...
GBS Paper in PLoSone: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019379
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"
- Project Initiation
- Requires personal contact with lab director
- Charlotte or Sharon sets up project in redmine
- 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
- Client sends DNA samples to the lab
- Client sets up customer registration at https://cores.lifesciences.cornell.edu/userdev/newuser.php
- DNA samples tested and if okay, Charlotte sets up a cost issue in redmine so Theresa knows what to bill.
- Customer is invoiced
- DNA samples begin moving through various lab steps; redmine updated at various steps
- SampTrac is used to update HTS database entries and create barcodes for DNA and library plates.
- Libraries are submitted for sequencing (sometimes more than once)
- Raw Data -> Data Files
- QC scripts run
- Pipeline can be Tassel, or Fei Li's pipeline
- Data Interpretation
- "manual" / "art"
- Data Distribution
- Data storage for X period of time
...
- 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
- Can probably use the order forms in minilims
- Billing probably ultimately still goes through LSCLC LIMS - perhaps we should talk with Brianne because low volume billing might be doable with minlims capability and some low impact manual process by the office staff (unlike the high volume LSCLC invoicing). It keeps GBS separate completely from LSCLC (not sure if that is good bad or indifference)
- if not using LSCLC for billing, not so strong of a need to tie authentication/authorization from minilims to LSCLC LIMS.
- if not using LSCLC, credit card processing NOT possible
- 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.
...
- if ordering is handled through LSCLC LIMS, invoicing will be easier (less manual) but this may not be necessary
- perhaps we should talk with Brianne because low volume billing might be doable with minlims capability and some low impact manual process by the office staff (unlike the high volume LSCLC invoicing). It keeps GBS separate completely from LSCLC (not sure if that is good bad or indifference)
- if not using LSCLC for billing, not so strong of a need to tie authentication/authorization from minilims to LSCLC LIMS.
- if not using LSCLC, credit card processing NOT possible
Misc operations
- Configure new adapter plate configurations
- self service interface/upload?