workflow high level overview

  1. Project Initiation
    • Requires personal contact with lab director
    • Charlotte or Sharon sets up project in redmine
  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. Client sets up customer registration at https://cores.lifesciences.cornell.edu/userdev/newuser.php
  5. DNA samples tested and if okay, Charlotte sets up a cost issue in redmine so Theresa knows what to bill.
  6. Customer is invoiced
  7. DNA samples begin moving through various lab steps; redmine updated at various steps
  8. SampTrac is used to update HTS database entries and create barcodes for DNA and library plates.
  9. Libraries are submitted for sequencing (sometimes more than once)
  10. Raw Data -> Data Files
    • QC scripts run
    • Pipelines change can be Tassel, or Fei Li's pipeline
  11. Data Interpretation
    • need to know Biology / skilled analyst
  12. Data Distribution
  13. Data storage for X period of time

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

  • Project initiation
    •   create project in redmine
  • Individual plate tracking
    • Can note if a plate failed somewhere in the process and link it to the redone plate.
    • Can link billing information so we know if the plate has been paid for
  • I don't like:
    • Having to click through so many screens to get to the next sample in a project
    • Hard to look at samples in groups, like all of the samples on a flowcell

Data Distribution

  • manual
    • either "hapmap table" by email, or dropbox or physical hard drive if client wants raw data

billing

current billing workflow

*invoicing handled through LSCLC cores LIMS

Theresa's comments on GBS billing issues

Misc operations

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