4180 biopython part 2

  

== 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: 

review of bioinformatic basic concepts

+Basic biology concept and data, 

Central Dogma: DNA (ATCG), RNA (AUCG), proteins (20 AA). Translation. Transcription. Replication. Genetic table. 

Genes. Genomes. 

Genome sequences. Expression levels.  

+biopython modules

 genbank file format; fasta file format

Breakout on final projects. 

TODO: 

retrieve a CDS? 

D614G mutation annotation

https://github.com/QinLab/aln2snv-2020format/blob/a670b48b00dffac244dc6a63bcd12cf6439c73fc/annotate_gwas_with_GFF.ipynb

Flu + RSV hybrid

 

https://medicalxpress.com/news/2022-10-flu-rsv-viruses-fuse-hybrid.html

https://www.nature.com/articles/s41564-022-01242-5

single phase versus triple phase power

https://www.fluke.com/en-us/learn/blog/power-quality/single-phase-vs-three-phase-power

In electricity, the phase refers to the distribution of a load. What is the difference between single-phase and three-phase power supplies? Single-phase power is a two-wire alternating current (ac) power circuit. Typically, there is one power wire—the phase wire—and one neutral wire, with current flowing between the power wire (through the load) and the neutral wire. Three-phase power is a three-wire ac power circuit with each phase ac signal 120 electrical degrees apart.

cpsc4180 biopython

 

== 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: 

+Basic biology concept and data, 

Central Dogma: DNA (ATCG), RNA (AUCG), proteins (20 AA). Translation. Transcription. Replication. Genetic table. 

Genes. Genomes. 

Genome sequences. Expression levels.  

+biopython modules

biopython tutorial

py4bio

https://github.com/agmcfarland/biopython_workshop

cpsc4180/5180 covid19-pandas, project discussion

== 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: 

Pandas on covid

GoogleDrive link in CoLab

final project milestones

N3C self study notes

how to duplicate code workbook 

https://unite.nih.gov/workspace/slate/documents/test-vector-duplication

https://unite.nih.gov/workspace/compass/view/ri.compass.main.folder.7403d6c8-3bab-4282-8904-6bcca88c08b9

https://unite.nih.gov/workspace/compass/view/ri.compass.main.folder.7403d6c8-3bab-4282-8904-6bcca88c08b9

NLM R25 program

SeattleStatSummer for Biomedical Data Science Research Training

https://reporter.nih.gov/search/SN29ZULFFUSU5OR1aFTQiw/project-details/10631342

Attracting Talented and Diverse Students to Biomedical Informatics and Data Science Careers Through Short-Term Study at OHSU

https://reporter.nih.gov/search/SN29ZULFFUSU5OR1aFTQiw/project-details/10630618

Place-based Culturally Responsive Health Informatics Research Education (PHIRE) Program

https://reporter.nih.gov/search/SN29ZULFFUSU5OR1aFTQiw/project-details/10631819

Buffalo Research Innovation in Genomic and Healthcare Technology (BRIGHT) Short-Term Training and Education

https://reporter.nih.gov/search/SN29ZULFFUSU5OR1aFTQiw/project-details/10631367

DataWiz-IN scholars program for Biomedical Informatics workforce in Indiana

https://reporter.nih.gov/search/SN29ZULFFUSU5OR1aFTQiw/project-details/10631297

Biomedical Informatics and Data Science at Institute for Informatics (BIDS@I2)

https://reporter.nih.gov/search/SN29ZULFFUSU5OR1aFTQiw/project-details/10631739

Training and Experiential Learning in Biomedical Informatics (TExBioMed)

https://reporter.nih.gov/search/SN29ZULFFUSU5OR1aFTQiw/project-details/10631457

Culturally Augmented Learning In Biomedical Informatics Research (CALIBIR) Program

https://reporter.nih.gov/search/SN29ZULFFUSU5OR1aFTQiw/project-details/10631379

OSU Summer Internship Program in Biomedical Informatics and Data Science

https://reporter.nih.gov/search/SN29ZULFFUSU5OR1aFTQiw/project-details/10631689

The Biomedical Informatics and Behavioral Sciences (BIBS) Summer Research Program

https://reporter.nih.gov/search/SN29ZULFFUSU5OR1aFTQiw/project-details/10631581

Building Accessible and Inclusive Paths for Students in Biomedical Informatics and Data Science

https://reporter.nih.gov/search/SN29ZULFFUSU5OR1aFTQiw/project-details/10630855

cpsc 4180/5180 pandas

 == pre-class to do: 

socrative questions (questions on contents from last lecture ): Q what do you think are the most important concept or skill 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: 

midterm-review (volunteer to share their videos? )

cpsc4180/5180 python lec3 numpy

== pre-class to do: 

socrative questions (questions on contents from last lecture ): Q what do you think are the most important concept or skill 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 

PET challenge

Python lec 3. Numpy (numpy backend is C). 

Go over CoLab and GoogleDrive demo

Midterm exam peer-review

How to compete (Phase 2)

1. Only blue teams who participated in Phase 1 and met minimum requirements are eligible to participate in Phase 2. Eligible teams are automatically registered. If you need to make changes to your team, please contact info@drivendata.org.
2. Get familiar with the problem through the problem description and code submission format pages.
3. Develop and submit your centralized solution. Check out the centralized code submission format page for more details.
4. Develop and submit your federated solution. Check out the federated code submission format page for more details.

Data overview

Code skeleton

https://github.com/drivendataorg/pets-prize-challenge-runtime

 

cpsc4180 20221005Wed Python lec 2, data type

   == pre-class to do: 

socrative questions (questions on contents from last lecture ): Q what do you think are the most important concept or skill 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 

Conda environment. 

Python lec 2. Data types. 

 

MPC and data privacy

MPC and data privacy

note:

 threshold cryptography is often superior to block chain in many situation, because block chain are often used as a way of encryption?!

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

+ joshua baron, DARPA

+ kurt nielsen, partisia blockchain

+ dan boneh, Stanford, https://crypto.stanford.edu/~dabo/pubs/pubs.html 

+ mariana raykova, google/columbia

zero knowledge authentication, distributed prover

N3C data download policy

 https://zenodo.org/record/4743249#.Yzx0pOzMLzf

cpsc4180 20221003 Mon

  == pre-class to do: 

socrative questions (questions on contents from last lecture ): Q what do you think are the most important concept or skill 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 

Conda environment. 

Show the hidden file .RData. A student show that RStudio can disable the loading of workspace. 

Python 1a. Quick start, Jupyter-notebook, 

adobe image highlights incompatible with Apple Preview

 

adobe image highlights incompatible with Apple Preview (show as yellow area that blocked the original view). 

Adobe filled box can work. 

GISAID and NCBI sars-cov-2 reference genomes

NCBI uses wuhan-hu-1

GISAID uses wuhan-hu-4. 

The two sequences only differ in the polyA tails. Qin verified this using MEGA alignment. 

So, wuhan-hu-1 and wuhan-hu-4 share the same gene coordinates, same GFF