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</p><p>Created outline for testing and validation. | </p><p>Created outline for testing and validation. | ||
</p><p>Explored MLP's for multivariate regression on time series. | </p><p>Explored MLP's for multivariate regression on time series. | ||
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</p><p><h6>Economic Modelling (Italian Wedding Soup)</h6> | </p><p><h6>Economic Modelling (Italian Wedding Soup)</h6> | ||
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</p><p><h6>protein modelling: </h6> | </p><p><h6>protein modelling: </h6> | ||
</p><p>Started gathering RMSDs, videos, and summaries to inform wetlab based on the 6gix modifications presented last week. | </p><p>Started gathering RMSDs, videos, and summaries to inform wetlab based on the 6gix modifications presented last week. | ||
− | Generated Summmary graphs to compare stability between 6gix and tagged proteins. | + | Generated Summmary graphs to compare stability between 6gix and tagged proteins. |
</p> | </p> | ||
</div> | </div> | ||
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Hybrid PNMM model completed. | Hybrid PNMM model completed. | ||
Sunny Days writeup begins. | Sunny Days writeup begins. | ||
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</p><p><h6>Salad Dressings (SCALE UP):</h6> | </p><p><h6>Salad Dressings (SCALE UP):</h6> | ||
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</p><p>Created McCabe-Thiele Script for Liquid-Liquid Extractions at low concentrations. Will derive a kremser equation as well to analytically determine stage number. Goal is to consider alternative process operations to syn-bio for comparative assesment (we want syn-bio approach to be clearly better). | </p><p>Created McCabe-Thiele Script for Liquid-Liquid Extractions at low concentrations. Will derive a kremser equation as well to analytically determine stage number. Goal is to consider alternative process operations to syn-bio for comparative assesment (we want syn-bio approach to be clearly better). | ||
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</p><p>More practice with emulsions. testing different formulations and observing size (emulsion structure). Began to look into possible neural net approach - different types of hybrid nets are used in similar studies, but existing approaches have illogical mehtods - like using 1 net to predict different ampiphile effects, and not including HBL or OHBLD measurement. Jake, Rylan, and Andrew mentioned that a classification approach using SVM and/or k-means clustering might be able to interporlate rather than using a neural net. | </p><p>More practice with emulsions. testing different formulations and observing size (emulsion structure). Began to look into possible neural net approach - different types of hybrid nets are used in similar studies, but existing approaches have illogical mehtods - like using 1 net to predict different ampiphile effects, and not including HBL or OHBLD measurement. Jake, Rylan, and Andrew mentioned that a classification approach using SVM and/or k-means clustering might be able to interporlate rather than using a neural net. | ||
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Created Supply/Demand Plot for Farmers | Created Supply/Demand Plot for Farmers | ||
</p><p> | </p><p> | ||
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Found cost of clays/shipping as well as many other factors for the project | Found cost of clays/shipping as well as many other factors for the project | ||
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</p><p>Created a prototype SVM and neural net model for ternary phase diagrams through changing temperature in order to extrapolate and interpolate the phase behaviour of systems in temperature. | </p><p>Created a prototype SVM and neural net model for ternary phase diagrams through changing temperature in order to extrapolate and interpolate the phase behaviour of systems in temperature. | ||
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</p><p><h6>Weather Modelling:</h6> | </p><p><h6>Weather Modelling:</h6> | ||
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<p><h6>Clay Filtration: </h6> | <p><h6>Clay Filtration: </h6> | ||
</p><p>We filtered chlorophyllated oil through acid activated clay. These pictures show the before/after filtration. it filters well but these conditions cause a 20% mass loss in canola oil (yikes.) | </p><p>We filtered chlorophyllated oil through acid activated clay. These pictures show the before/after filtration. it filters well but these conditions cause a 20% mass loss in canola oil (yikes.) | ||
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</p><p><h6>Economic Modelling:</h6> | </p><p><h6>Economic Modelling:</h6> | ||
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</p> | </p> | ||
</div> | </div> | ||
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</p><p><h6>Phase Diagrams:</h6> | </p><p><h6>Phase Diagrams:</h6> | ||
</p><p>Worked on SVM, K-nearest-neighbours, and MLP primary stage phase diagram interpolation. | </p><p>Worked on SVM, K-nearest-neighbours, and MLP primary stage phase diagram interpolation. | ||
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Used the first batch of real experimental results to get MLP secondary stage phase diagram interpolation. | Used the first batch of real experimental results to get MLP secondary stage phase diagram interpolation. | ||
</p><p> | </p><p> | ||
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Worked on data visualization. | Worked on data visualization. | ||
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<h6>Clay Filtration:</h6> | <h6>Clay Filtration:</h6> | ||
</p><p>Standard dilution curves were built for comparative extraction of chlorophyll. Results were taken at absorbances 649, 664, 670 | </p><p>Standard dilution curves were built for comparative extraction of chlorophyll. Results were taken at absorbances 649, 664, 670 | ||
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</p><p>Explain T1, t2, t3, then explain what langmuir and freundlich are, not in detail but enough to know what is happening | </p><p>Explain T1, t2, t3, then explain what langmuir and freundlich are, not in detail but enough to know what is happening | ||
T1 fits langmuir and freundlich well - T2 (60) and T3 (100) don't - might be due to change in physical characteristic of pore site - equivalence in in binding energy is no longer valid. There is a model that described sigmoid-like adsorption, assumptions are different. Refered to as langmuir s-type or sigmoid type. | T1 fits langmuir and freundlich well - T2 (60) and T3 (100) don't - might be due to change in physical characteristic of pore site - equivalence in in binding energy is no longer valid. There is a model that described sigmoid-like adsorption, assumptions are different. Refered to as langmuir s-type or sigmoid type. | ||
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</p><p>Performed a second round of experiments on T1 with 0.5%, 1%, 2%, 2.5% and 5% loadings at T1. Isotherm results are given below. Still need an effective way to describe oil loss mathematically as a function. It seems that the chlorophyll absorbance data fits the langmur isotherm at this temp well. Still need to include the quality of fitting parameters in the scripts. | </p><p>Performed a second round of experiments on T1 with 0.5%, 1%, 2%, 2.5% and 5% loadings at T1. Isotherm results are given below. Still need an effective way to describe oil loss mathematically as a function. It seems that the chlorophyll absorbance data fits the langmur isotherm at this temp well. Still need to include the quality of fitting parameters in the scripts. | ||
</p><p> | </p><p> | ||
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</p><p>Experimental results also have begun to show the relationship between %removal and temperature. Higher temperature, as predicted, allows improved removal of chlorophyll, but also causes a lower loss in oil. Thus, higher temperature operaiton has a higher oil recovery ratio. However it is more expensive to operate at a higher temperature - will attempt to adress this with economic trade off. A possible approach would be co-optimization of clay and protein bleaching. Still need to formulate continuum models. Possible approach would be to build solid/liquid separation into a black box model, and allow it to operate continously. Perform heat exchanger calculations off of slurry output. | </p><p>Experimental results also have begun to show the relationship between %removal and temperature. Higher temperature, as predicted, allows improved removal of chlorophyll, but also causes a lower loss in oil. Thus, higher temperature operaiton has a higher oil recovery ratio. However it is more expensive to operate at a higher temperature - will attempt to adress this with economic trade off. A possible approach would be co-optimization of clay and protein bleaching. Still need to formulate continuum models. Possible approach would be to build solid/liquid separation into a black box model, and allow it to operate continously. Perform heat exchanger calculations off of slurry output. | ||
</p><p> | </p><p> | ||
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</p><p><h6>Phase Diagrams:</h6> | </p><p><h6>Phase Diagrams:</h6> | ||
</p><p>SVM hyperparameter (gamma and cost) optimization algorithms implemented in addition to the K optimizations for K nearest neighbours. Improved results seen. | </p><p>SVM hyperparameter (gamma and cost) optimization algorithms implemented in addition to the K optimizations for K nearest neighbours. Improved results seen. | ||
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</p><p><h6>Protein Modelling:</h6> | </p><p><h6>Protein Modelling:</h6> | ||
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Also started looking into utility costs. Utilities can extrapolate the total cost of the operation. utilities generally are 15% of the cost of operation. using [Towler,_Gavin;_Sinnott,_Ray_K.]_Chemical_Engineer(z-lib.org).pdf | Also started looking into utility costs. Utilities can extrapolate the total cost of the operation. utilities generally are 15% of the cost of operation. using [Towler,_Gavin;_Sinnott,_Ray_K.]_Chemical_Engineer(z-lib.org).pdf | ||
</p><p> | </p><p> | ||
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</p> | </p> | ||
</div> | </div> | ||
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</p><p><h6>Phase Diagrams:</h6> | </p><p><h6>Phase Diagrams:</h6> | ||
Continued working on data visualization techniques. | Continued working on data visualization techniques. | ||
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</p><p><h6>Protein Modelling:</h6> | </p><p><h6>Protein Modelling:</h6> | ||
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</p><p>Created a script based on multiple assumptions that calculates the needed recycling capablities to have a decent return on investment. If we recycle less than 99.8% of protein there will not be a return on investment whilst there is a return on investment just shy of 5 years with a recycle factor of 99.91% | </p><p>Created a script based on multiple assumptions that calculates the needed recycling capablities to have a decent return on investment. If we recycle less than 99.8% of protein there will not be a return on investment whilst there is a return on investment just shy of 5 years with a recycle factor of 99.91% | ||
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</p> | </p> | ||
</div> | </div> | ||
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Created and printed first seed holder. The PLA formed in such a way that the divots were too shallow to use. | Created and printed first seed holder. The PLA formed in such a way that the divots were too shallow to use. | ||
Generated another seed holder with more breathing room but it ultimately failed due to being processed with too low of a fill percentage | Generated another seed holder with more breathing room but it ultimately failed due to being processed with too low of a fill percentage | ||
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</p><p><h6>Codon Optimization:</h6> | </p><p><h6>Codon Optimization:</h6> | ||
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A successful print of the seed holder was also stolen from the printer this week :( | A successful print of the seed holder was also stolen from the printer this week :( | ||
Refined the colour analysis software. | Refined the colour analysis software. | ||
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</p><p><h6>Codon Optimization:</h6> | </p><p><h6>Codon Optimization:</h6> | ||
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</p><p><h6>Codon Optimization:</h6> | </p><p><h6>Codon Optimization:</h6> | ||
</p><p>GREAT SUCCESS ACTUALLY PASSES TESTS | </p><p>GREAT SUCCESS ACTUALLY PASSES TESTS | ||
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Next step: Make my changes run without issue, pass arguments through a script, and then submit a pull request | Next step: Make my changes run without issue, pass arguments through a script, and then submit a pull request | ||
PULL REQUEST SENT IN, decreases code coverage whatever that means. It is extremely easy for django to use it so it should be fine | PULL REQUEST SENT IN, decreases code coverage whatever that means. It is extremely easy for django to use it so it should be fine | ||
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</p><p>Brian hates the aesthetic. | </p><p>Brian hates the aesthetic. | ||
</p><p>Proposes solutions that are incompatible with tox (py version 3.6 gets angry) | </p><p>Proposes solutions that are incompatible with tox (py version 3.6 gets angry) | ||
− | </p><p>When told he said to "Just bump the requirements up to python 3.7" Which i | + | </p><p>When told he said to "Just bump the requirements up to python 3.7" Which i don't know how to do. So I'm in a bit of a pickle |
</p><p>I've also been working on the look of the website. | </p><p>I've also been working on the look of the website. | ||
</p><p>I also tested the software, (unoptimized) on sequences. I ran it on modGIX, and it worked very well, no issue. | </p><p>I also tested the software, (unoptimized) on sequences. I ran it on modGIX, and it worked very well, no issue. | ||
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</p><p>The modified flood fill algorithm used by the program was visualized. | </p><p>The modified flood fill algorithm used by the program was visualized. | ||
</p><p> | </p><p> | ||
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</p><p><h6> | </p><p><h6> | ||
Codon Optimization:</h6> | Codon Optimization:</h6> |
Latest revision as of 03:14, 22 October 2019