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Team:Davidson-MissouriW/Notebook
From 2010.igem.org
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<li>Added histograms to the Java Code | <li>Added histograms to the Java Code | ||
<li>Researched and analyzed the effectiveness of Cre | <li>Researched and analyzed the effectiveness of Cre | ||
| + | <li>Size verification of ptet+variant lox sites | ||
</ul> | </ul> | ||
<br> | <br> | ||
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<ul><li>Added the option for the user to input the weights of the various modules and began work on custom construct builder | <ul><li>Added the option for the user to input the weights of the various modules and began work on custom construct builder | ||
<li>Picked colonies from TetA segment 1 & 2 optimized & deoptimized plates. </li> | <li>Picked colonies from TetA segment 1 & 2 optimized & deoptimized plates. </li> | ||
| + | <li>Planned to ligate pBad+RBS+Cre in ampicillin resistant vectors | ||
| + | <li>Researched plasmid partitioning | ||
</ul> | </ul> | ||
<br> | <br> | ||
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<li>Explored the set covering problem | <li>Explored the set covering problem | ||
<li>Researched applications of the knapsack problem in cryptography | <li>Researched applications of the knapsack problem in cryptography | ||
| + | <li>Ligated ptet+LoxP+RBS+RFP | ||
</ul> | </ul> | ||
<br> | <br> | ||
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<li>Some final work on the simulation program | <li>Some final work on the simulation program | ||
<li>Discussed new ideas such as integer programming | <li>Discussed new ideas such as integer programming | ||
| + | <li>PCR screening of “RFP construct” | ||
| + | <li>Ptet+variant lox sites were frozen down | ||
</ul> | </ul> | ||
<br> | <br> | ||
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<li>Added terminators to the program | <li>Added terminators to the program | ||
<li>Ran test trials of the program and analyzed its results | <li>Ran test trials of the program and analyzed its results | ||
| + | <li>Planned experiments for using Cre as “front” and “back” vector | ||
| + | <li>Ligated first “floxed” constructs | ||
</ul> | </ul> | ||
<br> | <br> | ||
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<li>Continued work on the categorization of the knapsack problem | <li>Continued work on the categorization of the knapsack problem | ||
<li>Researched Instant Insanity problem | <li>Researched Instant Insanity problem | ||
| + | <li>PCR screening for “floxed sites” | ||
</ul> | </ul> | ||
<br> | <br> | ||
Revision as of 15:57, 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
- Learned lab protocols and organized lab
- Created list of needed parts and parts we need
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
- Learned miniprep and digestion protocols
- Learned how to document gels
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
- Learned about biobrick restriction sites and sticky ends
- Ordered lox oligos
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
- Sent off parts for sequencing
- Learned the transformation protocol
June 7, 2010
- Ligate and plasmid check for pSB1A2 or pSB1AK3
- Began working to improve the Lancelator and created histograms for simulations
- Gel purified vector for lox ligations
- Divided up constructs to be ligated
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
- Analyzed sequencing results using ApE program
- BOUGHT HAWAIIAN SHIRTS!!!!!
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
- Annealed lox oligos together
- Gel purified pBad+RBS+Cre (“Cre construct” from 2010 igem kit plate)
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
- Performed ligations involving lox sites
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
- Size verified lox forward and lox reverse sites
- Ligated “cre construct” into low, medium, and high copy kanamycin resistant vectors
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
- Planning for Amp+Tet experiments
- First “cre construct” ligations failed
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
- Religated “cre construct”
- Lox sites sent off for sequencing
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
- Lox sites were frozen down and entered in GCAT-alog
- Agar plates were prepared for Amp+Tet experiments
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
- Planned kanamycin experiments
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
- Successfully ligated ptet+different lox sites
- Planned different combinations of variant lox sites
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
- Confirmed successful ligations of lox sites from sequencing results
- First pilot test for Amp+Tet experiments
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
- Researched data on possible transcription terminator in Tet A
- Failure of cre experiments
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
- Ligations to construct tet constructs
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
- Size verification of ptet+variant lox sites
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.
- Planned to ligate pBad+RBS+Cre in ampicillin resistant vectors
- Researched plasmid partitioning
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
- Ligated ptet+LoxP+RBS+RFP
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
- PCR screening of “RFP construct”
- Ptet+variant lox sites were frozen down
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
- Planned experiments for using Cre as “front” and “back” vector
- Ligated first “floxed” constructs
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
- PCR screening for “floxed sites”
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.
- Fixed the error in the CAI optimization program
- Continued analyzing systems of recursive relations
July 20, 2010
- Flourimeter data collected on IPTG experiment.
- Adapted the Oligator page for the Optimization program, now called the Optimus
- Made progress on solving the system of recursive relations that we have
July 21, 2010
- IPTG experiment started on optimized and deoptmized TetA constructs.
- Passage I715039-1 and I715039-2 experiments started.
- Started to link the ruby program on the webpage
- Finished theoretical probabilities for Construct A of size 4
July 22, 2010
- IPTG experiment started using varying tetracycline concentrations.
- Cell count data collected on IPTG TetA experiment.
- Linked the Optimus on the webpage
- Started theoretical probabilities for Construct A of size 5
July 23, 2010
- Cell count data collected from IPTG experiment..
- Flourimeter data collected from IPTG experiment.
- Worked on the tutorial for the Optimus and added various features
- Worked on a Matlab tool based on the pancake problem that can find the theoretical probabilities of different modules in different positions
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
