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 Removed}

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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• 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.
• What we like about redmine-  A really nice way to see the history of a particular plate of DNA or project:
  • Project summary: enzyme to use, contact information, expected sample number, comments for data analysis
  • Project workflow where we can check off status and note if something did not go as expected
  • Links that cross-reference.  I link all costs to plates so I know what has been paid for.  We also can link redo plates with the original preps.
  • Upload submission sheet, quantification, experion files (.pdf)
  • Note payment status
  • Track optimization results and R&D

GBS Database Schema

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

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• re-implement
• sample submission change requests
• 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
• Sample submissions are required to be in a plate format with 95 samples and 1 random blank. 
• We ask for concentration, but we re-quantify and it would be great to be able to enter those new numbers into the database.

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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• It would be great to get some reports off of the Illumina machine.

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

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