ATC:

• time change working out?

• GTEx

1. The Genotype-Tissue Expression (GTEx) project

Home page at https://gtexportal.org, integration with Ensembl. Let's have a quick look at the APIs,  https://observablehq.com/@episphere/gtex

Question from Daina Eiser

How can I acces pancreatic tissue and HNF1A gene expression

Notes

• Discuss serverless deployment model, 

• consider arguments for context agnostic analytical modules, 

• consider deploying serverless (FaaS) APIs 

• ...

New questions from Oscar Florez-Vargas 

(Daina was not in attendance ;-) )

• Focus on PSCA 

• Start with gene expression in all tissues, all cancers

• Oscar wants to start with cbio and only then move to gdc 

• He changed his mind and now prefers http://firebrowse.org/api-docs/#!/Samples/mRNASeq 

• ... and we got to http://firebrowse.org/api/v1/Samples/mRNASeq?format=json&gene=PSCA&cohort=BLCA&protocol=RSEM&page=1&page_size=250&sort_by=cohort

• ICGC has a SSL API :-) - https://docs.icgc.org/portal/api/

[Jonas] experimenting with Oscar's PSCA question using firebrowse https://observablehq.com/@episphere/firebrowse, libs at https://github.com/cloud4bio/firebrowse

2. Serverless data management and analysis for Confluence 

https://episphere.github.io/confluence

3. Serverless Hello Cloud4Bio

Write your own, 

this is mine https://cloud4bio.github.io/serverless/jonas/ :-D

really, I mean it: 

a) branch server out (video) to make it your own ...

b) ... while keeping your own client folder in the master branch ...

c) ... and being nice about explaining in the client UI what your API does and what is URL endpoint

4. Eric exploring Terra 

....

### Some notes from Ben

-- we did a bunch of work on Terra at Bio-IT world.  

https://github.com/NCBI-Hackathons/Bringing-the-Power-of-Synthetic-Data-Generation-to-the-Masses

https://github.com/NCBI-Hackathons/The-Broad-Institute-Single-Cell-RNA-Seq-Data-Set

also, theres some chance we might run this on the Terra platform (you heard it here first) -- https://hackathon.colorado.edu

-- Eric, let me know if you are interested in going?

###

5. Praful developing DCEG API

...