING_SEQUENCE_2.doc Frameshift Mutation Leader PCR primers]

'''Team Progress Table'''

{| border="1" cellpadding="2"
!width="200"|Student Name
!width="30"|5mer Codon
!width="40"|Anticodon Sequence
!width="40"|Codon Short Name
!width="150"|tRNA Status
!width="150"|5mer+RFP Status
!width="150"|5mer+Tet Resistance Status
|-
| Olivia Ho-Shing || CCAUC || GUGAUCCAA-9 || Pro4 || x clones being sequenced || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
| Olivia Ho-Shing || CCAUC || UUUGAUGGAG-10 || Pro5 || x clones being sequenced || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet 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|| tRNA Status || 5mer+RFP Status || 5mer+Tet Resistance Status
|-
|}

Math Based: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."

Missouri Western/Davidson iGEM2009

2009-05-27T02:54:09Z

Shsuresh:

This space will be used starting April, 2009 for brainstorming and a shared whiteboard space.

[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] 
[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] 
[http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] 
[http://gcat.davidson.edu/GCATalog-r2.1/GCATalog.htm GCAT-alog Freezer Stocks] 

We need to learn more about these topics:
<center>'''Biology-based'''</center>

#[[What is msDNA?]]
#[[How is msDNA normally produced?]] Olivia/Alyndria
#[[How many copies are carried per cell?]] Alyndria
#[[What would we need to do to turn this into a BioBrick device?]] Romina
#[[ How could we swap out msDNA sequences?]] Shamita
#[[What role can physical modeling of protein structure play in our project?]]
#[[What role can physical modeling of proteins play in our project? Eric Sawyer]]
#[[What other cool reporters are there? (Discrete On/Off or Continuous) Bryce Szczepanik]]
#[[Can we use promoter strength/opposite directions to subtract? Clif Davis]]
#[[Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?]]
#[[How is msDNA stored in E. coli?]] Olivia
#[[What is the sequence of bacterial reverse transcriptase and can we clone that gene?]] Shamita
#[[Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing?]] All
#[[What are other available reverse transcriptases?]] Leland
#[[What other math problems (e.g. NP- complete) are accessible to us? Annie Siya Sun]]
#[[What is the relationship between 3-SAT and map coloring? Ashley Schnoor]]
#[[What activators are there that turn on a promoter without any help?]]
#[[Can we use protein interactions to compute? (Post-translation, proteases, quaternary structure) Will Vernon]]
#[[Could we do something with clocks/counting?]]
#[[Could we have/use multiple synthetic organelles in a cell?]]
#[[What ideas from previous iGEM teams are useful to us?]]

<center>'''Math-based'''</center>
#[[Can we get bacteria to solve a problem large enough to challenge a person?]]
#[[What interesting challenges or problems does origami offer?]]
#[[Can we produce a series of increasingly difficult goals that might be possible to produce in the lab?]]
#[[What has been done before and how can we improve upon that?]]
#[[We can perform some pilot experiments using synthesized DNA and later switch to msDNA (maybe).]]
#[[Can we address the Boolean Satisfiability (SAT) problem with a bacterial computer?]]
#[[How has 3SAT been addressed with a DNA computer? Can we use those methods?]]

#Can we get bacteria to solve a problem large enough to challenge a computer (probably not, but it is fun to think about)?
#[[What are some linear algebra applications for DNA origami?]]
#[[How can we use origami to solve 3-SAT problems?]]

<center>'''Behavior-based'''</center>
#[[What constructs are we testing?]]
#[[What school districts do we have access to?]]
#[[Where is the Synthetic Biology page we want high school teachers to use after the survey?]]
#[[Do you need any more input from the veterans before the survey is ready?]]

<center>'''Solving The 3SAT Problem Using Suppressor Logic'''</center>
#[[Can we solve a 3-SAT problem with supressor logic?]]

<center>'''Hin/Hix System'''</center>
Here is a link to the animation of the Hin/Hix system created by the "E. HOP living computer project folks.
[http://www.bio.davidson.edu/people/kahaynes/FAMU_talk/Living_computer.swf Hin/Hix Animation]

Missouri Western/Davidson iGEM2009

2009-05-27T02:52:54Z

Shsuresh:

This space will be used starting April, 2009 for brainstorming and a shared whiteboard space.

[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] 
[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] 
[http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] 
[http://gcat.davidson.edu/GCATalog-r2.1/GCATalog.htm GCAT-alog Freezer Stocks] 

We need to learn more about these topics:
<center>'''Biology-based'''</center>

#[[What is msDNA?]]
#[[How is msDNA normally produced?]] Olivia/Alyndria
#[[How many copies are carried per cell?]] Alyndria
#[[What would we need to do to turn this into a BioBrick device?]] Romina
#[[ How could we swap out msDNA sequences?]] Shamita
#[[What role can physical modeling of protein structure play in our project?]]
#[[What role can physical modeling of proteins play in our project? Eric Sawyer]]
#[[What other cool reporters are there? (Discrete On/Off or Continuous) Bryce Szczepanik]]
#[[Can we use promoter strength/opposite directions to subtract? Clif Davis]]
#[[Can we use suppressor tRNAs to encode logical operators (suppressor suppressor logic, SSL)?]]
#[[How is msDNA stored in E. coli?]] Olivia
#[[What is the sequence of bacterial reverse transcriptase and can we clone that gene?]] Shamita
#[[Can we redesign the normal msDNA pathway to produce new segments of DNA of our choosing?]] All
#[[What are other available reverse transcriptases?]] Leland
#[[What other math problems (e.g. NP- complete) are accessible to us? Annie Siya Sun]]
#[[What is the relationship between 3-SAT and map coloring? Ashley Schnoor]]
#[[What activators are there that turn on a promoter without any help?]]
#[[Can we use protein interactions to compute? (Post-translation, proteases, quaternary structure) Will Vernon]]
#[[Could we do something with clocks/counting?]]
#[[Could we have/use multiple synthetic organelles in a cell?]]
#[[What ideas from previous iGEM teams are useful to us?]]

<center>'''Math-based'''</center>
#[[Can we get bacteria to solve a problem large enough to challenge a person?]]
#[[What interesting challenges or problems does origami offer?]]
#[[Can we produce a series of increasingly difficult goals that might be possible to produce in the lab?]]
#[[What has been done before and how can we improve upon that?]]
#[[We can perform some pilot experiments using synthesized DNA and later switch to msDNA (maybe).]]
#[[Can we address the Boolean Satisfiability (SAT) problem with a bacterial computer?]]
#[[How has 3SAT been addressed with a DNA computer? Can we use those methods?]]

#Can we get bacteria to solve a problem large enough to challenge a computer (probably not, but it is fun to think about)?
#[[What are some linear algebra applications for DNA origami?]]
#[[How can we use origami to solve 3-SAT problems?]]

<center>'''Behavior-based'''</center>
#[[What constructs are we testing?]]
#[[What school districts do we have access to?]]
#[[Where is the Synthetic Biology page we want high school teachers to use after the survey?]]
#[[Do you need any more input from the veterans before the survey is ready?]]

<center>'''Solving The 3SAT Problem Using Suppressor Logic'''</center>
#[[Can we solve a 3-SAT problem with supressor logic?]]

<center>'''Hin/Hix System'''</center>
Here is a link to the animation of the Hin/Hix system created by the "E. HOP living computer project folks. [http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols]