Team:Davidson-MissouriW/Notebook

From 2010.igem.org

(Difference between revisions)
(Notebook)
(Notebook)
Line 196: Line 196:
<li>Preparative BamHI/NheI digest performed on TetA.  
<li>Preparative BamHI/NheI digest performed on TetA.  
<li>New experiment protocol developed for reduced vector background noise.  </li>
<li>New experiment protocol developed for reduced vector background noise.  </li>
 +
<li>Added terminators to the program
 +
<li>Ran test trials of the program and analyzed its results
</ul>
</ul>
<br>
<br>
Line 202: Line 204:
<ul>
<ul>
<li>Mini prepped, diagnostic RP digest, preparative digest, ligation, pBAD+RBS-RFP </li>
<li>Mini prepped, diagnostic RP digest, preparative digest, ligation, pBAD+RBS-RFP </li>
 +
<li>Continued work on the categorization of the knapsack problem
 +
<li>Researched Instant Insanity problem
</ul>
</ul>
<br>
<br>
Line 209: Line 213:
<li>Ligated S04446 and S04447 to J31007.
<li>Ligated S04446 and S04447 to J31007.
<li>Tet titration experiment performed on pLac and pLacI +RBS-RFP-RBS-TetA. </li>
<li>Tet titration experiment performed on pLac and pLacI +RBS-RFP-RBS-TetA. </li>
 +
<li>Added direction of terminators in the simulation
 +
<li>Researched cryptography application
</ul>
</ul>
<br>
<br>
Line 216: Line 222:
<li>Ligated S04448 to RBS-TetA.
<li>Ligated S04448 to RBS-TetA.
<li>Ligated S04449 to RBS-TetA.</li>
<li>Ligated S04449 to RBS-TetA.</li>
 +
<li>Fixed memory leak in the simulation program
 +
<li>Researched integer programming
</ul>
</ul>
<br>
<br>
Line 223: Line 231:
<li>IPTG experiment started using pre-induced method.   
<li>IPTG experiment started using pre-induced method.   
<li>IPTG experiment started using varying levels of tetracycline.  </li>
<li>IPTG experiment started using varying levels of tetracycline.  </li>
 +
<li>Worked on animation for the simulation and continued analysis of the results of the simulation
 +
<li>Discussed integer programming as a group
</ul>
</ul>
<br>
<br>
Line 230: Line 240:
<li>Picked optimized and deoptimized TetA colonies.
<li>Picked optimized and deoptimized TetA colonies.
<li>Flourimeter data collected from IPTG experiment.  </li>
<li>Flourimeter data collected from IPTG experiment.  </li>
 +
<li>Revised some features on the program
 +
<li>Began working on theoretical probability models of the different constructs
</ul>
</ul>
<br>
<br>
Line 237: Line 249:
<li>Used RFLP to screen for candidate TetA clones.  
<li>Used RFLP to screen for candidate TetA clones.  
<li>Transformed various pLac and pLacI constructs into MG1655 cells. </li>
<li>Transformed various pLac and pLacI constructs into MG1655 cells. </li>
 +
</ul>
 +
<br>
 +
'''July 12, 2010'''
 +
<hr>
 +
<ul>
 +
<li>Used RFLP to screen for candidate TetA clones.
 +
<li>Transformed various pLac and pLacI constructs into MG1655 cells. </li>
 +
<li>Added slider feature to the simulation program
 +
<li>Continued work on the theoretical probability model for Construct A of size 3
</ul>
</ul>
<br>
<br>
Line 244: Line 265:
<li>Used RFLP to screen for candidate TetA clones.  
<li>Used RFLP to screen for candidate TetA clones.  
<li>EcoRI/PstI diagnostic digest performed on K199150. </li>
<li>EcoRI/PstI diagnostic digest performed on K199150. </li>
 +
<li>Added custom prefixes and suffixes to the Oligator
 +
<li>Found a general equation for finding theoretical probabilities for Construct A of size 3
</ul>
</ul>
<br>
<br>
Line 251: Line 274:
<li>Ligated segment 2 optimized and deoptimzed TetA behind segment 1.
<li>Ligated segment 2 optimized and deoptimzed TetA behind segment 1.
<li>IPTG experiment started on I715039-1 and I715039-2. </li>
<li>IPTG experiment started on I715039-1 and I715039-2. </li>
 +
<li>Began analyzing MW optimization code
 +
<li>Finished theoretical probabilities for Construct A of size 3
</ul>
</ul>
<br>
<br>
Line 258: Line 283:
<li>Cell count data collected from IPTG experiments.
<li>Cell count data collected from IPTG experiments.
<li>Flourimeter data collected from IPTG experiments.  </li>
<li>Flourimeter data collected from IPTG experiments.  </li>
 +
<li>Worked on a separate program using the CAI equation
 +
<li>Began working on theoretical probabilities for Construct A of size 4
</ul>
</ul>
<br>
<br>
Line 265: Line 292:
<li>Tet titration experiment started using pSB3T5 vector.
<li>Tet titration experiment started using pSB3T5 vector.
<li>Tet titration experiment started using optimized and deoptimized TetA. </li>
<li>Tet titration experiment started using optimized and deoptimized TetA. </li>
 +
<li>Added changes to the optimizer code
 +
<li>Researched how to solve a system of recursive relations into closed form
</ul>
</ul>
<br>
<br>

Revision as of 15:30, 27 July 2010

Notebook

June 1, 2010


  • Tested to find lethal concentration of Tet in plated and liquid mediums
  • Verified RCBS with our sequences and researched codon optimization methods
  • Analyzed probabilities for constructs A and B


June 2, 2010


  • Mini prepped, diagnostic RP digest, preparative digest, ligation, pBAD+RBS-RFP
  • Researched different ways to optimize a gene
  • Began simulation for Constructs A and B


June 3, 2010


  • Mini prepped, diagnostic RP digest, preparative digest, ligation, pBAD+RBS-RFP
  • Researched restriction sites and created proposal for gene optimization
  • Continued work on simulation in Java and Matlab


June 4, 2010


  • Mini prepped RBS-TetA-TT
  • RX Fragment digestion for RBS-TetA-TT
  • Analyzed the optimization of tetA sequence and researched properties of Lox sites
  • Debugged Simulations


June 7, 2010


  • Ligate and plasmid check for pSB1A2 or pSB1AK3
  • Began working to improve the Lancelator and created histograms for simulations


June 8, 2010


  • Double digest on pBAD-RBS-RFP to make an RS fragment insert.
  • Worked on a Perl program that check for Bio Brick Restriction Sites


June 9, 2010


  • EcoRI and PstI digest on pLac and pBad colonies.
  • Arabinose and IPTG concentration experiments started.
  • Continued work on the Lancelator program and began working on a different simulation for Construct C and D


June 10, 2010


  • Picked 14 colonies from pLac-RBS-RFP and pLac-RBS-RFP-RBS plates.
  • Started inducer curve experiments.
  • Linked Lancelator code to the website and continued simulations


June 11, 2010


  • Ligated S03736 into pSB1A7 vector.
  • EcoRI/PstI digest on pLac-RBS-RFP-RBS colonies.
  • Added new features to the Lancelator and worked on numerically representing Construct C for the Matlab simulation


June 14, 2010


  • EcoRI/PstI diagnostic digest performed on pBad-RBS-RFP colonies.
  • Inducer curve experiment started on pBad and pLac constructs.
  • Debugged Lancelator and finished numerical representation for the simulation


June 15, 2010


  • Ligated pLac-RBS-RFP + RBS-TetA.
  • IPTG experiment started on pLacI-RBS-RFP
  • Worked on the color schemes for the new Oligator
  • Created a new construct that might be helpful for the biologists


June 16, 2010


  • EcoRI/PstI diagnostic digest performed on pLac-RBS-RFP in pSB1A7 vector.
  • IPTG experiment started on plates with pLac and pLacI constructs.
  • Began working on a Java code that will run simulations for all the constructs
  • Researched on NP-Complete problems


June 17, 2010


  • Flourimeter data collected from IPTG experiment.
  • Ligated pLacI-RBS-RFP + RBS-TetA.
  • Worked on graphics of the Java program
  • Studied specific NP-Complete problems and brainstormed ways to incorporate them in our project


June 18, 2010


  • Picked 4 colonies from pLacI-RBS-RFP-RBS-TetA plates.
  • IPTG experiment started using newly created IPTG.
  • Debugged the Java program
  • Created a new page for the GCAT server


June 21, 2010


  • Digested TetA with EcoRI/NheI.
  • Annealed oligos for optimized and deoptimized TetA segment 1.
  • Improved the Java program
  • Began categorizing the knapsack problem into subparts


June 22, 2010


  • Ligated annealed TetA oligos into digested TetA.
  • Inducer curve experiment started on pLac and pLacI constructs.
  • Added buttons to the java program
  • Brainstormed biological implications in different NP-Complete problems


June 23, 2010


  • Preparative NheI/BamHI digest performed on TetA.
  • Preparative EcoRI/NheI digest performed on TetA.
  • Restructuring and reorganizing the Java program
  • Reviewed numerical algorithms and its relation to NP-Complete problems


June 24, 2010


  • Annealed optimized and deoptimized segment 1 TetA ligated into vector.
  • Annealed optimized and deoptimized segment 2 TetA ligatied into vector.
  • Added weight characteristic to the fluorescent proteins in the Java code
  • Continued exploration of NP-Complete problems


June 27, 2010


  • Inducer curve experiment started on pLac and pLacI constructs.
  • Picked colonies from TetA segment 1 & 2 optimized & deoptimized plates.
  • Added histograms to the Java Code
  • Researched and analyzed the effectiveness of Cre


June 28, 2010


  • Added the option for the user to input the weights of the various modules and began work on custom construct builder
  • Picked colonies from TetA segment 1 & 2 optimized & deoptimized plates.


June 29, 2010


  • Screened segment 1 optimized and deoptimized candidate clones using RFLP
  • Screened segment 2 optimized and deoptimized candidate clones using RFLP
  • Finished the simulation program and exported it
  • Explored the set covering problem
  • Researched applications of the knapsack problem in cryptography


June 30, 2010


  • Tet titration experiment performed on pLac and pLacI +RBS-RFP-RBS-TetA.
  • Ligated TetA onto pLac and pLacI +RBS-RFP-RBS-TetA with no terminator.
  • Some final work on the simulation program
  • Discussed new ideas such as integer programming


July 1, 2010


  • Preparative BamHI/NheI digest performed on TetA.
  • New experiment protocol developed for reduced vector background noise.
  • Added terminators to the program
  • Ran test trials of the program and analyzed its results


July 2, 2010


  • Mini prepped, diagnostic RP digest, preparative digest, ligation, pBAD+RBS-RFP
  • Continued work on the categorization of the knapsack problem
  • Researched Instant Insanity problem


July 6, 2010


  • Ligated S04446 and S04447 to J31007.
  • Tet titration experiment performed on pLac and pLacI +RBS-RFP-RBS-TetA.
  • Added direction of terminators in the simulation
  • Researched cryptography application


July 7, 2010


  • Ligated S04448 to RBS-TetA.
  • Ligated S04449 to RBS-TetA.
  • Fixed memory leak in the simulation program
  • Researched integer programming


July 8, 2010


  • IPTG experiment started using pre-induced method.
  • IPTG experiment started using varying levels of tetracycline.
  • Worked on animation for the simulation and continued analysis of the results of the simulation
  • Discussed integer programming as a group


July 9, 2010


  • Picked optimized and deoptimized TetA colonies.
  • Flourimeter data collected from IPTG experiment.
  • Revised some features on the program
  • Began working on theoretical probability models of the different constructs


July 10, 2010


  • Used RFLP to screen for candidate TetA clones.
  • Transformed various pLac and pLacI constructs into MG1655 cells.


July 12, 2010


  • Used RFLP to screen for candidate TetA clones.
  • Transformed various pLac and pLacI constructs into MG1655 cells.
  • Added slider feature to the simulation program
  • Continued work on the theoretical probability model for Construct A of size 3


July 13, 2010


  • Used RFLP to screen for candidate TetA clones.
  • EcoRI/PstI diagnostic digest performed on K199150.
  • Added custom prefixes and suffixes to the Oligator
  • Found a general equation for finding theoretical probabilities for Construct A of size 3


July 14, 2010


  • Ligated segment 2 optimized and deoptimzed TetA behind segment 1.
  • IPTG experiment started on I715039-1 and I715039-2.
  • Began analyzing MW optimization code
  • Finished theoretical probabilities for Construct A of size 3


July 15, 2010


  • Cell count data collected from IPTG experiments.
  • Flourimeter data collected from IPTG experiments.
  • Worked on a separate program using the CAI equation
  • Began working on theoretical probabilities for Construct A of size 4


July 16, 2010


  • Tet titration experiment started using pSB3T5 vector.
  • Tet titration experiment started using optimized and deoptimized TetA.
  • Added changes to the optimizer code
  • Researched how to solve a system of recursive relations into closed form


July 19, 2010


  • Cell count data collected from Tet titrations.
  • Tet titration experiment started using optimized and deoptimized TetA.


June 3, 2010


  • Mini prepped, diagnostic RP digest, preparative digest, ligation, pBAD+RBS-RFP


July 20, 2010


  • Flourimeter data collected on IPTG experiment.


July 21, 2010


  • IPTG experiment started on optimized and deoptmized TetA constructs.
  • Passage I715039-1 and I715039-2 experiments started.


July 22, 2010


  • IPTG experiment started using varying tetracycline concentrations.
  • Cell count data collected on IPTG TetA experiment.



July 23, 2010


  • Cell count data collected from IPTG experiment..
  • Flourimeter data collected from IPTG experiment.



July 26, 2010


  • Presented Missouri Western data to Davidson colleagues.
  • Presented Davidson data to Missouri Western colleagues.



July 27, 2010


  • Worked on team wiki.



July 28, 2010


  • n/a
  • n/a



July 30, 2010


  • n/a
  • n/a