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Commit 8947003a authored by Sishir Sivakumar's avatar Sishir Sivakumar
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Merge branch 'garv' into 'main' 

Update notebook.html

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<div style="width: 1440px; height: 2782px; position: relative; background: white">
<div style="width: 1440px; height: 76px; left: 0px; top: 24px; position: absolute; background: black"></div>
<div style="width: 1440px; height: 111px; left: 0px; top: 181px; position: absolute; background: #34304D"></div>
<div
style="width: 681px; height: 80px; left: 380px; top: 196px; position: absolute; text-align: center; color: white; font-size: 60px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Lab Notebook</div>
<div style="width: 681px; height: 80px; left: 380px; top: 196px; position: absolute; text-align: center; color: white; font-size: 60px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Lab Notebook
</div>
<div style="width: 1440px; height: 97px; left: 0px; top: 328px; position: absolute">
<div style="width: 1440px; height: 97px; left: 0px; top: 0px; position: absolute; background: #9C93C9"></div>
<div
style="width: 1079px; left: 181px; top: 23px; position: absolute; text-align: center; color: black; font-size: 42px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Dry Lab</div>
<div style="width: 1079px; left: 181px; top: 23px; position: absolute; text-align: center; color: black; font-size: 42px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Dry Lab
</div>
</div>
<div style="width: 1201px; height: 803px; left: 128px; top: 495px; position: absolute">
<div style="width: 200px; height: 785px; left: 0px; top: 0px; position: absolute">
<div style="width: 200px; height: 156px; left: 0px; top: 0px; position: absolute"><span
style="color: #221023; font-size: 36px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">June<br /></span><span
style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">Week
1</span></div>
<div
style="width: 200px; height: 156px; left: 0px; top: 248px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 2</div>
<div
style="width: 200px; height: 156px; left: 0px; top: 424px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 3</div>
<div
style="width: 200px; height: 156px; left: 0px; top: 629px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 4</div>
<div style="width: 200px; height: 156px; left: 0px; top: 0px; position: absolute">
<span style="color: #221023; font-size: 36px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
June<br>
</span>
<span style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
<br />
</span>
<span style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 1
</span>
</div>
<div style="width: 200px; height: 156px; left: 0px; top: 212px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 2
</div>
<div style="width: 200px; height: 156px; left: 0px; top: 380px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 3
</div>
<div style="width: 200px; height: 156px; left: 0px; top: 520px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 4
</div>
</div>
<div style="width: 1079px; left: 122px; top: 72px; position: absolute">
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
Recruitment of the team completed<br />
Review of the original work by Salis et al. for better technical understanding of the problem statement<br>
Review of other work on predictive design of ribosome binding sites - thermodynamic
models, kinetic models, stochastic models, machine learning models<br>
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
Review of other work on predictive design of ribosome binding sites - thermodynamic models, kinetic models,
stochastic models, machine learning models<br />
Installing the ViennaRNA library for RNA sequence analysis using Python<br />
Downloading a dataset of 1014 RBS sequences with experimentally determined expression levels
from Reis and Salis (2020)<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br>
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
Defining the interaction between the rRNA and mRNA so as to have minimum hybridisation energy<br />
Including the effect of spacing between the SD sequence and the start codon<br />
Defining the interaction between the rRNA and the ribosomal S1 protein<br />
Accounting for the transient regional folding of the mRNA that can hinder RBS accessibility<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word" >
Including the presence of standby sites upstream of the SD sequence to which the ribosome can bind if the SD sequence is
transiently folded<br />
Accounting for the effect of various start codons on translation efficiency by using
data from Hecht et al. (2017)<br />
Training and testing different machine learning models to see which works
best for the data at hand
</span>
</div>
<div style="width: 1079px; left: 122px; top: 72px; position: absolute"><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Recruitment
of the team completed<br />Review of the original work by Salis et al. for better technical understanding of
the problem statement<br />Review of other work on predictive design of ribosome binding sites - thermodynamic
models, kinetic models, stochastic models, machine learning models<br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Review
of other work on predictive design of ribosome binding sites - thermodynamic models, kinetic models,
stochastic models, machine learning models<br />Installing the ViennaRNA library for RNA sequence analysis
using Python<br />Downloading a dataset of 1014 RBS sequences with experimentally determined expression levels
from Reis and Salis (2020)<br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Defining
the interaction between the rRNA and mRNA so as to have minimum hybridisation energy<br />Including the effect
of spacing between the SD sequence and the start codon<br />Defining the interaction between the rRNA and the
ribosomal S1 protein<br />Accounting for the transient regional folding of the mRNA that can hinder RBS
accessibility<br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Including
the presence of standby sites upstream of the SD sequence to which the ribosome can bind if the SD sequence is
transiently folded<br />Accounting for the effect of various start codons on translation efficiency by using
data from Hecht et al. (2017)<br />Training and testing different machine learning models to see which works
best for the data at hand</span></div>
</div>
<div style="width: 1201px; height: 484px; left: 128px; top: 1386px; position: absolute">
<div style="width: 1201px; height: 484px; left: 128px; top: 1200px; position: absolute">
<div style="width: 200px; height: 478px; left: 0px; top: 0px; position: absolute">
<div style="width: 200px; height: 156px; left: 0px; top: 0px; position: absolute"><span
style="color: #221023; font-size: 36px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">July<br /></span><span
style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">Week
1</span></div>
<div
style="width: 200px; height: 156px; left: 0px; top: 219px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 2</div>
<div
style="width: 200px; height: 156px; left: 0px; top: 279px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 3</div>
<div
style="width: 200px; height: 23px; left: 0px; top: 455px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 4</div>
<div style="width: 200px; height: 156px; left: 0px; top: 0px; position: absolute">
<span style="color: #221023; font-size: 36px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
July<br />
</span>
<span
style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br />
</span>
<span style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 1
</span>
</div>
<div style="width: 200px; height: 156px; left: 0px; top: 212px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 2
</div>
<div style="width: 200px; height: 156px; left: 0px; top: 270px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 3
</div>
<div style="width: 200px; height: 23px; left: 0px; top: 435px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 4
</div>
</div>
<div style="width: 1079px; left: 122px; top: 72px; position: absolute">
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
Downloading a dataset of 16779 RBS sequences characterised by FlowSeq from Reis and Salis (2020) and testing the model on
it<br />
Reading up on different optimisation algorithms that can be used to "mutate" an RBS sequence in silico
in order to achieve a desired expression level<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
Simulated annealing and gradient descent optimisers were created and tested<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
Optimiser performance was tested by varying its intrinsic parameters, work is ongoing<br />
A partially working genetic algorithm was created, work is yet to be finished on this<br />
The two working optimisers were used to generate RBS sequences with varying expression levels. These sequences will be used in the wet lab using
GFP-expressing Lactococcus lactis to see if the optimisation was successful.<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
All India iGEM Meet
</span>
</div>
<div style="width: 1079px; left: 122px; top: 72px; position: absolute"><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Downloading
a dataset of 16779 RBS sequences characterised by FlowSeq from Reis and Salis (2020) and testing the model on
it<br />Reading up on different optimisation algorithms that can be used to "mutate" an RBS sequence in silico
in order to achieve a desired expression level<br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Simulated
annealing and gradient descent optimisers were created and tested<br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Optimiser
performance was tested by varying its intrinsic parameters, work is ongoing<br />A partially working genetic
algorithm was created, work is yet to be finished on this<br />The two working optimisers were used to
generate RBS sequences with varying expression levels. These sequences will be used in the wet lab using
GFP-expressing Lactococcus lactis to see if the optimisation was successful.<br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">All
India iGEM Meet</span></div>
</div>
<div style="width: 1201px; height: 397px; left: 128px; top: 1958px; position: absolute">
<div style="width: 1201px; height: 397px; left: 128px; top: 1750px; position: absolute">
<div style="width: 200px; height: 391px; left: 0px; top: 0px; position: absolute">
<div style="width: 200px; height: 156px; left: 0px; top: 0px; position: absolute"><span
style="color: #221023; font-size: 36px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">August<br /></span><span
style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">Week
1</span></div>
<div
style="width: 200px; height: 156px; left: 0px; top: 132px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 2</div>
<div
style="width: 200px; height: 112px; left: 0px; top: 279px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 3</div>
<div
style="width: 200px; height: 23px; left: 0px; top: 339px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 4</div>
<div style="width: 200px; height: 156px; left: 0px; top: 0px; position: absolute">
<span style="color: #221023; font-size: 36px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
August<br />
</span>
<span style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br />
</span>
<span style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 1</span>
</div>
<div style="width: 200px; height: 156px; left: 0px; top: 128px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 2
</div>
<div style="width: 200px; height: 112px; left: 0px; top: 240px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 3
</div>
<div style="width: 200px; height: 23px; left: 0px; top: 297px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 4
</div>
</div>
<div style="width: 1079px; left: 122px; top: 72px; position: absolute">
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Genetic
algorithm completed. Found to have the best performance.
<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
Attempted to combine different aspects to the optimization algorithms.<br />
Started work on adding new parameters to the model to improve accuracy of predictions. Literature review on RNA folding kinetics and RNA degradation was
initiated.<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
Literature review continued<br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
<br />
</span>
<span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
Starting working with the Kinfold library of ViennaRNA to find the folding time. There was a need to integrate command
line operations with Python code.
</span>
</div>
<div style="width: 1079px; left: 122px; top: 72px; position: absolute"><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Genetic
algorithm completed. Found to have the best performance.<br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Attempted
to combine different aspects to the optimization algorithms.<br />Started work on adding new parameters to the
model to improve accuracy of predictions. Literature review on RNA folding kinetics and RNA degradation was
initiated.<br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Literature
review continued<br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Starting
working with the Kinfold library of ViennaRNA to find the folding time. There was a need to integrate command
line operations with Python code.</span></div>
</div>
<div
style="width: 1201px; height: 339px; padding-bottom: 33.82px; left: 128px; top: 2443px; position: absolute; justify-content: center; align-items: center; display: inline-flex">
<div style="width: 1201px; height: 339px; padding-bottom: 33.82px; left: 128px; top: 2180px; position: absolute; justify-content: center; align-items: center; display: inline-flex">
<div style="width: 1201px; height: 305.18px; position: relative">
<div style="width: 226px; height: 305.18px; left: 0px; top: 0px; position: absolute">
<div style="width: 226px; height: 146.09px; left: 0px; top: 0px; position: absolute"><span
style="color: #221023; font-size: 36px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">September<br /></span><span
style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">Week
1</span></div>
<div
style="width: 200px; height: 146.09px; left: 0px; top: 159.09px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 2</div>
<div style="width: 226px; height: 146.09px; left: 0px; top: 0px; position: absolute">
<span style="color: #221023; font-size: 36px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
September<br />
</span>
<span style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br />
</span>
<span style="color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 1
</span>
</div>
<div style="width: 200px; height: 146.09px; left: 0px; top: 154px; position: absolute; color: #221023; font-size: 24px; font-family: Montserrat; font-weight: 700; word-wrap: break-word">
Week 2
</div>
</div>
<div style="width: 1079px; height: 137.66px; left: 122px; top: 67.43px; position: absolute">
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
Kinfold used to generate folding time data for the dataset.<br />
Prototype for degradation model built<br />
</span>
<span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br />
</span>
<span style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">
Folding kinetics and degradation did not improve model performance.<br />
Model finalised without using these parameters.
</span>
</div>
<div style="width: 1079px; height: 137.66px; left: 122px; top: 67.43px; position: absolute"><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Kinfold
used to generate folding time data for the dataset.<br />Prototype for degradation model
built<br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word"><br /></span><span
style="color: black; font-size: 24px; font-family: Montserrat; font-weight: 400; word-wrap: break-word">Folding
kinetics and degradation did not improve model performance.<br />Model finalised without using these
parameters.</span></div>
</div>
</div>
</div>
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>
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></div>
<div
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height: 111px;
left: 0px;
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position: absolute;
background: #34304d;
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></div>
<div
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width: 681px;
height: 80px;
left: 300px;
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position: absolute;
text-align: center;
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word-wrap: break-word;
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Lab Notebook
</div>
<div
style="
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left: 0px;
top: 328px;
top: 10px;
position: absolute;
"
>
......@@ -246,7 +275,7 @@
width: 1119px;
height: 2459px;
left: 128px;
top: 495px;
top: 200px;
position: absolute;
"
>
......@@ -764,8 +793,8 @@
style="
width: 1079px;
height: 1981px;
left: 181px;
top: 3068px;
left: 128px;
top: 2600px;
position: absolute;
"
>
......@@ -1300,8 +1329,8 @@
style="
width: 1079px;
height: 431px;
left: 181px;
top: 5171px;
left: 128px;
top: 4400px;
position: absolute;
"
>
......@@ -1422,10 +1451,12 @@
width: 907px;
height: 793px;
left: 267px;
top: 687px;
top: 400px;
position: absolute;
"
src="https://static.igem.wiki/teams/4931/wiki/wetlab.png"
/>
</div>
</div>
{% endblock %}
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