Page History

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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

GBS Paper in PLoSone: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019379^{Image Added}

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"

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GBS Database Schema

• GBS DatabaseSchema Image
• based on The Genomic Diversity and Phenotype Data Model (GDPDM)

sample submission interface fields and database schema

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• 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

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Map current components/workflow to new system(s)

Project management

• not clear if redmine is the right solution, but it has its place now. would need similar functionality, probably with better integration with other components.

GBS Database Schema

• May not need full implementation, especially pmost of "passport" info.
• should be extended for Stat and QC management. right now the tables for "stat" and "qc" are really just placeholders.

Sample Submission

• re-implement
• suggest implementing as part of LSCLC Cores LIMS
  • Single Sign-in with other cores. consistent customer interface for all services.
• could populate information in Minilims module, or customer development within LSCLC LIMS

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.

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

Billing

• if ordering is handled through LSCLC LIMS, invoicing will be easier (less manual)

Misc operations

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