Page History

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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 Pipelines change can be Tassel, or Fei Li's pipeline
11. Data Interpretation
    • "manual" / "art"need to know Biology / skilled analyst
12. Data Distribution
13. Data storage for X period of time

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• no changes required at this time ???
• - possibly change SOP to record that data was released-
• Our current scope does not include any changes to data distribution, which is currently done manually via dropbox or hard drive.
• 1) We will need to produce a detailed specification for the information/format of data and metadata distribution:
  • Rob Elshire will be producing a standard for information (In my mind I think of it like MIAME or MIAPE standards)
  - this should be able to help us produce the spec
  • .
    there may be different definitions for different classes of customers
    • customers that receive only sequence data and metadata about panel
  etc (is "key file" a standard term?)
  • • in the form of a "Key File".
    • customers for whom the facility has produced genotypes. they may or may not also want the sequence data.
• Do we want to consider build a distribution mechanism that defines the contents of an archive file that can be accessed via web link, including programmatically (curl or wget) and suitable notification
  • could be modelled on the distribution that our sequencing facility produces
  • CLC will provide storage available to minilims from which files can be served

Billing

• if ordering is handled through LSCLC LIMS, invoicing will be easier (less manual) but this may not be necessary
• My thoughts right now are centering around whether or not it makes sense to have customers actually place orders through the LSCLC LIMS system. I would like to avoid it if possible.
• Theresa's comments on GBS billing issues

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