over-registered, and the stipend is a major concern of participants.
16 teacher showed up.
Basic python is OK.
HCDE gmail account does not allow COLAB by default. Needs to ask HCDE-IT for add COLAB.
COVID-19 analysis is a lot and about half of the teachers clearly did not follow.
[Previously saved workspace restored]
> b1 = 1
> b1 = 2
> b2= 1.8
> I1 = c(0.005, 0.5, 0.9)
> I2 = c(0.8, 0.5, 0.1)
> b1*I1 / b2 * I2
[1] 0.004444444 0.277777778 0.100000000
> ratio = b1*I1 / b2 * I2
> t = 1:3
> plot( ratio ~ t)
> t = 1:5
> t
[1] 1 2 3 4 5
> I1 = 0.005*2^5
> I1
[1] 0.16
> I1 = 0.005*2^t
> I1
[1] 0.01 0.02 0.04 0.08 0.16
> I2 = 1 - I1
> ratio = b1*I1 / b2 * I2
> plot( ratio ~ t)
> plot( log(ratio) ~ t)
-1 means rows are unknown.
1 means column is 1.
https://stackoverflow.com/questions/18691084/what-does-1-mean-in-numpy-reshape
Only one student show up. Other students could not find rides to UTC, because they are living off campus this week.
zoom, screen sharing,
ipad
Socrative
CoLab
Basic R.
Socrative Questions:
What is SARS-CoV-2? How is SARS-CoV-2 related to COVID-19?
Have you been able to use COLab?
What are the difference between code and text sections on CoLab?
How to run code on CoLab?
What is the R coding language?
What does the equal sign "=" do in R?
What does the sign "#" do in R?
What is a vector in R?
What is a function in R?
What is a data frame in R?
How to pick the 9th element of an array in R?
What does $ do in R?
How to pick the second row in a data frame tb?
How to pick the third column in a data frame tb?
df = pd.read_csv("variant_surveillance.tsv", sep = '\t',dtype = {'Variant': 'string','Is reference?': 'string'})
array(['Alpha', 'Beta', 'Delta', 'Epsilon', 'Eta', 'GH/490R', 'Gamma',
'Iota', 'Kappa', 'Lambda', 'Mu', 'Omicron', 'Theta', 'Zeta'],
dtype=object)North America
zoom, screen sharing,
ipad
Socrative
CoLab
Basic R.
Socrative Questions:
What is SARS-CoV-2? How is SARS-CoV-2 related to COVID-19?
Have you been able to use COLab?
What are the difference between code and text sections on CoLab?
How to run code on CoLab?
What is the R coding language?
What does the equal sign "=" do in R?
What does the sign "#" do in R?
What is a vector in R?
What is a function in R?
What is a data frame in R?
How to pick the 9th element of an array in R?
What does $ do in R?
How to pick the second row in a data frame tb?
How to pick the third column in a data frame tb?
LB notes:
Here is a link to a quick program that shows all of the pango lineages in GRA submissions for the updated GISAID variant surveillance dataset. There are 199 unique pango lineages out of all GRA submissions.
Also, here are a couple links that might explain some of the unexpected ones:
https://pubmed.ncbi.nlm.nih.gov/34987185/
https://github.com/AYMoralesArce/sims_DFE_virus
Amber M. Smith, Academic Editor and Ruian Ke, Academic Editor
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8310006/
QIN: This is within-host competition based fitness model, which is different from SARS-CoV-2 genomic surveillance data!
https://www.nature.com/articles/s43587-022-00233-9#data-availability
re we present and validate a TF activity estimation method for single cells from the hematopoietic system that is based on TF regulons, and apply it to a mouse single-cell RNA-sequencing atlas, to infer age-associated differentiation activity changes in the immune cells of different organs
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56046
| ||||
| Status | Public on Nov 24, 2014 | |||
| Title | Transcriptomics and methylomics of human monocytes [methylome] | |||
| Organism | Homo sapiens | |||
| Experiment type | Methylation profiling by genome tiling array | |||
| Summary | The MESA Epigenomics and Transcriptomics Study has been launched to investigate potential gene expression regulatory methylation sites in humans by examining the association between CpG methylation and gene expression in purified human monocytes from a large study population (community-dwelling participants in the Multi-Ethnic Study of Atherosclerosis (MESA)). The MESA Epigenomics and Transcriptomics Study was funded by a National Heart, Lung and Blood Institute grant (R01HL101250) through the NIH Roadmap Epigenomics Program in 2009. | |||
CRISPi + scRNA
https://gwps.wi.mit.edu/
matrix file in H5AD format
https://doi.org/10.25452/figshare.plus.20029387
Genome wide screen targeted n=9867 genes.
Essential-wide screen targeted n=2285 essential genes.
Growth phenotypes were measured log2-guide enrichment per cell doubling (gamma)
"The relative homogeneity of CRISPRi reduces selection for unperturbed cells, especially when studying essential genes. Unlike CRISPR knockout, CRISPRi does not lead to activation of the DNA damage response which can alter transcriptional signatures (Haapaniemi et al., 2018)."
"We use a compact, multiplexed CRISPR interference (CRISPRi) library to assay thousands of loss-of-function genetic perturbations with single-cell RNA sequencing (scRNA-seq) in chronic myeloid leukemia (CML) (K562) and retinal pigment epithelial (RPE1) cell lines."
There are four datasets on SRA:
Instructors,
Please refer to these online resources for creating a stellar Biosketch (https://nexus.od.nih.gov/all/2019/04/02/looking-for-help-developing-your-biosketch/). Also, refer to the workshop video https://vimeo.com/706149781/d58bcee44e for tips on creating the full application. Thank you again for your interest in the AIM-AHEAD Research Fellowship.
| This is "Research Fellowship Application Preparation Workshop Recording" by AIM-AHEAD on Vimeo, the home for high quality videos and the people who love them. vimeo.com |
The biosketch provides an opportunity for each senior/key person listed in an NIH grant application to describe why they are well-suited for their role(s) in the project through a personal statement and cite publications/ research products, among other things. nexus.od.nih.gov |
