Journal Club

LDlink - https://ldlink.nci.nih.gov (Mitchell Machiela)

1. Machiela MJ, Chanock SJ. LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants. Bioinformatics. 2015 Jul 2.

2. Machiela MJ, Chanock SJ. LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation. Bioinformatics. 2017 Sept 12.

3. Alexander TA, Machiela MJ. LDpop: an interactive online tool to calculate and visualize geographic LD patterns. BMC Bioinformatics. 2020 Jan 10.

4. Myers TA, Chanock SJ, Machiela MJ. LDlinkR: An R Package for Rapidly Calculating Linkage Disequilibrium Statistics in Diverse Populations. Front. Genet. 2020 Feb 28.

Notes

• API: https://ldlink.nci.nih.gov/?tab=apiaccess

• Resources/documentation: https://ldlink.nci.nih.gov/?tab=help 

...

Hackathon 

brief interactive analytics

PRS, Jacob, Aaron double clustering, Lee's SOM

P2P framework (Praful)

...

GPT

• API note how AI is at an engineering level about a mixture of a) wrapping API calls for what is computationally intensive and b) client-side execution for what it is not. Into this FAIR throws a governance requirement about which we need to be honest.

• Auth: https://platform.openai.com/account/api-keys  , example: https://episphere.github.io/gpt/jonas 

• Pricing: https://openai.com/pricing 

• Overview: https://openai.com/research/overview (research),
  https://openai.com/product (application),
  https://platform.openai.com/overview (platform)

• joint session with SBU,

• Immediate opportunities for GPT - ongoing for epiVerse and PRS, what others? is there a WSI angle ? ...

• Remember PRS calculator? not giving up that team work applies here too: https://episphere.github.io/gpt 

• Miniconferences throughout April ? (check poll)