Difference between revisions of "Team:William and Mary/Notebook"

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<html>
 
<html>
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<head>
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<style>
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/* Three image containers (use 25% for four, and 50% for two, etc) */
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.row {
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  display: flex;
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float: center;
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}
  
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<div class="column full_size">
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div {
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<h1>Notebook</h1>
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</style>
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<p> Document the dates you worked on your project. This should be a detailed account of the work done each day for your project.</p>
+
</head>
  
 +
<body>
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<div style='padding-top: 50px;'></div>
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<h1 style="color: black;text-align:center;">Notebook</h1>
 +
<div style='padding-top: 10px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 1: 180528 -180604</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Began cloning 3G parts based off the library sent from the Murray lab</li>
 +
<li>Researched literature on dual inducible promoters</li>
 +
<li>Sent out several cloned 3G parts for sequencing</li>
 +
<li> Planned out several IFFLs to test. </li>
 +
</ul>
 
</div>
 
</div>
−
<div class="clear"></div>
+
 +
<div style='padding-top: 40px;'></div>
  
  
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 2: 180604 -180610</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
  
−
<div class="column two_thirds_size">
+
 
−
<h3>What should this page have?</h3>
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<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 
<ul>
 
<ul>
−
<li>Chronological notes of what your team is doing.</li>
+
<li>Continued cloning 3G parts onto our standard WM Pad backbone</li>
−
<li> Brief descriptions of daily important events.</li>
+
<li> Redesigned primers for cloning 3G promoter parts, as previous ones were faulty</li>
−
<li>Pictures of your progress. </li>
+
<li>Received results from sequencing, confirmed parts</li>
−
<li>Mention who participated in what task.</li>
+
<li> Beginning to assemble circuits using 3G assembly</li>
 +
<li> Making inducible reporter construct and an mf-Lon based IFFL</li>
 
</ul>
 
</ul>
 +
</div>
  
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 3: 180611 -180617</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Completed cloning the portion of our comprehensive 3G assembly part library needed for our circuits</li>
 +
<li> Adding remaining 3G parts from Murray’s lab to our library</li>
 +
<li>Working on designing and building a dual inducible promoter and low copy backbone for assembly</li>
 +
<li>  Confirmed minipreps based on sequencing results </li>
 +
<li>  Started plate reader for experiments on circuits with IPTG and ATC inducer</li>
 +
<li>  Started using FACS machine for experiments</li>
 +
</ul>
 
</div>
 
</div>
  
−
<div class="column third_size">
+
<div style='padding-top: 40px;'></div>
−
<div class="highlight decoration_A_full">
+
−
<h3>Inspiration</h3>
+
−
<p>You can see what others teams have done to organize their notes:</p>
+
  
−
<ul>
+
 
−
<li><a href="https://2014.igem.org/Team:ATOMS-Turkiye/Notebook">2014 ATOMS-Turkiye</a></li>
+
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 4: 180618 - 180624</b></div>
−
<li><a href="https://2014.igem.org/Team:Tec-Monterrey/ITESM14_project.html#tab_notebook">2014 Tec Monterrey</a></li>
+
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
−
<li><a href="https://2014.igem.org/Team:Kyoto/Notebook/Magnetosome_Formation#title">2014 Kyoto</a></li>
+
<div style='padding-top: 0px;'></div>
−
<li><a href="https://2014.igem.org/Team:Cornell/notebook">2014 Cornell</a></li>
+
 
 +
 
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Microscopy training with Jacob Sawyer, advanced imaging specialist from Nikon</li>
 +
<li> Spin down inducer tests to see if we can remove inducer from media to create pulses</li>
 +
<li>Plate reader experiment of pulse timing in different conditions</li>
 +
<li> FACs experiment of how long cells can be incubated on ice without changing results</li>
 +
<li> Decided to stop sequencing 3G parts and start functionally screening them instead</li>
 +
<li> Set up our first Golden Gate reaction</li>
 +
<li> Madilyn & Friends Outreach event</li>
 
</ul>
 
</ul>
 
</div>
 
</div>
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 5: 180625 -180701</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Continue designing and building circuits</li>
 +
<li>Continue inducer spin down tests for plate reader experiment</li>
 +
<li>Reached out to St. Andrews to solidify collaboration partnership</li>
 +
<li>Considering alternatives for the inducer spin down tests due to multiple complications</li>
 +
<li>Looked into light-induced gene expression systems</li>
 +
<li>SEP 8th graders</li>
 +
</ul>
 
</div>
 
</div>
  
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 6: 180702 -180708</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Experienced some leakiness with our FACS machine, spent time fixing this</li>
 +
<li>Abandoned light-induced gene expression system, as it appears impractical in lab and less relevant to in vivo systems</li>
 +
<li> Began looking into temperature-induced circuits</li>
 +
<li>Continue inducer spin down tests</li>
 +
<li>Making different variants of the same circuit with different strength repressors</li>
 +
<li>Made and characterized Oscillator Circuit</li>
 +
<li>Cell sorting with GS, image dissociated cells on the slides</li>
 +
<li>Started Interlab Study measurements</li>
 +
</ul>
 +
</div>
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 7: 180709 -180715</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Successfully cloned our entire 3G library, except recently added parts</li>
 +
<li>Demonstrated cells can be frozen in 15% glycerol without changing results</li>
 +
<li>Successfully tested whether inducers can be removed from media</li>
 +
<li>Using parts from last year, tested an IFFL with a single 20 minute pulse</li>
 +
<li>Tested an IFFL with a single 40 minute pulse</li>
 +
<li>Began assembling and testing circuits utilizing temperature as an inducer (TS-C1 system)</li>
 +
<li>Attended the Mid-Atlantic Meetup hosted by University of Maryland</li>
 +
<li>Submitted Interlab measurements</li>
 +
</ul>
 +
</div>
 +
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 8: 180716 -180722</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Reached out to UVA for collaboration</li>
 +
<li>Continued with plate reader experiments</li>
 +
<li> Continued testing heat inducible circuits</li>
 +
<li>Cloned and transformed Oscillator parts for functional testing</li>
 +
<li>Medical Explorers Outreach Event Visit Day 1 and 2</li>
 +
<li>Building with Biology event</li>
 +
<li>Camp Launch</li>
 +
</ul>
 +
</div>
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 9: 180723 -180729</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Contacted University of Pittsburgh for collaboration</li>
 +
<li>Continued plate reader experiments</li>
 +
<li>Testing lower temperature inductions</li>
 +
<li>Successfully created working high copy inducible parts and possible working low copy parts</li>
 +
<li>Addressing  issues with microscopy</li>
 +
<li>Plus S Ice Cream and iGEM</li>
 +
</ul>
 +
</div>
 +
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 10: 180730 -180805</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Continuing plate reader experiments</li>
 +
<li>Interlab data got rejected due to accidentally switching the Od600 and fluorescence in the form. Minor issue, easily resolved and submitted</li>
 +
<li> Investigated parameters for oscillator</li>
 +
<li>Sent collaboration package to UVA and University of Pittsburgh</li>
 +
<li>Started considering clontegration and requisite parts and primers</li>
 +
<li>First MUN Meeting</li>
 +
</ul>
 +
</div>
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 11: 180827 -180902</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Designed primers for pOSIP 3G amplification</li>
 +
<li>Continued plate reader experiments with heat inducible circuits</li>
 +
<li> Updated safety form</li>
 +
</ul>
 +
</div>
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 12: 180903 -180909</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Continued plate reader experiments</li>
 +
<li>Focused on testing variations of Tlp- heat sensitive promoter</li>
 +
<li>Collaboration data was received from UVA and University of Pittsburgh</li>
 +
<li>Design logo</li>
 +
</ul>
 +
</div>
 +
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 13: 180910 -180916</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>CTested circuit with two different promoters, tlp mflon and tlp mscarlet</li>
 +
<li>Hurricane Florence hit, school was evacuated and closed from Tuesday to Sunday</li>
 +
<li>No wetlab was able to commence</li>
 +
<li>Analyzed data from integrated circuits</li>
 +
<li>Presentation at Windsor Mead Nursing Home</li>
 +
</ul>
 +
</div>
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 14: 180917 - 180923</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Picked up after Hurricane Florence</li>
 +
<li>Made competent flped cells</li>
 +
<li>Tested circuits transformed in pre-flped and flped cells</li>
 +
<li>Tested new ptd tag</li>
 +
<li> Experiments with integrated cells</li>
 +
<li>Created parts pages for UVA parts</li>
 +
<li>Presentation at Williamsburg Landing Nursing Home</li>
 +
<li>Poster Presentation at the Women’s Weekend</li>
 +
</ul>
 +
</div>
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 15: 180924 - 180930</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Plate reader experiment with older parts- tsc1 mscarlet with tlp mflon</li>
 +
<li>Tested more ptd tag parts</li>
 +
<li> Continue experiments with integrated cells</li>
 +
<li>Analyzed different strength 3k3 parts</li>
 +
<li>Outbreak presentation with guest entrepreneurship speaker</li>
 +
</ul>
 +
</div>
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 16: 181001 - 181007</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Plate reader experiment of combined circuits with tlp mflon and tlp mscarlet</li>
 +
<li>Cloned multiple circuits to be sequenced and submitted</li>
 +
<li>Presentation to Model UN</li>
 +
</ul>
 +
</div>
 +
 +
 +
<div style='padding-top: 40px;'></div>
 +
 +
 +
<div style = 'padding-left: 14%; padding-bottom: 10px;font-size: 25px' ><b>Week 17: 181008-181017</b></div>
 +
<div style='background: #808080; margin: 0px 14% 20px 14%; height:1px;></div>
 +
<div style='padding-top: 0px;'></div>
 +
 +
 +
<div style = 'padding-right: 14%; padding-left: 14%; text-indent: 0px;line-height: 25px;'>
 +
<ul>
 +
<li>Wrapped up on outstanding wetlab tasks</li>
 +
<li>Worked on Wiki!</li>
 +
<li>Ladies in the Lab</li>
 +
</ul>
 +
</div>
 +
<div style='padding-top: 50px;'></div>
 +
</body>
 
</html>
 
</html>
 +
 +
{{William_and_Mary/SOURCE JS}}
 +
{{William_and_Mary/FOOTER}}

Latest revision as of 01:31, 18 October 2018

Notebook

Week 1: 180528 -180604
  • Began cloning 3G parts based off the library sent from the Murray lab
  • Researched literature on dual inducible promoters
  • Sent out several cloned 3G parts for sequencing
  • Planned out several IFFLs to test.
Week 2: 180604 -180610
  • Continued cloning 3G parts onto our standard WM Pad backbone
  • Redesigned primers for cloning 3G promoter parts, as previous ones were faulty
  • Received results from sequencing, confirmed parts
  • Beginning to assemble circuits using 3G assembly
  • Making inducible reporter construct and an mf-Lon based IFFL
Week 3: 180611 -180617
  • Completed cloning the portion of our comprehensive 3G assembly part library needed for our circuits
  • Adding remaining 3G parts from Murray’s lab to our library
  • Working on designing and building a dual inducible promoter and low copy backbone for assembly
  • Confirmed minipreps based on sequencing results
  • Started plate reader for experiments on circuits with IPTG and ATC inducer
  • Started using FACS machine for experiments
Week 4: 180618 - 180624
  • Microscopy training with Jacob Sawyer, advanced imaging specialist from Nikon
  • Spin down inducer tests to see if we can remove inducer from media to create pulses
  • Plate reader experiment of pulse timing in different conditions
  • FACs experiment of how long cells can be incubated on ice without changing results
  • Decided to stop sequencing 3G parts and start functionally screening them instead
  • Set up our first Golden Gate reaction
  • Madilyn & Friends Outreach event
Week 5: 180625 -180701
  • Continue designing and building circuits
  • Continue inducer spin down tests for plate reader experiment
  • Reached out to St. Andrews to solidify collaboration partnership
  • Considering alternatives for the inducer spin down tests due to multiple complications
  • Looked into light-induced gene expression systems
  • SEP 8th graders
Week 6: 180702 -180708
  • Experienced some leakiness with our FACS machine, spent time fixing this
  • Abandoned light-induced gene expression system, as it appears impractical in lab and less relevant to in vivo systems
  • Began looking into temperature-induced circuits
  • Continue inducer spin down tests
  • Making different variants of the same circuit with different strength repressors
  • Made and characterized Oscillator Circuit
  • Cell sorting with GS, image dissociated cells on the slides
  • Started Interlab Study measurements
Week 7: 180709 -180715
  • Successfully cloned our entire 3G library, except recently added parts
  • Demonstrated cells can be frozen in 15% glycerol without changing results
  • Successfully tested whether inducers can be removed from media
  • Using parts from last year, tested an IFFL with a single 20 minute pulse
  • Tested an IFFL with a single 40 minute pulse
  • Began assembling and testing circuits utilizing temperature as an inducer (TS-C1 system)
  • Attended the Mid-Atlantic Meetup hosted by University of Maryland
  • Submitted Interlab measurements
Week 8: 180716 -180722
  • Reached out to UVA for collaboration
  • Continued with plate reader experiments
  • Continued testing heat inducible circuits
  • Cloned and transformed Oscillator parts for functional testing
  • Medical Explorers Outreach Event Visit Day 1 and 2
  • Building with Biology event
  • Camp Launch
Week 9: 180723 -180729
  • Contacted University of Pittsburgh for collaboration
  • Continued plate reader experiments
  • Testing lower temperature inductions
  • Successfully created working high copy inducible parts and possible working low copy parts
  • Addressing issues with microscopy
  • Plus S Ice Cream and iGEM
Week 10: 180730 -180805
  • Continuing plate reader experiments
  • Interlab data got rejected due to accidentally switching the Od600 and fluorescence in the form. Minor issue, easily resolved and submitted
  • Investigated parameters for oscillator
  • Sent collaboration package to UVA and University of Pittsburgh
  • Started considering clontegration and requisite parts and primers
  • First MUN Meeting
Week 11: 180827 -180902
  • Designed primers for pOSIP 3G amplification
  • Continued plate reader experiments with heat inducible circuits
  • Updated safety form
Week 12: 180903 -180909
  • Continued plate reader experiments
  • Focused on testing variations of Tlp- heat sensitive promoter
  • Collaboration data was received from UVA and University of Pittsburgh
  • Design logo
Week 13: 180910 -180916
  • CTested circuit with two different promoters, tlp mflon and tlp mscarlet
  • Hurricane Florence hit, school was evacuated and closed from Tuesday to Sunday
  • No wetlab was able to commence
  • Analyzed data from integrated circuits
  • Presentation at Windsor Mead Nursing Home
Week 14: 180917 - 180923
  • Picked up after Hurricane Florence
  • Made competent flped cells
  • Tested circuits transformed in pre-flped and flped cells
  • Tested new ptd tag
  • Experiments with integrated cells
  • Created parts pages for UVA parts
  • Presentation at Williamsburg Landing Nursing Home
  • Poster Presentation at the Women’s Weekend
Week 15: 180924 - 180930
  • Plate reader experiment with older parts- tsc1 mscarlet with tlp mflon
  • Tested more ptd tag parts
  • Continue experiments with integrated cells
  • Analyzed different strength 3k3 parts
  • Outbreak presentation with guest entrepreneurship speaker
Week 16: 181001 - 181007
  • Plate reader experiment of combined circuits with tlp mflon and tlp mscarlet
  • Cloned multiple circuits to be sequenced and submitted
  • Presentation to Model UN
Week 17: 181008-181017
  • Wrapped up on outstanding wetlab tasks
  • Worked on Wiki!
  • Ladies in the Lab