Page History

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IGD-GBS MiniLIMS Proposal v1_2.doc

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action items

• Rob Elshire and IGD generate minimum distribution information standard
• Theresa defines details of billing dashboard page
• IGD create lists of pages (data objects and dashboards?)
• Charlotte rework workflow
• IGD detailed sample submission spec
• IGD define roles and authorization levels for each page
• James define APIs for billing and ordering integration with CLC LIMS

items for discussion

• pull qc data into minilims and report on it - including possibility of illumina data reports but only possibility of getting this would be Peter's facility, not other providers. fastqc is easy to run and staff can do it themselves easily.

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.

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• 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.
• It would be great to get some Am excited by the possibility of pulling reports off of the Illumina machine.the Illumina machines to further our QC.  I was also introduced to a Java based program, FastQC, which may be helpful for us.
• Assuming qc reports are pulled into minilims and parsed, how flexible can we do queries to find statistics over time and although each report is by lane, it contains plate information. slice and dice

• 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?
  Am excited by the possibility of pulling reports off the Illumina machines to further our QC.  I was also introduced to a Java based program, FastQC, which may be helpful for us.

Data Distribution

• 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.
• 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).
    there may be different definitions for different classes of customers
    • customers that receive only sequence data and metadata about panel 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.
• 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
    • note use of "cntrl" parameter which is a keycode so that anyone with that link that includes that parameter can download the file without explicit authentication. Since it could be brute forced it nags at me a little bit, but it does make programmatic downloads easier and security by obscurity should be sufficient enough for this purpose.
  • CLC will provide storage available to minilims from which files can be served. whoever runs the pipeline analysis will assemble archive and place in filesystem

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