sars-cov-2 nextstrain phylogeny

 

Omicron is from an 'ancient' branch, different from Delta. It seems that phylogenetic success is not a good measure to compare Delta and Omicron fitness. 

omicron, sars-cov-2 variants of concerns

# Omicron GRA (B.1.1.529+BA.* 

• B.1.1.7 (Alpha): isolate C69.1, GISAID ID EPI_ISL_3277382; 
• B.1.351 (Beta): isolate C24.1, GISAID ID EPI_ISL_1123262; 
• B.1.617.2 (Delta): isolate SARS-CoV-2-hCoV-19/USA/NYMSHSPSP-PV29995/2021, GISAID ID EPI_ISL_2290769; 
• B.1.1.529 (Omicron): isolate E16.1, GISAID ID EPI_ISL_6902053

Ref: 

https://cdn.who.int/media/docs/default-source/blue-print/janine-kimpel_c19_whoconsulation_15dec2021.pdf?sfvrsn=2f6fc437_7

https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

https://cov-lineages.org/lineage_list.html

VMware workstation player

 VMware workstation player

VirtualBox very slow on MacOS

 VirtualBox very slow on MacOS

VirtualBox errors on MacOS BigSurf

 

Kernel driver not installed (rc=-1908) Getting Errors in macOS Big Sur 11.0.1

https://stackoverflow.com/questions/65149373/kernel-driver-not-installed-rc-1908-getting-errors-in-macos-big-sur-11-0-1

(base) hqin@CS313BQin ~ % sudo kextload -b org.virtualbox.kext.VBoxDrv

Password:

Executing: /usr/bin/kmutil load -b org.virtualbox.kext.VBoxDrv

Error Domain=KMErrorDomain Code=27 "Extension with identifiers org.virtualbox.kext.VBoxNetAdp,com.apple.nke.rvi,com.paloaltonetworks.kext.pangpd,org.virtualbox.kext.VBoxUSB,org.virtualbox.kext.VBoxDrv,org.virtualbox.kext.VBoxNetFlt not approved to load. Please approve using System Preferences." UserInfo={NSLocalizedDescription=Extension with identifiers org.virtualbox.kext.VBoxNetAdp,com.apple.nke.rvi,com.paloaltonetworks.kext.pangpd,org.virtualbox.kext.VBoxUSB,org.virtualbox.kext.VBoxDrv,org.virtualbox.kext.VBoxNetFlt not approved to load. Please approve using System Preferences.}

(base) hqin@CS313BQin ~ % 

Checked the "Security & Privacy", Restart the laptop to make the update function. 

This worked, and the error went over. 

REU cost effectiveness

 ratio of F / G in budget = REU cost effectivness

Common reasons for returned REU reports:

* including students outside of the reporting period

* not include a print copy of SALG URSSA survey report

* not filling in all info on each REU participant

* not including title and abstracts of student research

cpsc4900 2022 01 27, team role breakout room discussion,

  == pre-class to do: 

calendar email invitation: including guests;  NA 

socrative questions.  done

update Canvas course materials, update learning objectives. assignments as needed.   NA

* make sure grades are NOT shown on Canvas. 

 learning objectives:  ??

== In-class to do: 

restart computer to make sure ZOOM works. make sure Bluetooth mouse are turned off. 

clean up desktop space, calendars: 

team formation, shared excel sheet, 

ZOOM, live transcript (start video recording).  Turn the computer speaker on. 

* breakout rooms, team roles and product vision discussion. Some team has only one student. 

10:50-11:30, 

* in the main room, each team report discussion process. Team 1 used discord. Team 2 discuss in breakout. Team 4 used groupme. 

* start Ch3. socrative.  I stopped at Q19 (explan how can identify feature from a scenario). 

UTC bylaws

 

chemistry and physics: https://www.utc.edu/sites/default/files/2020-11/department-bylaws.pdf

CPSC4900 ESP Ch2 Agile (finish), Ch3 Features, Scenario, Stories (start).

 == pre-class to do: 

calendar email invitation: including guests;  NA 

socrative questions.  done

update Canvas course materials, update learning objectives. assignments as needed.   NA

* make sure grades are NOT shown on Canvas. 

 learning objectives:  ??

== In-class to do: 

restart computer to make sure ZOOM works. make sure Bluetooth mouse are turned off. 

clean up desktop space, calendars: 

team formation, shared excel sheet, 

ZOOM, live transcript (start video recording).  Turn the computer speaker on. 

* review Ch2 AGILE socrative questions

* start Ch3. socrative. 

todo: update protoria , Kaltura on syllabus

UTC Canvas sandbox request

 

 If you ever need another sandbox, you can let us know using this form: https://forms.office.com/r/95Zs91FHCQ

 

Research Assistantships for High School Students (RAHSS): Funding to Broaden Participation in the Biological Sciences

 

https://www.nsf.gov/pubs/2018/nsf18088/nsf18088.jsp

DoD CySP letter requirement

 

cpsc4900 Ch2 Agile, part 2

== pre-class to do: 

calendar email invitation: including guests;  NA 

socrative questions.  done

update Canvas course materials, update learning objectives. assignments as needed.   NA

* make sure grades are NOT shown on Canvas. 

 learning objectives:  ??

== In-class to do: 

restart computer to make sure ZOOM works. 

clean up desktop space, calendars: 

team formation, shared excel sheet, 

ZOOM, live transcript (start video recording).  Turn the computer speaker on. 

My bluetooth mouse caused my touchpad disfunctional during lecture. Make sure bluetooth mouse is disconnected. 

todo: update protosoria , Kaltura on syllabus

stability theory

 

Stability diagram classifying Poincaré maps of linear autonomous system ${\displaystyle x'=Ax,}$ as stable or unstable according to their features. Stability generally increases to the left of the diagram.^[1] Some sink, source or node are equilibrium points.

https://en.wikipedia.org/wiki/Stability_theory

Entrepreneurial Mindset, 3C

 curiosity, connections, creating values

https://engineeringunleashed.com/