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/

genome privacy

 

XiaoFeng Wang is a James H. Rudy Professor of Computer Science and Engineering at Indiana University Bloomington. His research focuses on system security and data privacy with a specialization on security and privacy issues in mobile and cloud computing, and privacy issues in dissemination and computation of human genomic data.

https://homes.luddy.indiana.edu/xw7/

CPSC4900 Ch2, AGILE

  == 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. 

scrum rugby video: https://www.youtube.com/watch?v=VIfD0nuocVo

todo: update protosoria , Kaltura on syllabus

MG on maskRNN

 

 

I have managed to fix the code error. Due to new version of “TensorFlow”, It requires to modify some part of the code. You should be able to train the code by running “train1.py” or “train2.py” file from link below: 

 

https://github.com/QinLab/HSYAA/tree/master/model_playground/mrcnn

 

 

replit does not compile Linux code of Siberschatz v10 c code

 

git cloned Sibler OS v10 C codes into replit. It does not compile, because it cannot find <linux/init.h> 

various types of computer storages

 size: registers < cache < main memory < solid state disk < magnetic disk

access speed: registers > cache > main memory > solid state disk > magnetic disk

UTC honor college, associate dean, position

 The responsibilities associated with this position include assisting in the overall management of the Honors College and calls for extensive collaboration with the dean and the other administrative staff in the Honors College; in addition, serving as the primary administrator of all honors courses, the Associate Dean works closely with all department heads and faculty across campus as well as with community members. Specific responsibilities may include, but are not limited to: 

-    Supervision and evaluation of the Honors College Lecturer, the Director of Innovations in Honors and Professor of Practice, and whatever other faculty are assigned part or full-time to the Honors College 

-    Managing all honors curricula including oversight of the honors seminar proposal process, schedule creation, and recertification of general education courses

-    Administering the honors thesis process including teaching at least one section of UHON 3000 (1 credit) each semester, our honors thesis support course, managing thesis director contracts and their departmental approvals, scheduling all sections of 4995R, tracking student progress and completion, working with the Registrar on final outcomes and graduation designations, and approving theses in the digital archive

-    Participate in the overall recruitment and selection processes for Honors College admissions and serving ex officio on the Honors College Advisory Committee and the Honors College Advisory Board

-    Manage all faculty development opportunities for faculty teaching in honors and serve on the Council of Academic Department Heads

-    Teach one section of UHON 2000 (1 credit) each year

-    Join and be active in the National Collegiate Honors Council and the Southern Regional Honors Council

 

This position is full-time in the Honors College with no home departmental responsibilities. 

 

COVID19 disinformation accounts

 

https://twitter.com/jikkykjj?lang=en , which created on November 2021. 

https://archive.is/18Ho4

cpsc4900 2022 Jan 13, 2nd lecture

 == pre-class to do: 

calendar email invitation: including guests;  done. 

socrative questions.  done

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

* make sure grades are NOT shown on Canvas. 

 learning objectives:  updated on canvas

== In-class to do: 

clean up desktop space, calendars": 

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

Qin forgot to add a conclusion and summary question in Socrative. 

I finished Ch1 today. 

team formation

todo: update proctosoria , Kaltura? on syllabus

plot neural network in Latex

 

https://github.com/HarisIqbal88/PlotNeuralNet

leadership notes

 

position power vs personal power

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

4900 first day

== pre-class to do: 

calendar email invitation: including guests;  done. 

socrative questions.  done

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

* make sure grades are NOT shown on Canvas. 

 learning objectives:  updated on canvas

== In-class to do: 

clean up desktop space, calendars": 

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

Syllabus

ice break socrative

scheduling

team formation

todo: update proctosorio , Kultra? on syllabus

student major search at UTC

 Go to advising hold -> my mocsdegree  -> advanced search 

https://dwdash.utc.edu/

tips, preparing for job interviews

 

https://twitter.com/GarciaLabMS/status/1478738213074264066 

confusion matrix in machine learning

 

accuracy, F1

NVIDIA hardware acadmic application

NVIDIA Academic Hardware Grant Program

 

https://mynvidia.force.com/HardwareGrant/s/Application?ncid=em-targ-697994-vt16&mkt_tok=MTU2LU9GTi03NDIAAAGBxJTwo0FcmjskSDhEY0OVkkP7gIOoq6pz0vfXtL2Vt-8YTdnJITl8jxQRRVAtVwXfFF0krx0LRXTvcDGYAyd-Owp-0PPngLs4tNJ_n2OjX-arYE8#cid=ix01_em-targ_en-us

 

A large-scale COVID-19 Twitter chatter dataset for open scientific research - an international collaboration

https://zenodo.org/record/5816329#.YdPiNRPMLzc