Server code for STRESS
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README.md

Allosteric Web

Repo for website of an allosteric project in Gersten lab

All code from DC in code folder

Tasks

  • Allow users to upload files
  • Allow users to give PDB ID and then fetch files from PDB
  • Let users select which module they want to run (BL or/and GN)
  • Run two programs and report results
    • Pipeline all programs using bash (Shantao)
    • Install & configure MMTK on an AWS instance (Richard)
  • Email notification for users after the job is done
  • Archive finished results in SQL database, automatically query
  • Fix GN module
  • [N] Batch processing (user can submit multiple PDB ids or upload multiple PDB files and retrieve all the results in one zip file)
  • Random job id
  • [N] Delete user submitted PDB files and results after 1 week
  • [N] Prepopulate database with selected PDB IDs and results
  • Front end design, descriptions, instructions, email content, etc.
  • [N] Progress indicator
  • Quick mode?
  • Docker image
  • Make code available: BL/GN, server code, sample data & output, docker image
  • Database flat file showing all results: Bulk paper results and accumulated results
  • Documentation
  • [N] Caps to prevent overuse
  • [N] DNS naming
  • [N] Visualization (optional)?
  • [D] Fix autoscaling
  • Web server setup packaging and distribution

Implementation Notes

  • Paperclip used to manage PDB file attachments
  • Validations for user-uploaded PDB files and user-specified PDB ids
  • Run pipeline_BL [INPUTPDB] to execute BL module and pipeline_GN [INPUTPD]
    • But in order to remove MMTK dependency, pass fnm_10 as the 2nd param
    • GN Module not working now...I need to ask DC about the weird VMD dependency and python script (Shantao)
    • pipeline_BL.sh writes output files to the current working directory

AWS Notes

  • 1 web server tier for processing HTTP requests, 1 worker tier for processing background jobs. Auto-scaling enabled.
  • 1 RDS database and 1 S3 bucket for cloud-based storage. Allows both tiers to share data.
  • RDS t2.micro: max_connections is 26