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
   • 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
    • Pipeline can be Tassel, or Fei Li's pipeline
11. Data Interpretation
    • "manual" / "art"
12. Data Distribution
13. Data storage for X period of time

Current Components

Overview

GBS Database Schema

sample submission interface fields and database schema

QC Scripts

• 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

• 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

Data Distribution

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

billing

Misc operations

• Configure new adapter plate configurations
  • example adapter plate spreadsheet

Map current components/workflow to new system(s)

QC Scripts

• QC Scripts
• Comments and request changes for QC output
• Besides the changes I listed above, but the biggest bug is that the scripts look for the cut site overhang and then the barcode.  Barcodes containing the cut-site overhang are not recognized and we see it as 0 reads.  The data pipeline does barcode and cut-site recognition simultaneously and so you still get data for these barcodes.

Samptrack

• build rich enough interface for web? extend and maintain c# "product"?
• Custom DB queries desired added functionality:
  • example custom queries

• Make more editable.  Need to be able to edit web submission fields after they are entered into database.
  • Sometimes we find mistakes after data has been analyzed, these revisions must be tracked somehow.
  • Other things we may want to change
    • Allow edits to submission before approval?  Keeps from having to reject over small issue, can just edit and approve.
    • Other mistakes (i.e. taxa names, standardizing project names) only a special person can enter these and it isn't easy- keep it that way?

Data Distribution

• no changes required at this time
• possibly change SOP to record that data was released

Misc operations

• Configure new adapter plate configurations
  • self service interface/upload?