journal of emerging investigator (high school research publication)
https://careernavigator.gradeducation.hms.harvard.edu/journal-emerging-investigators-jei
Frontier for young minds
https://kids.frontiersin.org/article/10.3389/frym.2020.566235
Sunday, January 31, 2021
bootcamp, data science crash course
guest login to check screen, audio
introduce myself, recording locally
anonymous survey, zoom,
github readme, overview, link to chat.
went overtime.
Colab need a gmail account.
Thursday, January 28, 2021
git with ssh key
git with ssh key can only run with git URL, not http
One way is to set the URL to git
https://docs.github.com/en/github/using-git/changing-a-remotes-url
$ git remote set-url origin https://github.com/USERNAME/REPOSITORY.git
cpsc2100, agile
tutor service announcement
https://new.utc.edu/engineering-and-computer-science/center-for-student-success/student-services/peer-peer-tutoring
breakout rooms
Discussion topics on AGILE software design:
- what are your expectations of an excellent software?
- When you noticed some problematics issues on softwares, apps, websites, have you tried to come up with potential solutions?
- What ways do you think are effective to develop a software, app, or website?
- Describe the basic idea of AGILE software development
- Describe the 12 principles of AGILE using your own words.
Breakout room group report.
An interesting/funny story on when a software did not function as expected?
I then spent 5 minutes to go over the AGILE slides.
The following content were not discussed.
Breakout room discussion on Git, GitHub
- what is git, github?
- what does "commit" do?
- what does "push" do?
- what does "pull" do?
Github repo cerate, readme, editi, demo
Wednesday, January 27, 2021
Tuesday, January 26, 2021
interview questions
“Tell me about some of the most difficult problems you worked on and how you solved them.”
https://www.cnbc.com/2021/01/26/elon-musk-favorite-job-interview-question-to-ask-to-spot-a-liar-science-says-it-actually-works.html
Monday, January 25, 2021
exp(ix) = cosx + i sinx
Reference:
https://physics.stackexchange.com/questions/53005/how-to-get-complex-exponential-form-of-wave-equation-out-of-sinusoidal-form
graph-convolutional-networks-deep learning
graph convolutional networks (GCN) used Lapalacian matrix = Degree matrix - Adjacency materix
https://towardsdatascience.com/graph-convolutional-networks-deep-99d7fee5706f
Sunday, January 24, 2021
advancing data curation, book , vorgelegt von
advancing data curation, book , vorgelegt von
https://www.depositonce.tu-berlin.de/bitstream/11303/10811/4/visengeriyeva_larysa.pdf
COVID19 B1.1.7 strain Alpha variant
https://en.wikipedia.org/wiki/SARS-CoV-2_Alpha_variant
Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England
https://virological.org/t/transmission-of-sars-cov-2-lineage-b-1-1-7-in-england-insights-from-linking-epidemiological-and-genetic-data/576
https://virological.org/t/transmission-of-sars-cov-2-lineage-b-1-1-7-in-england-insights-from-linking-epidemiological-and-genetic-data/576
https://www.medrxiv.org/content/10.1101/2020.12.24.20248822v1
One study showed that N501Y had only a weak transmission advantage on its own, rising rapidly only when coupled with the suite of mutations observed in B.1.1.7.
Early empirical assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020
https://www.medrxiv.org/content/10.1101/2020.12.20.20248581v2
redfinger cloud amulators
https://www.cloudemulator.net/?fbclid=IwAR1HzQRjGqemAilVEMwnYGeDHJBra72H5qKwCfp1mcaZufZEPhavX-Wyo8s
Saturday, January 23, 2021
COVID19 hospitalization data USA
COVID19 hospitalization data USA
https://healthdata.gov/dataset/covid-19-reported-patient-impact-and-hospital-capacity-facility
https://healthdata.gov/sites/default/files/reported_hospital_capacity_admissions_facility_level_weekly_average_timeseries_20210117.csv
Hospital meta information:
https://healthdata.gov/dataset/covid-19-hospital-data-coverage-report
https://healthdata.gov/sites/default/files/20210119_Hospital%20Data%20Coverage%20Report.xlsx
Reference: https://sites.google.com/view/hamiltoncounty-tn-covid19/data?authuser=0
Friday, January 22, 2021
comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2599-6
In general, agreement among the tools in calling DE genes is not high. There is a trade-off between true-positive rates and the precision of calling DE genes. Methods with higher true positive rates tend to show low precision due to their introducing false positives, whereas methods with high precision show low true positive rates due to identifying few DE genes. We observed that current methods designed for scRNAseq data do not tend to show better performance compared to methods designed for bulk RNAseq data. Data multimodality and abundance of zero read counts are the main characteristics of scRNAseq data, which play important roles in the performance of differential gene expression analysis methods and need to be considered in terms of the development of new methods.
A few studies have compared differential expression analysis methods for scRNAseq data. Jaakkola et al. [40] compared five statistical analysis methods for scRNAseq data, three of which are for bulk RNAseq data analysis. Miao et al. [41] evaluated 14 differential expression analysis tools, three of which are newly developed for scRNAseq data and 11 of which are old methods for bulk RNAseq data. A recent comparison study [42] assessed six differential expression analysis tools, four of which were developed for scRNAseq and two of which were designed for bulk RNAseq. In this study, we consider all differential gene expression analysis tools that have been developed for scRNAseq data as of October 2018 (SCDE [21], MAST [29], scDD [39], D3E [33], Monocle2 [38], SINCERA [34], DEsingle [36], and SigEMD [37]). We also consider differential gene expression analysis tools that are designed for heterogeneous expression data (EMDomics [31]) and are commonly used for bulk RNAseq data (edgeR [4], DESeq2 [43]).
As of October 2018, we have identified eight software tools for differential expression analysis of scRNAseq data, which are designed specifically for such data [21, 29, 30, 33, 34, 36,37,38] (SCDE, MAST, scDD, D3E, Monocle2, SINCERA, DEsingle, and SigEMD).
2021 ReSEARCH Dialogues Conference
Greetings,
The 2021 ReSEARCH Dialogues Conference is going virtual!
ReSEARCH Dialogues is an annual, campus-wide academic conference celebrating research and creative activities happening on campus and in the Chattanooga community.
Presenters represent nearly all UTC disciplines, centers, programs and include:
- Undergraduate and graduate students, faculty, and staff
- Chattanooga community members
- Local high school students
- Local community college students
RD 2021 will be held during the first-ever UTC Research and Creative Activities Week. The virtual conference format will feature online presentations available on demand, daily, live webcasts including panels and talks, and live Q&A sessions with conference presenters. Learn more about UTC Research and Creative Activities Week and submit an event HERE.
RD 2021 Conference Details
WHEN: Monday, April 12 – Thursday, April 15, 2021.
WHERE: Virtual via the Symposium by ForagerOne online conference platform. Live webcasts will be scheduled each day of the conference.
Ready to Register? Visit the RD website.
Other Ways to Participate in RD 2021
- Attend live conference webcast events.
- Encourage colleagues and students to present at RD 2021, and attend live conference webcasts.
- Publicize RD 2021 and UTC Research and Creative Activities Week within your department, college, or unit.
- Participate in UTC Research and Creative Activities Week. Submit an event HERE.
- Promote the conference on social media.
- Volunteer at RD 2021. To volunteer sign up HERE or contact researchdialogues@utc.edu.
Questions? Contact the RD 2021 Team.
Sincerely,
RD 2021 Team
Thursday, January 21, 2021
UT compensation project, 2020
https://hr.tennessee.edu/pay/compensation-project/
https://hr.tennessee.edu/job-families/research/researcher/
https://hr.tennessee.edu/pay/market-ranges/
Researcher 2, MR09, mid-point salary $59.3K
RESEARCHER 2
- Provides professional contributions to research programs and projects requiring specialized knowledge and experience.
- Independently performs components of a research program with general guidance by a senior member of the research team or principal investigator.
- Performs complex research-related work assignments.
- Solves a range of straightforward problems that may include proposing and implementing procedural and design modifications.
- Makes independent judgments and decisions, including theoretical approaches, design of experiments and conclusions.
Education/Experience
Typically requires an advanced degree in a relevant field and two years of relevant experience, or an equivalent combination of education, training, and experience.
Market Range: MR09
Wednesday, January 20, 2021
cpsc2100 day 2, Jupyter notebook quick start, CoLab
start zoom recording, ( I forgot to record this)
Socrative questions
=> go over self-video presentation again
=>Anaconda: local installation
=>Jupyter-notebook: code blocks, mark-down blocks, run, kernel, "!", "%"
=>Google CoLab: free cloud, code blocks, text blocks, table of content, run codes, file uploading, linking GoogleDrive, download ipynb files
=>Google Cloud Platform ( need subscription)
=>Breakout room discussion:
anaconda installation, jupyter-notebook, coLab
Tuesday, January 19, 2021
Monday, January 18, 2021
Sunday, January 17, 2021
Saturday, January 16, 2021
Friday, January 15, 2021
cpsc2100 day 1
slides, introduce myself
Socrative, Room HongQin
syllabus
video requirement
video submission with hyper-link. Examples of past student submissions.
sample student videos
Colab; COVID19 data analysis
https://github.com/hongqin/python-covid19-analysis-sandbox/blob/master/PD_demo_jhu_covid19.ipynb
why python
x Email list to calendar invitation
Wednesday, January 13, 2021
Machine Learning for Fluid Mechanics
Machine Learning for Fluid Mechanics
https://arxiv.org/abs/1905.11075
Tuesday, January 12, 2021
try to download PDF from google drive (unsuccessful attemp)
import sys
sys.path.append("/opt/anaconda3/lib/python3.7/site-packages")
import requests
from bs4 import BeautifulSoup as soup
from urllib import parse
import os
import re
import pandas as pd
tb = pd.read_excel('Submission of Report _ Lesson plan, online-R-coding bootcamp Dec 2020 (Responses).xlsx')
doc_urls = tb['Please upload your report (for students) or lesson plans (for teachers) in PDF format']
type( doc_urls )
doc_urls[1]
content = requests.get(doc_urls[1] )
with open(("test.pdf"), 'wb') as pdf:
pdf.write(content.content)
dir(content)
#The generated pdf cannot be open. It is an html file.
Sunday, January 10, 2021
A Tidy Transcriptomics introduction to RNA-Seq analyses
A Tidy Transcriptomics introduction to RNA-Seq analyses
https://stemangiola.github.io/bioc_2020_tidytranscriptomics/articles/tidytranscriptomics.html
Friday, January 8, 2021
Thursday, January 7, 2021
identical twin 5.2 SNP
https://www.newser.com/story/301012/identical-twins-not-as-identical-as-we-thought.html
"On average, identical twins have 5.2 of these early genetic differences, the researchers found. But about 15% of identical twin pairs have more genetic differences, some of them up to 100, said Stefansson"
Wednesday, January 6, 2021
scDNA-seq
Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Single-Cell Sequencing
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114520
Using sequencing data from single sperms, we quantitatively compare two prevailing amplification methods that extensively applied in single-cell sequencing, multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Our results show that MALBAC, as a combination of modified MDA and tweaked PCR, has a higher level of uniformity, specificity and reproducibility.
this paper argues that MDA has serious amplification bias.
allele specific protein expression in a diploid yeast hybrid by LC-MS
Khan, 2012, MSB, allele specific protein expression in a diploid yeast hybrid by LC-MS
https://www.embopress.org/doi/epdf/10.1038/msb.2012.34
This paper used LC-MS to study protein from yeast hybrid S cerevisie X S. bayanas. It likely the polymorphism in the same species has too few changes at the protein level.
yeast allelic differential expression
https://www.embopress.org/doi/epdf/10.1038/msb.2009.31
genome wide allele and strand-specific expression in yeast. Gagneur 2009. MSB.
Tiling array. 371 (13%) of the transcripts have >1.5 fold difference. So, total transcripts is about 2854 in this paper.
In Dang's CR and NR data sets, there are over 3K transcripts.
Tuesday, January 5, 2021
yeast cell DNA, RNA, protein
DNA: 0.034 pg/diploid cell, 0.017 pg/ haploid cell
RNA: 1.9 pg /diploid cell, 1.2 pg / haploid cell
Protein: 8 pg/ diploid cell, 6 pg/ haploid cell
Range: Table - link pg/cell
https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105079&ver=5
Reference: Sherman, getting started with yeast. Mehods Enzymol. 2002.
So, if Illuminia require 1 ng for sequencing, a single cell DNA needs to be amplified by:
1ng / 0.017 pg = 1000 pg / 0.017 pg ~ 1000* 1000 / 20 = 50, 000 X amplification.
50,1000 = 2**15, so 15 rounds of PCR amplification.
UTC graduate assistantship
https://new.utc.edu/research/graduate-school/student-resources/graduate-assistantships#SACS
H3K36me3
https://en.wikipedia.org/wiki/H3K36me3#:~:text=H3K36me3%20is%20an%20epigenetic%20modification,have%20many%20important%20biological%20processes.
single cell DNA reagent kits, library preparation
Solid Phase Reversible Immobilization (SPRI) beads are used to optimize the DNA size range for library preparation. see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944320/
This paper sheared all single-cell and bulk DNA, https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105585 , "A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods", de Bounrcy, 2014. This is an old paper though. This paper said that Illumina require 1 ng of DNA for sequencing. A single bacterial cell has 1 fg (femtogram) DNA, so, 1E6 application is needed.
https://support.10xgenomics.com/single-cell-dna/library-prep/doc/user-guide-chromium-single-cell-dna-reagent-kits-user-guide
Solid Phase Reversible Immobilization (SPRI) beads are used to optimize the DNA size range for library preparation. see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944320/
https://en.wikipedia.org/wiki/Single_cell_sequencing#Single-cell_genome_(DNA)_sequencing
Monday, January 4, 2021
scDNA-seq and LOH monitoring in yeast aging
single cell DNA seq
Natural communication, 2019, Luquette, .. Peter Park, Identification of somatic mutations in single cell DNA-seq using a spatial model of allelic imbalance.
somatic SNV (single nucleotide variation).
variant allele fraction (VAF), the fraction of sequencing reads supporting allele a heterozygous variant.
Qin: VAF on loss of heterozygosity during aging can be done with young cells as the background. The young cells provide a reference distribution of VAF at allelic positions genome-wide. Comparison between VAF of aging cells and young cells. If loss of heterozygocity occurs a loci, VAF at a loci can only be caused by amplification artifacts, which are expect to be 'random' and has a very small probability to overlap with the natural variations. S288c and RM is 0.5-1%.
Luquette19 proposed a genome-location spatial model for Amplification Balance to evaluate VAF. Luquette used nearby known SNP VAF to show the allele imbalance. Luquette19 used a 'smooth curve' to model the spatial distribution of allele imbalance on chromosomes.
Sunday, January 3, 2021
weighted correlation network analysis
https://en.wikipedia.org/wiki/Weighted_correlation_network_analysis
Saturday, January 2, 2021
Friday, January 1, 2021
anterior (ventral), posterior (dorsal), superior (cephalic), caudal, inferior (distal), medial, lateral
anterior (ventral), posterior (dorsal), superior (cephalic), caudal, inferior (distal), medial, lateral
https://courses.lumenlearning.com/ap1x94x1/chapter/anatomical-orientation-and-directions/
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