cpsc4180 how to do presentation

 

How to do a research presentation

Qin AI 101 slides

CoLab tutorial on DNA.

cpsc4180 final project discussion

 go over student projects, poll about which project to discuss. 

go over a example research paper

https://www.nature.com/articles/s42256-022-00536-x

transition rate theory

 

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

Langevin equation

 

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

cpsc4180

 SFS

deep learning prediction

final project

final presentation

PULSE survey

 

State Information

I am sending you the data dictionary of the PULSE data. Once you open the file, you should be able to find a variable, named "EST_ST." As you can see, this variable indicates which state each of the respondents was from.

 

cpsc4180 one-hot encoding; project discussions

 

one-hot encoding

project presentations. 

NIH F31 Ruth L. Kirschstein National Research Service Award (NRSA) Individual Predoctoral Fellowship to Promote Diversity in Health-Related Research (Parent F31-Diversity)

 Ruth L. Kirschstein National Research Service Award (NRSA) Individual Predoctoral Fellowship to Promote Diversity in Health-Related Research (Parent F31-Diversity)

https://grants.nih.gov/grants/guide/pa-files/PA-21-052.html#_Section_II._Award

https://www.nia.nih.gov/research/training/f31-individual-fellowships-phd-students

F31 Individual Fellowships for PhD Students

NIA supports three F31 awards, one open to all PhD Students conducting aging research (PA-21-051), one open to students from underrepresented backgrounds conducting aging research (PA-21-052), and one specifically for students from underrepresented backgrounds conducting research on Alzheimer’s Disease and related dementias (PAR-21-218). All F31 recipients must be U.S. citizens or permanent residents at the time of award. View other NIA fellowships available to graduate students.

AD/ADRD

https://grants.nih.gov/grants/guide/pa-files/PAR-21-218.html

fairness in machine learing

independence

separation

sufficiency 

group fairness definitions, confusion matrix

Bias mitigation methods: preprocessing; reweighting; inprocessing; adversarial debiasing; postprocessing; reject option based classification

https://en.wikipedia.org/wiki/Fairness_(machine_learning)

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

cpsc4180 from gisaid alignment to mutations

 == pre-class to do: 

socrative questions (questions on contents from last lecture ): Q what do you think are the most important concepts or skills that we have discussed today? 

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

Test-run code: 

== In-class to do: 

clean up destktop space, calendars, 

ZOOM, live transcript (start video recording). 

Socrative sign in: 

How to identify mutations or variations? 

https://www.ebi.ac.uk/Tools/msa/clustalo/

>one
ChattanoogaIsAGreatPlace
>two
ChattanoogaMaybeAGreatPlace

Use AliView to explain the FASTA alignment file (gaps)

https://github.com/hongqin/Python-CoLab-bootcamp/blob/master/align2snv.ipynb

upload 0613 files to CoLab. This is too slow. So, I switched to run jupyter-notebook on my laptop

* UTC Course Evaluation 

* student presentation.

UTC individual study contract form

 

https://www.utc.edu/enrollment-management-and-student-affairs/registrar/individual-studies-contracts

network permutation

 

https://www.nature.com/articles/s43588-020-00009-4

cpsc 4180/5180 project discussion

zoom recording, live transcript

two student presentations. 

 

funding opportunites

 

https://beta.nsf.gov/funding/opportunities/research-mentoring-postbaccalaureates-biological

https://beta.nsf.gov/funding/opportunities/building-research-capacity-new-faculty-biology-brc

paperswithcode

 

https://paperswithcode.com/

python bioinfor in cpsc4180, D614G mutation

 == pre-class to do: 

socrative questions (questions on contents from last lecture ): Q what do you think are the most important concepts or skills that we have discussed today? 

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

Test-run code: 

== In-class to do: 

clean up destktop space, calendars, 

ZOOM, live transcript (start video recording). 

Socrative sign in: 

https://github.com/hongqin/Python-CoLab-bootcamp/blob/master/notebooks/Chapter_9-v2_Introduction_to_Biopython.ipynb 

D614G mutation annotation

mutation

TODO: 

FASTA format (GISAID)

2022 Fall acknowledgement

HQ thanks the USA NSF  award 1761839 and #2200138,  a catalyst award from the USA National Academy of Medicine, and the support from the Office of Vice Chancellor of Research at the University of Tennessee at Chattanooga. 

For covid19

HQ thanks the support of USA NSF PIPP #2200138, BD Spoke #1761839, SFS #1663105,  REU #1852042 and #2149956, and an internal CEACSE award and support from the Office of the Vice Chancellor of Research at the University of Tennessee at Chattanooga.

For REU: 

We thank the support of NSF REU #1852042 and  #2149956, and the support from the Office of Vice Chancellor of Research at the University of Tennessee at Chattanooga. 

For image related works
We thank the support of NSF Career award #1453078 and #1720215, BD Spoke  #1761839, and internal support of the University of Tennessee at Chattanooga. 


For yeast aging:
We thank the support of NSF Career award #1453078 and #1720215, BD Spoke  #1761839,  REU   #1852042, and the internal support of the University of Tennessee at Chattanooga. 

For Machine Learning
We thank the support of NSF Career award #1453078 and #1720215, BD Spoke  #1761839, and internal support of the University of Tennessee at Chattanooga. TP, DM thanks the support of a DoD capacity building grant. 

cpsc4180 biopython CDS, retrieve,

== pre-class to do: 

socrative questions (questions on contents from last lecture ): Q what do you think are the most important concepts or skills that we have discussed today? 

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

Test-run code: 

== In-class to do: 

clean up destktop space, calendars, 

ZOOM, live transcript (start video recording). 

Socrative sign in: 

https://github.com/hongqin/Python-CoLab-bootcamp/blob/master/notebooks/Chapter_9-v2_Introduction_to_Biopython.ipynb 

retrieve a CDS? spike gene example. 

TODO: 

D614G mutation annotation

negative sense 

FASTA sequence

CCF journal and conference ranking

 CCF journal and conference ranking

中国计算机学会推荐国际学术会议和期刊目录

https://www.ccf.org.cn/Academic_Evaluation/By_category/