Journal Club ~ 9:30

Alignment+Scale-free iterated maps

sandbox for SW alignment: https://usm.github.io/align

CGR 1990 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC330698

The original paper with initial evidence for a bijective map between discrete symbolic and continuous numeric sequences: https://academic.oup.com/bioinformatics/article-pdf/17/5/429/777494/170429.pdf

Foundations - alignment-free sequence alignment - https://academic.oup.com/bioinformatics/article/19/4/513/218529

Twilight zone - https://academic.oup.com/peds/article/12/2/85/1550637

The last short review of advances in the field (we may be due a new one because of the many applications to COVID genomes … ): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4017330

benchmarking in 2019 - https://pubmed.ncbi.nlm.nih.gov/31345254

The web tool used today where you can try genomics, proteomics, poetry or music: https://usm.github.io (also https://almob.biomedcentral.com/articles/10.1186/1748-7188-7-12)

Sequences as pictures - a generic 2d projection: https://pubmed.ncbi.nlm.nih.gov/19335894

Hackaton ~ 10:30

Documenting JS functions (Eric, Erika)

https://episphere.github.io/plco/out/plco.html

updated automatically upon pushing via github action https://github.com/episphere/plco/actions

ISB BigQuery exploits

https://isb-cgc.appspot.com/workflowhttps://github.com/isb-cgchttps://isb-cgc.appspot.com/bq_meta_search https://isb-cgc.appspot.com/workflow

I see that observable has a decent level of integration with BigQuery: https://observablehq.com/@observablehq/databases

RShiny as a middle layer to operating BQ: https://academic.oup.com/jamiaopen/article/4/2/ooab038/6291419

Data management solution via https://groups.google.com

Nicole.

recall ISB + our VCF next to each other

calling BQ from SAS ... SDK? starting exploration here ...

branch deployment

Bhaumik