# TO DO - DEV TASKS

## ML Capabilities
Curator functions
Leaderboard functions

Ollama??
GPT at scale on Ravenclaw?

## Curator

 * Migrate angularjs to reactjs 
 	- First do some POC based on the angularjs plugin (eg. frankenplot plugin, table plugin)
 * VariantDB - Identify if the item in current variant column is already present in the previously curated sample lists.
 * Access the igv session file from NETApp S3 bucket.
 * IGV browser -- igv.js
 * QC overview plots
 * Oncopolot - MAFtools summary in the bottom section of Dashboard page
 * Upload curated json directly to MTBP from curator
 * Help and setup documentation.

## Launcher
* Migrate jquery to reactjs
* Update the new pipeline command -- buttons,UI and steps for snakemake pipeline
* Enable notification - slack and mail
* View curator
- Now - we can redirect into curator login page.
- In Future - we can access the curator app using single login.
* Help and setup documentation.

## Genomic Leaderboard
* Migrate jquery to reactjs (Use AWS Amplify Studio + ChatGPT )
* Cleanup the backend script
* View curator
- Now we can redirect to curator login page.
- In Future - we can access the curator app using single login.
* Help and setup documentation.

## iPCM
* Migrate jquery to reactjs (explore AWS Amplify Studio)
* In eCRF form, add one new column for additional information about tissue sample issues.
* Enable export json & pdf
* View curator
- Now we can redirect into curator login page.
- In Future - we can access the curator app using single login.
* Help and setup documentation.

## Database
* Cleanup the column data type for all application
* Daily Backup
* Migration postgresql to (MongoDB or elastic search)? required or not? Open for discussion with Karthick, Sarath & Solbritt
* Common DB for all three apps

## Common DB integration
* Integrate - Leaderboard => Launcher => Curator
* Admin interface to access all the databases with CURD functionality.

## Webpage
* Content update from old to new
* Browser compatibility
* Patient content dynamic change every week need to update in the webpage

## c/o Solbritt -- New webpage design for PROBIO, regular updates and testing

UI/UX FIGMA (Mockup - Wireframe)
Dev - HTML5, bootstrap

## c/o Sarath & Solbritt -- SLURM Monitoring Dashboard

Grafana SLURM dashboard  based on logging information from SLURM exporter for Prometheus.

references:
https://grafana.com/grafana/dashboards/4323
https://github.com/vpenso/prometheus-slurm-exporter

See implemented example --- https://it.fysik.su.se/hpc/grafana.html#cpu-and-memory-statistics

## run k-mer analysis kvar on ductal vs acinar

https://github.com/collaborativebioinformatics/kvar

## MAFtools implementation in Dashboard (ln 12)

1. convert all vcfs to vep.maf files
2. run MAFtools on them