Thursday, July 30, 2020

LIME - Local Interpretable Model-Agnostic Explanations

LIME - Local Interpretable Model-Agnostic Explanations
x

https://homes.cs.washington.edu/~marcotcr/blog/lime/

https://www.oreilly.com/content/introduction-to-local-interpretable-model-agnostic-explanations-lime/

geneious bioiformatics platform

a comercial competitor to usegalaxy.com

https://www.geneious.com/

Multiple alignment program for amino acid or nucleotide sequences

https://mafft.cbrc.jp/alignment/software/

Sunday, July 26, 2020

MyNCI My Bibliography

For NIH Biosketch

https://www.ncbi.nlm.nih.gov/myncbi/16Kujylt58I/bibliography/public/

Thursday, July 23, 2020

Why humidity matters, covid19

From
https://medicalxpress.com/news/2020-06-humidity-linked-covid-.html

Why humidity matters

Professor Ward said there are biological reasons why humidity matters in transmission of airborne viruses.

"When the humidity is lower, the air is drier and it makes the aerosols smaller," he said. "When you sneeze and cough those smaller infectious aerosols can stay suspended in the air for longer. That increases the exposure for other people. When the air is humid and the aerosols are larger and heavier, they fall and hit surfaces quicker."

https://www.medicalnewstoday.com/articles/how-humidity-may-affect-covid-19-outcome
Specifically, differences in temperature and humidity affect how stable and transmissible viruses are. For instance, some data reviewed in the new paper suggest that cold, dry, unventilated air may contribute to the transmission of influenza in the winter.

transcription fidelity and yeast aging

reviewers asks for mutation in DNA as a model. This is not correct (No, this is relavent 2020Oct), because yeast aging is a single-cell event. Its chromosome DNA unlikely to be mutated.

Experimental verification

Single cell variation

Old cell variation,

Test of some mutants ???. On transcription fidelity,

Candidate genes:

Transcriptional noise regulators.

Maybe histone methylation, K4 methyltransferase? Transcript inititiation? KO? Over-expression?

K4-methy hot in human aging. Six paralogs in human, involved in leukemia.

Only one copy gene in yeast. No clear phenotype on growth fitness and aging in yeast. ?!!!!

*** SET1 maybe not a general transcription initiation??? Only in stress-response.

https://www.yeastgenome.org/locus/S000001161

Aging is a stress condition.

TODO: SET1 expression during aging in eLife Data set. and Dang’s lab RNA and protein level data.

Gene Ontology Term: maintenance of transcriptional fidelity during DNA-templated transcription elongation

https://www.yeastgenome.org/go/GO:0001192

**** RPB9-deletion shorten RLS by 44% with p=1E-9. -> expect to increase expression noise -> aging.

General transcription elongation factor

https://www.yeastgenome.org/locus/DST1

DST1-deletion does change average RLS. (Need to check its distribution of RLS, gene expression).

RPB9
https://www.yeastgenome.org/locus/S000003038
RNA polymerase II subunit B12.6; contacts DNA; mutations affect transcription start site selection and fidelity of transcription

DST1 / YGL043W Overview

https://www.yeastgenome.org/locus/S000003011

K4 methyltransferase yeast cerevisiae is SET1

R write.csv versus write.csv2

write.csv uses "." for the decimal point and a comma for the separator.

write.csv2 uses a comma for the decimal point and a semicolon for the separator, the Excel convention for CSV files in some Western European locales.

2m dew point, ERA5

In Kelvin

Temperature to which the air, at 2 metres above the surface of the Earth, would have to be cooled for saturation to occur.It is a measure of the humidity of the air. Combined with temperature and pressure, it can be used to calculate the relative humidity. 2m dew point temperature is calculated by interpolating between the lowest model level and the Earth's surface, taking account of the atmospheric conditions. Temperature measured in kelvin can be converted to degrees Celsius (°C) by subtracting 273.15.

https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-land?tab=overview

Low dew point == low humidity according to wikipedia, because less vapor is need for condensation
https://en.wikipedia.org/wiki/Dew_point

Dew point		Relative humidity at 32 °C (90 °F)
Over 26 °C	Over 80 °F	73% and higher
24–26 °C	75–80 °F	62–72%
21–24 °C	70–74 °F	52–61%
18–21 °C	65–69 °F	44–51%
16–18 °C	60–64 °F	37–43%
13–16 °C	55–59 °F	31–36%
10–12 °C	50–54 °F	26–30%
Under 10 °C	Under 50 °F	25% and lower

This seems to explain that the condensation on leaves is often seen in the early morning, but not during the daytime. So, if a mutant strain has a lower dew point, it tend be in drier locations. If a strain has a higher dew point, it tends to be more humid locations

Tuesday, July 21, 2020

R versus Python

R versus Python

https://www.esparkinfo.com/r-vs-python.html

tensorflow play ground

playground.tensorflow.org

Monday, July 20, 2020

Saturday, July 18, 2020

mouse, protein noises

https://www.nature.com/articles/nature18270
Defining the consequences of genetic variation on a proteome-wide scale

Nature

Abstract

Genetic variation modulates protein expression through both transcriptional and post-transcriptional mechanisms. To characterize the consequences of natural genetic diversity on the proteome, here we combine a multiplexed, mass spectrometry-based method for protein quantification with an emerging outbred mouse model containing extensive genetic variation from eight inbred founder strains. By measuring genome-wide transcript and protein expression in livers from 192 Diversity outbred mice, we identify 2,866 protein quantitative trait loci (pQTL) with twice as many local as distant genetic variants. These data support distinct transcriptional and post-transcriptional models underlying the observed pQTL effects. Using a sensitive approach to mediation analysis, we often identified a second protein or transcript as the causal mediator of distant pQTL. Our analysis reveals an extensive network of direct protein–protein interactions. Finally, we show that local genotype can provide accurate predictions of protein abundance in an independent cohort of collaborative cross mice.

mutations ~ dewpoint in spike region

There are 3 mutations in the Spike region.

	msa_position	p	q	ref_position	ref_seq	type	gene	start	end	protein_id	feature_position	feature_position_mod3	triplet_start	triplet_end	ref_triplet	mut_triplet	ref_position_inProtein	ref_AA	ref_AAPosition	mut_AA	ref_freq	mut_freq	mut_seq	CHR
3654	36985	0.00453724672342917	0.0019392834243773	23730	C	CDS	S	21563	25384	YP_009724390.1	2169	0	23728	23730	ACC	ACT	7910	T	T723	T	40314	1381	T	1
3655	37185	0	0	23928	C	CDS	S	21563	25384	YP_009724390.1	2367	0	23926	23928	TAC	TAT	7976	Y	Y789	Y	41149	530	T	1
3653	36626	1.98774342659889E-68	4.81792614569765E-68	23402	A	CDS	S	21563	25384	YP_009724390.1	1841	2	23401	23403	GAT	GGT	7801	D	D614	G	11231	30413	G	1

ef_triplet

mut_triplet

ref_position_inProtein

ref_AA

ref_AAPosition

mut_AA

ref_freq

mut_freq

GAT

GGT

7801

D614

11231

30413

ACC

ACT

7910

T723

40314

1381

TAC

TAT

7976

Y789

41149

530

Are synonymous codon adaptation in play?
In bat, ACT > ACC, in human, ACC > ACT, so T723T from ACC -> ACT change from human major codon to human minor codon.

In human, TAT > TAC, so Y789Y change from human major codon to minor codon.
So, the answer seems to be NO.

Bat virus codon usage versus human codon bias usage

West Caucasian bat virus [gbvrl]: 4 CDS's (1478 codons)
http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=249584

West Caucasian bat virus [gbvrl]: 4 CDS's (1478 codons)

fields: [triplet] [frequency: per thousand] ([number])

UUU 18.9(    28)  UCU 29.8(    44)  UAU 22.3(    33)  UGU 12.9(    19)
UUC 21.0(    31)  UCC 18.9(    28)  UAC 18.3(    27)  UGC  8.8(    13)
UUA 10.8(    16)  UCA 18.9(    28)  UAA  0.7(     1)  UGA  1.4(     2)
UUG 20.3(    30)  UCG  4.1(     6)  UAG  0.7(     1)  UGG 12.9(    19)

CUU 14.2(    21)  CCU 18.3(    27)  CAU 12.9(    19)  CGU  3.4(     5)
CUC 12.9(    19)  CCC 13.5(    20)  CAC 16.2(    24)  CGC  1.4(     2)
CUA  8.8(    13)  CCA 14.2(    21)  CAA 16.9(    25)  CGA  2.7(     4)
CUG 16.2(    24)  CCG  2.7(     4)  CAG 10.1(    15)  CGG  1.4(     2)

AUU 16.2(    24)  ACU 15.6(    23)  AAU 26.4(    39)  AGU 16.2(    24)
AUC 27.1(    40)  ACC 12.2(    18)  AAC 17.6(    26)  AGC  6.8(    10)
AUA 18.3(    27)  ACA 22.3(    33)  AAA 23.7(    35)  AGA 29.8(    44)
AUG 23.7(    35)  ACG  3.4(     5)  AAG 35.2(    52)  AGG 17.6(    26)

GUU 17.6(    26)  GCU 15.6(    23)  GAU 37.9(    56)  GGU 10.1(    15)
GUC 18.9(    28)  GCC 13.5(    20)  GAC 23.0(    34)  GGC  6.1(     9)
GUA  9.5(    14)  GCA 14.2(    21)  GAA 38.6(    57)  GGA 21.7(    32)
GUG 21.0(    31)  GCG  2.0(     3)  GAG 32.5(    48)  GGG 19.6(    29)

Coding GC 43.96% 1st letter GC 46.75% 2nd letter GC 39.17% 3rd letter GC 45.94%
homo sapiens
http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606
Homo sapiens [gbpri]: 93487 CDS's (40662582 codons)

fields: [triplet] [frequency: per thousand] ([number])

UUU 17.6(714298)  UCU 15.2(618711)  UAU 12.2(495699)  UGU 10.6(430311)
UUC 20.3(824692)  UCC 17.7(718892)  UAC 15.3(622407)  UGC 12.6(513028)
UUA  7.7(311881)  UCA 12.2(496448)  UAA  1.0( 40285)  UGA  1.6( 63237)
UUG 12.9(525688)  UCG  4.4(179419)  UAG  0.8( 32109)  UGG 13.2(535595)

CUU 13.2(536515)  CCU 17.5(713233)  CAU 10.9(441711)  CGU  4.5(184609)
CUC 19.6(796638)  CCC 19.8(804620)  CAC 15.1(613713)  CGC 10.4(423516)
CUA  7.2(290751)  CCA 16.9(688038)  CAA 12.3(501911)  CGA  6.2(250760)
CUG 39.6(1611801)  CCG  6.9(281570)  CAG 34.2(1391973)  CGG 11.4(464485)

AUU 16.0(650473)  ACU 13.1(533609)  AAU 17.0(689701)  AGU 12.1(493429)
AUC 20.8(846466)  ACC 18.9(768147)  AAC 19.1(776603)  AGC 19.5(791383)
AUA  7.5(304565)  ACA 15.1(614523)  AAA 24.4(993621)  AGA 12.2(494682)
AUG 22.0(896005)  ACG  6.1(246105)  AAG 31.9(1295568)  AGG 12.0(486463)

GUU 11.0(448607)  GCU 18.4(750096)  GAU 21.8(885429)  GGU 10.8(437126)
GUC 14.5(588138)  GCC 27.7(1127679)  GAC 25.1(1020595)  GGC 22.2(903565)
GUA  7.1(287712)  GCA 15.8(643471)  GAA 29.0(1177632)  GGA 16.5(669873)
GUG 28.1(1143534)  GCG  7.4(299495)  GAG 39.6(1609975)  GGG 16.5(669768)

Coding GC 52.27% 1st letter GC 55.72% 2nd letter GC 42.54% 3rd letter GC 58.55%

Wednesday, July 15, 2020

SFS information

78. During the past 12 months, please indicate which Department level Federal agencies in which your SFS program partnered and describe the activity (e.g., worked on a "real world" project or research for publication or presentation, invited agency as guest speaker, gave presentation at agency, networked in an informal setting, placed SFS students for internships or permanent positions upon graduation). Listed below are the Department level Federal agencies.

Department of Agriculture

Department of Commerce – Bureau of Economic Analysis

Department of Commerce – Federal Trade Commission

Department of Commerce – National Institute of Standards & Technology

Department of Defense – Air Force/Air Force Material Command

Department of Defense – Air Force/Air Force Research Laboratory

Department of Defense – Army/Army CIO

Department of Defense – Army/Army Cyber Command and Second Army

Department of Defense – Army/Army Knowledge Leaders Program

Department of Defense – Army/Army Research Laboratory

Department of Defense – Army/Communications-Electronics Research, Development, and Engineering Center (CERDEC)

Department of Defense – Army/Engineering Research and Development Center (ERDC)

Department of Defense – Army/Intelligence Security Command (INSCOM)

Department of Defense – Army/US Army Corps of Engineers

Department of Defense - Defense Information Systems Agency

Department of Defense - Defense Intelligence Agency

Department of Defense - National Geospatial-Intelligence Agency

Department of Defense - National Security Agency

Department of Defense – Navy/Naval Air Systems Command (NAVAIR)

Department of Defense – Navy/Naval Criminal Investigative Service (NCIS)

Department of Defense – Navy/Naval Oceanographic Office

Department of Defense – Navy/Naval Post Graduate School

Department of Defense – Navy/Naval Research Laboratory

Department of Defense – Navy/Naval Sea Systems Command (NAVSEA)

Department of Defense – Navy/Office of Naval Research

Department of Defense – Navy/Space and Naval Warfare Systems Command (SPAWAR)

Department of Defense - Other DoD sub-agency

Department of Education

Department of Energy (if you partnered with the FFRDC, please select the FFRDC in question #78 below)

Department of Health and Human Services

Department of Homeland Security - Customs & Border Protection

Department of Homeland Security - Cybersecurity and Infrastructure Security Agency

Department of Homeland Security - Other DHS sub-agency

Department of Housing and Urban Development

Department of Interior

Department of Justice - Federal Bureau of Investigations

Department of Justice - Office of the Chief Information Officer

Department of Justice - Other DOJ sub-agency

Department of Labor

Department of State

Department of Transportation

Department of Treasury

Department of Veterans Affairs

(Enter up to 2000 characters)

79. During the past 12 months, please indicate which independent agencies in which your SFS program partnered and describe the activity (e.g., worked on a "real world" project or research for publication or presentation, invited agency as guest speaker, gave presentation at agency, networked in an informal setting, placed SFS students for internships or permanent positions upon graduation). Listed below are the Independent Federal agencies.

Administrative Conference of the United States

African Development Foundation

Central Intelligence Agency

Commission on Civil Rights

Commission on Presidential Scholars

Commission on Security and Cooperation in Europe

Consumer Financial Protection Bureau

Corporation for National and Community Service

Defense Nuclear Facilities Safety Board

Denali Commission

Environmental Protection Agency

Equal Employment Opportunity Commission

Export-Import Bank of the United States

Farm Credit Administration

Executive Office of the President

Federal Communications Commission

Federal Deposit Insurance Corporation

Federal Election Commission

Federal Housing Finance Agency

Federal Labor Relations Authority

Federal Maritime Commission

Federal Mediation and Conciliation Service

Federal Mine Safety and Health Review Commission

Federal Reserve System

Federal Retirement Thrift Investment Board

Federal Trade Commission

General Accountability Office

General Services Administration

Institute of Museum and Library Services

Inter-American Foundation

Merit Systems Protection Board

Millennium Challenge Corporation

National Aeronautics and Space Administration

National Archives and Records Administration

National Capital Planning Commission

National Credit Union Administration

National Endowment for the Humanities

National Labor Relations Board

National Mediation Board

National Railroad Passenger Corporation

National Science Foundation

National Transportation Safety Board

Nuclear Regulatory Commission

Occupational Safety and Health Review Commission

Office of Government Ethics

Office of Personnel Management

Office of Special Counsel

Office of the Director of National Intelligence

Overseas Private Investment Corporation

Peace Corps

Pension Benefit Guaranty Corporation

Postal Regulatory Commission

Privacy and Civil Liberties Oversight Board

Railroad Retirement Board

Securities and Exchange Commission

Selective Service System

Small Business Administration

Smithsonian Institution

Social Security Administration

Surface Transportation Board

Tennessee Valley Authority

U.S. Agency for Global Media

U.S. Agency for International Development

U.S. Commodity Futures Trading Commission

U.S. International Trade Commission

U.S. Nuclear Regulatory Commission

U.S. Postal Service

U.S. Trade and Development Agency

U.S. Courts

U.S. Senate

80. During the past 12 months, please indicate which Federally Funded Research Development Centers (FFRDC) in which your SFS program partnered and describe the activity (e.g., worked on a "real world" project or research for publication or presentation, invited FFRDC as guest speaker, gave presentation at FFRDC, networked in an informal setting, placed SFS students for internships or permanent positions upon graduation). Listed below are the FFRDCs.

Aerospace Corporation

Ames Laboratory

Argonne National Laboratory

Arroyo Center

Brookhaven National Laboratory

Center for Advanced Aviation System Development

Center for Communications and Computing

Center for Enterprise Modernization

Center for Naval Analyses

Center for Nuclear Waste Regulatory Analyses

CMS Alliance to Modernize Healthcare

Fermi National Accelerator Laboratory

Frederick National Laboratory for Cancer Research

Homeland Security Operational Analysis Center

Homeland Security Systems Engineering and Development Institute

Idaho National Laboratory

Institute for Defense Analyses

Jet Propulsion Laboratory

Johns Hopkins Applied Physics Laboratory

Judiciary Engineering and Modernization Center

Lawrence Berkeley National Laboratory

Lawrence Livermore National Laboratory

Lincoln Laboratory

Los Alamos National Laboratory

MITRE Corporation

National Biodefense Analysis and Countermeasures Center

National Center for Atmospheric Research

National Cybersecurity Center of Excellence

National Defense Research Institute

National Optical Astronomy Observatory

National Radio Astronomy Observatory

National Renewable Energy Laboratory

National Security Engineering Center

National Solar Observatory

Oak Ridge National Laboratory

Pacific Northwest National Laboratory

Princeton Plasma Physics Laboratory

Project Air Force

Sandia National Laboratories

Savannah River National Laboratory

Science and Technology Policy Institute

SLAC National Accelerator Laboratory

Software Engineering Institute

Systems and Analyses Center

(Enter up to 2000 characters)
81. During the past 12 months, please indicate which city, county, state, or tribal organizations in which your SFS program partnered and describe the activity (e.g., worked on a "real world" project or research for publication or presentation, invited organization as guest speaker, gave presentation at organization, networked in an informal setting, placed SFS students for internships or permanent positions upon graduation). (Enter up to 2000 characters)

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