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