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. Pricing table and procedures can be found here http://www.igd.cornell.edu/index.cfm/page/projects/GBS/GBSpricing.htm

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
  2. Sample submission: client goes to http://sorghumdiversity.maize.cornell.edu/ to get the required steps, and upload their information to attempt to get approved to send DNA samples
  3. Client sends DNA samples to the lab
  4. Charlotte sets up project in redmine
  5. DNA samples begin moving through various lab steps; redmine updated at various steps
  6. Client sets up customer registration at https://cores.lifesciences.cornell.edu/userdev/newuser.php
  7. Charlotte sets up a cost issue in redmine so Theresa knows what to bill
  8. Customer is invoiced
  9. Raw Data -> Data Files
  10. Data Interpretation
  11. Data Distribution
  12. Data storage for X period of time

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.

redmine project management

Data Distribution

billing

Misc operations

Map current components/workflow to new system(s)

QC Scripts

Samptrack

Data Distribution

Misc operations