Difference between revisions of "Team:Purdue/Notebook"

 
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<p>Notebook</p>
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<div><a href="#week01">Week 1</a></div>
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<p>Created GANTT chart, went over lab protocols, researched background information for yeast infections, discussed researchers and companies to reach out to for integrated human practices, made media, resuspended g blocks, created navigation and footer for wiki, purchased plane tickets, and reached out to companies for sponsorships.</p>
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<h1>Week 2 (6/1/19)</h1>
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<p>Began cloning of gBlocks into E. coli, contacted planned parenthood, local hospitals, and a gynecologist, began Promega and Learning Beyond the Classroom grant, created wiki quiz and updated aesthetics, ordered lab supplies, met with colleges to discuss iGEM funding.</p>
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<h1>Week 3 (6/7/18)</h1>
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<p>Used ampicillin plates to select for successfully cloned gBlocks, began model development using protein mass balance equation, scheduled meetings with professors on campus to discuss project, rough drafts for wiki content worked on, and began research on paper-based assay including discussions of design, type of paper, and characteristics.</p>
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<p>Ran digests of gBlocks to confirm transformation, PCR failed for positive control development, furthered model development to account for speed of liquid falling through paper assay and rate of enzyme reaction, modeled capillary action with washburn equation and enzyme kinetics with michaelis-menten, discussed mechanisms of paper-based assay with professors on campus, created navigation bar on wiki, worked on questions for IRB survey, met with College of Engineering for funding request.</p>
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<h1>Week 5 (6/19/18)</h1>
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<p>Successfully cloned most gBlocks into E. coli, discovered positive control development failed due to incorrect primers being ordered, contacted statistics department for preparation of IRB survey, began human subjects training, developed method to discover parameters for modeling, added navigational buttons to wiki, began training with professors for paper-based assay development.</p>
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<h1>Week 6 (6/28/18)</h1>
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<p>Met with Purdue Research Foundation to discuss potential of getting patents for research, decided on parameters, paper, and design for paper-based assay, did restyling of wiki, learned how to use flex station for biological and paper-based assay.</p>
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<h1>Week 7 (7/5/18)</h1>
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<p>Performed half of standardization experiments for interlab study, determined protein protein interaction constants for modeling, discovered error between simulation data and real parameter values, new positive control dimers continued to dimerize, casing PCR complications, met with girl scouts for potential human practices opportunity, applied design section added to wiki, and discussed paper-based assay shelf life and surfactant complications, as well as how to improve on cost, accuracy, durability, and speed.</p>
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<p>Began photo scanner training for paper-based assay, began TMB biological assay development, restarted interlab study due to accidental freezing of microspheres, ran MCMC bayesian parameter estimation code, ran sensitivity analyses for parameters, contacted vice-provost for potential funding, brainstormed project acronyms, and discussed target audience for project.</p>
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<p>Began aging experiments with TMB, characterized device using food colored water glucose solutions, whatman #1 chosen as paper-based assay paper, specifically 3mm thick due to ability to filter out red blood cells, projected costs ignoring reagents to roughly 8 cents, using plate reader we were able to quantify assay parameters with glucose solutions, adjusted parameters for developing positive control by changing annealing temperature of primers in PCR, completed all 3 calibrations for interlab study, and received Learning Beyond the Classroom Grant.</p>
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<p>Created HRP calibration curve, discovered HRP is extremely reactive and will react in minutes if left in aerobic environment, needs peroxide to react, discovered red/orange intermediate is formed before fully oxidized, set experiment for adjusting TMB, HRP, and peroxide concentration to improve assay, discovered frb-fkbp interactions are rate-limited, used Markov Chain Monte Carlo to assess Bayesian Parameter Estimation, successfully cloned positive control into E.coli, completed interlab study, and ran escape room with DNA scouts on campus.</p>
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<h1>Week 11 (8/2/18)</h1>
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<p>Sequenced positive control, proved successful transformation into E.coli, and transformed plasmid into yeast cells to be used in biological assay.</p>
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Latest revision as of 10:24, 17 October 2018

Bootstrap Example

Notebook

Week 1 (5/24/18)

Created GANTT chart, went over lab protocols, researched background information for yeast infections, discussed researchers and companies to reach out to for integrated human practices, made media, resuspended g blocks, created navigation and footer for wiki, purchased plane tickets, and reached out to companies for sponsorships.

Week 2 (6/1/19)

Began cloning of gBlocks into E. coli, contacted planned parenthood, local hospitals, and a gynecologist, began Promega and Learning Beyond the Classroom grant, created wiki quiz and updated aesthetics, ordered lab supplies, met with colleges to discuss iGEM funding.

Week 3 (6/7/18)

Used ampicillin plates to select for successfully cloned gBlocks, began model development using protein mass balance equation, scheduled meetings with professors on campus to discuss project, rough drafts for wiki content worked on, and began research on paper-based assay including discussions of design, type of paper, and characteristics.

Week 4 (6/14/18)

Ran digests of gBlocks to confirm transformation, PCR failed for positive control development, furthered model development to account for speed of liquid falling through paper assay and rate of enzyme reaction, modeled capillary action with washburn equation and enzyme kinetics with michaelis-menten, discussed mechanisms of paper-based assay with professors on campus, created navigation bar on wiki, worked on questions for IRB survey, met with College of Engineering for funding request.

Week 5 (6/19/18)

Successfully cloned most gBlocks into E. coli, discovered positive control development failed due to incorrect primers being ordered, contacted statistics department for preparation of IRB survey, began human subjects training, developed method to discover parameters for modeling, added navigational buttons to wiki, began training with professors for paper-based assay development.

Week 6 (6/28/18)

Met with Purdue Research Foundation to discuss potential of getting patents for research, decided on parameters, paper, and design for paper-based assay, did restyling of wiki, learned how to use flex station for biological and paper-based assay.

Week 7 (7/5/18)

Performed half of standardization experiments for interlab study, determined protein protein interaction constants for modeling, discovered error between simulation data and real parameter values, new positive control dimers continued to dimerize, casing PCR complications, met with girl scouts for potential human practices opportunity, applied design section added to wiki, and discussed paper-based assay shelf life and surfactant complications, as well as how to improve on cost, accuracy, durability, and speed.

Week 8 (7/12/18)

Began photo scanner training for paper-based assay, began TMB biological assay development, restarted interlab study due to accidental freezing of microspheres, ran MCMC bayesian parameter estimation code, ran sensitivity analyses for parameters, contacted vice-provost for potential funding, brainstormed project acronyms, and discussed target audience for project.

Week 9 (7/19/18)

Began aging experiments with TMB, characterized device using food colored water glucose solutions, whatman #1 chosen as paper-based assay paper, specifically 3mm thick due to ability to filter out red blood cells, projected costs ignoring reagents to roughly 8 cents, using plate reader we were able to quantify assay parameters with glucose solutions, adjusted parameters for developing positive control by changing annealing temperature of primers in PCR, completed all 3 calibrations for interlab study, and received Learning Beyond the Classroom Grant.

Week 10 (7/26/18)

Created HRP calibration curve, discovered HRP is extremely reactive and will react in minutes if left in aerobic environment, needs peroxide to react, discovered red/orange intermediate is formed before fully oxidized, set experiment for adjusting TMB, HRP, and peroxide concentration to improve assay, discovered frb-fkbp interactions are rate-limited, used Markov Chain Monte Carlo to assess Bayesian Parameter Estimation, successfully cloned positive control into E.coli, completed interlab study, and ran escape room with DNA scouts on campus.

Week 11 (8/2/18)

Sequenced positive control, proved successful transformation into E.coli, and transformed plasmid into yeast cells to be used in biological assay.

Special Thanks

to all those that made this possible

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West Lafayette, IN 47906