Allosteric Web

Repo for website of an allosteric project in Gersten lab

All code from DC in code folder

Note about potential security vulnerability

The current version of this server has a security vulnerability. This vulnerability, which is in the rack module, has been classified by GitHub as a moderate severity security vulnerability. More information can be found here: https://nvd.nist.gov/vuln/detail/CVE-2018-16471 and here: https://nvd.nist.gov/vuln/detail/CVE-2015-3225

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