GBS Project

Overview

This is a project to replace and enhance existing laboratory management systems supporting the Institute for Genomic Diversity's Genotyping By Sequencing (GBS) service.

As IGD has become more of a service facility, we need a more cohesive system for accepting samples, tracking samples, and customer billing. Currently these are all completely separate systems, with no linkage between them. We also have no centralized support, as all the web-based systems were designed by different people for different reasons.

Workflow

I'm thinking of a fairly high level text list of steps from project initiation to data distribution and billing - general terms like "run QC scripts" or "customer places online order"

1. Project Initiation
   • Requires personal contact with lab director
2. xxx
3. xxx
4. Raw Data -> Data Files
   • Pipeline can be Tassel, or Fei Li's pipeline
5. Data Interpretation
   • "manual" / "art"
6. Data Distribution

Current Components

Overview

GBS Database Schema

sample submission interface fields and database schema

QC Scripts

"SampTrack" C# windows program to interface with GBS for setting up pools etc.

manual SQL queries (supplement "samptrack")

redmine project management

• Project initiation
  • create project in redmine

    Data Distribution

• how accomplished now?

  billing

Misc operations

• Configure new adapter plate configurations
  • example adapter plate spreadsheet

Map current components/workflow to new system(s)

Misc operations

• Configure new adapter plate configurations
  • self service interface/upload?
• Custom DB queries
  • example custom queries