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.
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
Workflow
- 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
Current Components
Overview
GBS Database Schema
- GBS DatabaseSchema Image
- based on The Genomic Diversity and Phenotype Data Model (GDPDM)
sample submission interface fields and database schema
QC Scripts
"SampTrack" C# windows program to interface with GBS for setting up pools etc.
- manual SQL queries (supplement "samptrack")
- desire to have functionality build in
- SampTrack screenshots and notes
redmine project management
- Project initiation
- create project in redmine
- 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
- I don't like:
- Having to click through so many screens to get to the next sample in a project
- Hard to look at samples in groups, like all of the samples on a flowcell
Data Distribution
- manual
- either "hapmap table" by email, or dropbox or physical hard drive if client wants raw data
billing
*invoicing handled through LSCLC cores LIMS
Theresa's comments on GBS billing issues
Misc operations
- Configure new adapter plate configurations
Vision for new implementations
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.
- 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 most 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
- 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
- integrate with LSCLC LIMS authentication
- consider possible dual-path authentication that supports cuwebauth as an option
- 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.
Integration with Sequencing Submission
- Currently I have to enter sample information onto the Core Facility website by hand. Automation of this would be complicated by my need to assign billing to different accounts. In addition, after Tom has made the flowcell I go onto Wikilims to get the flowcell name and lane assignments for the samples I submitted.
- If it is a 384-plex I make a new name for the sample submitted that is not recorded anywhere (could be written in redmine, but I don't always remember). The database lane_id is also appended to the name so there is a numerical way to check back, but people like a human readable name that correlates to the project.
- If samples are going to be sequenced off site then, in addition to the above steps I need to create additional emails and packing slips.
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.
- 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:
- 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
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
Benefits:
1) Order is collected along with payment information with one set of credentials by the customer.
Disadvantage:
1) We would be asking bioteam to code within our LSCLC LIMS base - I don't think this is the best way to go
2) order information would have to be migrated to minilims(or custom) GBS LIMS.
Possible mitigation:
1) Configure minilims to use the LSCLC LIMS for authentication. This will require a development meeting with my group and bioteam to determine feasibility
- support for credit cards is required
- 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?