Twitter sentiment analysis

Tweepy

https://youtu.be/1gQ6uG5Ujiw

competency should have verbs.

competency should have verbs, so we can meet the competency by actions

TAGC notes

PgmNr 714C: Mistranslation elicits different cellular responses based on the amino acid substitution.

Authors:
Matthew Berg ¹; Yanrui Zhu ¹; Bianca Ruiz ²; Joshua Isaacson ¹; Julie Genereaux ¹; Raphael Loll-Krippleber ³; Bryan-Joseph San Luis ³; Charles Boone ³; Grant Brown ³; Judit Villen ²; Christopher Brandl ¹
1) Department of Biochemistry, University of Western Ontario, London, ON, Canada; 2) Department of Genome Sciences, University of Washington, Seattle, WA, USA; 3) Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada

---

Life does not require a perfectly accurate proteome. In fact, errors occur at a rate of one mis-incorporated amino acid in every 10⁴ to 10⁵ codons. Mistranslation, or the mis-incorporation of an amino acid that differs from what is specified by the “standard” genetic code, can also occur due to mutations in the translation machinery. Cells therefore have mechanisms to cope with the resulting errors in protein folding and aggregation. Defects in these pathways may contribute to disease due to a loss of proteostasis. Our goal was to examine how different types of mistranslation affect cells. Using three tRNA variants that mistranslate the genetic code, we investigated genetic interactions and effects of mistranslation on the proteome in Saccharomyces cerevisiae. The tRNA variants mistranslate alanine at proline codons, serine at proline codons or serine at arginine codons with frequencies of 2.9%, 4.7% and 2.8% respectively. The alanine at proline and serine at arginine mistranslating tRNAs cause ~10% increase in doubling time as measured by growth in liquid media, while the more severe serine at proline mistranslating tRNA causes ~20% increase. All mistranslating tRNAs induce a heat shock response. Synthetic genetic array analysis of the tRNAs against the yeast temperature sensitive collection revealed that all the tRNAs had negative genetic interactions with genes involved in protein folding. Interestingly, however, we found distinct differences in the genetic interactions of each tRNA. Similarly, proteome analysis using mass spectrometry identified different subsets of up and down regulated proteins, depending on the type of mistranslation. We conclude that while protein quality control mechanisms are required for all types of mistranslation, the specific amino acid substitutions effect cells in different ways. We previously found variants in human tRNAs that have the potential to mistranslate. Based on the unique genetic and proteomic responses observed for different mistranslating tRNAs, we believe that in addition to exacerbating diseases caused by protein mis-folding, naturally occurring mistranslating tRNAs have the potential to negatively influence a wider range of diseases, depending on the specific amino acid substitution caused by the mistranslation.

The above poster on residue level on protein translation fidelity. 

Solve the EndNote COM Exception, copy-past as text and reformat

How to solve the EndNote Com error?
I  copy-past the portion text. This clear the tag information of EndNote citations. I  reformated the bibliography, and it worked.

zero Eigen value

zero eigen value seems to give undefined eigen vector.

geometric multiplicity and algebraic multiplicity are equal for symmetric matrice

𝜆$\lambda$ be an eigen value of a symmetric matrix 𝐴$A$ then how to show that the geometric multiplicity and algebraic multiplicity are equal?

in general, geometric multiplicity <= algebraic multipliciy

https://youtu.be/Xcln3xG8QGQ

2D contour plot, Python notebook

CoLab notebook

https://colab.research.google.com/github/ageron/handson-ml2/blob/master/math_differential_calculus.ipynb#scrollTo=eOzDBgjndchn

dot product, nicely explained

https://youtu.be/LyGKycYT2v0

ms02 interaction probability landscape

ms02 interaction probability landscape

Z score -> probability

I need to check my power-law network permutation methods for its randomness. 

scRNAseq tutorials

MIT compbio lecture 21, single cell genomcis 2018.
https://youtu.be/mJKbnJO5gZk

dimensionality reduction, linear PCA, nonlinear t-distributed stochastic neighbor emdedding (TSNE)


https://youtu.be/2DkLihHvaJE

probability landscape versus waddington landscape

probability landscape complements Waddington landscape,

https://www.researchgate.net/figure/The-epigenetic-landscape-The-probability-distribution-upper-panel-and-the_fig1_235402808

session 5A, population mortality modeling

https://youtu.be/S8EPH7q3e5o

uncertainty principle of aging
Xiaoming Liu,  Western university in Ontario, Canada

Markov chain model

Lin and Liu 2007

2020, living o 100 symposium

SarsCov2 topics

Sweden, loose social distance

Wisconsin, April 8, in person primary election. R0 comparison before and after

Niagara?

graph sparfification and single cell network

Languraidan matrix


https://youtu.be/8XJes6XFjxM

Quantum Speedup for Graph Sparsification, Cut Approximation and Laplacian Solving

https://youtu.be/p2hZL38tqAs

*** spectral graph theory, clustering

https://youtu.be/8XJes6XFjxM

small eigen value indicate small bottleneck, which can be used for spectral clustering.

Matrix Eigen value

spectral theorem

https://youtu.be/KCANLl8z6PI

visual explanation
https://youtu.be/PFDu9oVAE-g

new york times sarscov2 model

warm temperature is assumed

https://www.nytimes.com/interactive/2020/03/25/opinion/coronavirus-trump-reopen-america.html

ESRI covid19

https://www.esri.com/en-us/covid-19/overview

Kaggle covid19

https://www.kaggle.com/covid-19-contributions

news, media, covid19 weather

A call to honesty in pandemic modelingMaria Chikina and Wesley Pegden2020 March 29

https://medium.com/@wpegden/a-call-to-honesty-in-pandemic-modeling-5c156686a64b

NEON workshop

Workshop page: https://www.neonscience.org/aag-20200408


https://www.neonscience.org/download-explore-neon-data


https://www.neonscience.org/neon-spatial-data-basics

https://www.neonscience.org/neon-spatial-data-basics

bootcamp to do list

Zoom introduction,
microphone, raise hand, yes-green, red-no, go slower, go faster,

NimbioS webinar, viruses in the ocean.

surface ocean, chroloryl, cycles seanonally from NASA models SeaWiFi.

model A: epidemics are everywhere
model B: nature flatten the curve.

SIR model  is connected to the resource, producer and consumer model

argue that oscillation is epidemics cycles.

attention based recurrent neural network for flu predictions

Attention-based recurrent neural network for influenza epidemic prediction

• Xianglei Zhu, 
• Bofeng Fu, 
• Yaodong Yang, 
• Yu Ma, 
• Jianye Hao, 
• Siqi Chen, 
• Shuang Liu, 
• Tiegang Li, 
• Sen Liu, 
• Weiming Guo & 
• Zhenyu Liao 

volume 20, Article number: 575 (2019) Cite this article
x

BMC Bioinformatics 

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3131-8

deep learning, weather prediction

deep learning -> parameterization for weather prediction

https://www.sciencedaily.com/releases/2019/11/191112164947.htm

this is similar to use deep learning to speed up ODE modeling for system biology

Research.gov request to change objectives and scope

1200 characters (250 words) for each section of changes and justification

GCP deep learning VM

Suggested next steps

• Set up the Cloud SDK.
  The Cloud SDK (gcloud) is the preferred command line tool for interfacing with your instance. Download it here. 
• (Optional) Copy files to your VM from your local machine.
  You can use the gcloud tool to upload files to your machine.

  
  $
  
  
  gcloud compute scp --project agile-magnet-273523 --zone us-east1-d --recurse <local file or directory> tensorflow-1-vm:~/
  
  
  
  
  
  

• Access the running Jupyter notebook.
  We've already started a Jupyter notebook instance on the VM for your convenience. In order to get link that can be used to access Jupyter Lab run the following command.

  
  $
  
  
  gcloud compute instances describe --project agile-magnet-273523 --zone us-east1-d tensorflow-1-vm | grep googleusercontent.com | grep datalab
  
  
  
  
  
  

• Assign a static external IP address to your VM instance
  An ephemeral external IP address has been assigned to the VM instance. If you require a static external IP address, you may promote the address to static. Learn more 

Documentation

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• StackOverflow: Deep Learning VM 
• Google Group: Deep Learning VM 

Support

If you have non-framework related issues, you can bring them up at the Deep Learning VM Stack Overflow .

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