Tinus Brown's open science talk slides

 

https://osf.io/bsner/

machine learning for health

 

https://ml4health.github.io/2021/pages/call-for-participation.html

x-omics tutrials

 

https://youtu.be/kzErX57Si9M

single cell transcriptomics with tidyverse

 

single cell transcriptomics with tidyverse

https://github.com/stemangiola/bioc_2020_tidytranscriptomics

https://github.com/stemangiola/tidySingleCellExperiment

 

Why anti-PD1/PDL1 therapy is so effective? Another piece in the puzzle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5756957/ 

github personal token

 

git config --global credential.helper cache

air quality data at EPA

 including air quality data measured daily in USA

https://www.epa.gov/outdoor-air-quality-data

potential data science projects:

 

twitter sentiment ~ election results

climate effect on a specific area, 

kaggle competitions

advantage of mitochondria as a organelle in system biology

 

advantage of mitochondria as an organelle in systems biology. Rule of Life (mitochondria as a control?)

Added controllability? fast response? temporal networks? 

CR on aging maybe a side effect of mitochondria control of cells as a system? 

metabolic control of longevity

 

metabolic control of longevity

microbiome -> u, B is the gene target, A -> gene/metabolite network

x = A x + B u

latex thesis cover

 

The front cover can be edited in “ utthesis.cls” ( last one)  lines 200 - 231 .

current variants

 

https://outbreak.info/situation-reports

quantum sequence alignment

 Quantum pattern recognition for local sequence alignment

https://ieeexplore.ieee.org/document/8269076 

https://github.com/spencerking/QiskitSummerJam-LocalSequenceAlignment 

amsantanubanerjee/quantum_sequence_alignment

 

QuASeR -- Quantum Accelerated De Novo DNA Sequence Reconstruction

https://arxiv.org/abs/2004.05078

https://github.com/QE-Lab/QuASeR

https://github.com/prince-ph0en1x/QuASeR

linear models in Python, Faraway

 

https://github.com/julianfaraway/LMP

natural language processing, bioinformatics

 

BERT-GT: cross-sentence n-ary relation extraction with BERT and Graph Transformer

https://academic.oup.com/bioinformatics/article-abstract/36/24/5678/6069538

LBERT: Lexically aware Transformer-based Bidirectional Encoder Representation model for learning universal bio-entity relations

https://academic.oup.com/bioinformatics/article-abstract/37/3/404/5893949

Attention-Based Transformers for Instance Segmentation of Cells in Microstructures

https://ieeexplore.ieee.org/abstract/document/9313305?casa_token=88kTMDn2LIUAAAAA:LxNIoFl-o24XoXV5PHpJ1T67-atx7ScUVKONPNGwKvPP6skEt4E99z1LmF6-8pGKSuuXtnCTSzo

transformer protein lanugage models are unsupervised structure learners

https://openreview.net/pdf?id=fylclEqgvgd 

BERTology meets biology: interpreting attention in protein language models

https://arxiv.org/abs/2006.15222

Burris Wheeler transformation

data science program assessment

 

data model 

Program Assessment Folder Link

covid19 mutations, github

 

https://github.com/cov-lineages/constellations/blob/main/constellations/data/mutations.csv

COVID19 lineages

 

https://cov-lineages.org/

https://github.com/cov-lineages

https://github.com/cov-lineages/constellations/blob/main/constellations/data/mutations.csv

covid19 variants

 

covid19 variants, CDC

 

https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

virus species

 virus metadata resource

https://talk.ictvonline.org/taxonomy/vmr/

Information on exemplar viruses for each species

The primary, definitive lists of exemplar viruses for each species is provided in chapters of the ICTV Report on Virus Classification and Taxon Nomenclature http://ictv.global/report). The list of exemplar viruses appears in the Member Species tables for each genus. For example, for the genus Cyclovirus, the Member Species table appears near the bottom of the following web page: https://talk.ictvonline.org/ictv-reports/ictv_online_report/ssdna-viruses/w/circoviridae/660/genus-cyclovirus.

On this page, we have made available a spreadsheet that contains this list of exemplars for each virus species, even those not yet described in a published ICTV Report chapter.

The Member Species tables and the VMR are the definitive sources for exemplar information, and are both updated based on new information and to correct errors. Taxonomy proposals (available from https://talk.ictvonline.org/files/ictv_official_taxonomy_updates_since_the_8th_report/) represent a snapshot in time and are not updated after the proposal is ratified. They are historical documents, and are therefore not a good source of current information on virus taxa and exemplar viruses.

data science lesson, youcubed

K12 data science lessons 

https://www.youcubed.org/data-science-lessons/

teacher bootcamp, day 1

 morning: 

TAs to add "TA" in their zoom name, 

start zoom breakout room

ask participant to mute themselves

remember to sign in

https://github.com/hongqin/R-bootcamp-for-teachers-2021July

lunch break. 

Afternoon, went over weather record for Chattanooga airport. 

The Facts – and Gaps – on the Origin of the Coronavirus

https://www.factcheck.org/2021/06/scicheck-the-facts-and-gaps-on-the-origin-of-the-coronavirus/?utm_source=twitter&utm_medium=social&utm_campaign=social-pug

 

neural network, sequence motif

 PSSM to nueral network 

control theory and machine learning

 

https://sites.google.com/view/control-meets-learning