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"
- Project Initiation
- Requires personal contact with lab director
- 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
- Client sends DNA samples to the lab
- Charlotte sets up project in redmine
- DNA samples begin moving through various lab steps; redmine updated at various steps
- Client sets up customer registration at https://cores.lifesciences.cornell.edu/userdev/newuser.php
- Charlotte sets up a cost issue in redmine so Theresa knows what to bill
- Customer is invoiced
- Raw Data -> Data Files
- Pipeline can be Tassel, or Fei Li's pipeline
- Data Interpretation
- "manual" / "art"
- Data Distribution
- 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.
- manual SQL queries (supplement "samptrack")
- desire to have functionality build in
redmine project management
- Project initiation
- create project in redmine
Data Distribution
- either "hapmap table" by email, or dropbox or physical hard drive if client wants raw data
billing
Misc operations
- Configure new adapter plate configurations
Map current components/workflow to new system(s)
QC Scripts
Samptrack
- build rich enough interface for web? extend and maintain c# "product"?
- Custom DB queries desired added functionality:
Data Distribution
- no changes required at this time
Misc operations
- Configure new adapter plate configurations
- self service interface/upload?