Pre-proposal for the Institute for Genomic Diversity

Scientists at Cornell University and the ARS have developed a method called Genotyping-By-Sequencing (GBS), a multiplexed approach based on next-generation sequencing technologies that is suitable for a wide variety of species. The GBS method is currently used in a production environment at the Institute for Genomic Diversity (IGD) such that outside laboratories can submit samples to the IGD and pay for the GBS results.

The current systems used at the IGD for handling sample submission, tracking, and billing are disparate and incomplete with respect to functionality. BioTeam proposes that a custom MiniLIMS system could both replace those systems that are currently sub-optimal and interact with those systems that are useful and widely used. The end result should be more efficient and easy-to-use for those submitting and for those handling samples and data in the lab.

Systems to be replaced by MiniLIMS

Functionality in Redmine like workflow summaries, plate tracking for the purposes of pricing, and billing/payment status would be implemented in MiniLIMS.

Functionality in the IGD Tracking database like image upload and documentation would be implemented in MiniLIMS.

Systems that must interact with MiniLIMS

  • Customer registration at https://cores.lifesciences.cornell.edu/userdev/newuser.php interact with CLC LIMS using RESTful interfaces** Customer registers, logs in, initiates order, providing payment info (and generating invoice) then is passed to minilims to place order** Staff use minilims to bounce over to CLC LIMS to modify and process invoices.  CLC LIMS will provide restful interfaces for managing invoice from within minilims.
  • SampTrack application look very hard at implementing functionality within minilims, along with the GBS database
  • WikiLIMS Wikilims is internal to one of many sequencing services retained by IGD.  No integration.

Customer information from the Core Laboratories Center LIMS (CLC LIMS) should be visible and searchable in MiniLIMS (REST queries). This would allow straightforward generation of PO’s and invoices.billing is the in the CLC LIMS domain. The pages that display customer information should only be visible to privileged users in MiniLIMS. MiniLIMS could also implement an email notification system based on specific triggers. MiniLIMS should NOT store information currently not stored by the Core Laboratories system, such as payment mode or account number. There are outstanding issues regarding access to CLC LIMS from MiniLIMS, however.???

The SampTrack application is a sophisticated interface for entering and portraying Sample and container data. This application is in use and its functionality does not have to be re-created in MiniLIMS.  I'm not so sure about that.  we will need to discuss this functionality and interface in detail to determine the best course of action.  Charlotte actually demo-ing its use would be helpful.  I actually dislike SampTrac and assumed we would be getting rid of it.  There are a ton of bugs, which I could document if necessary.

MiniLIMS should retrieve or display flowcell and and lane data from WikiLIMSWikilims is not associated with the IGD GBS Core facility.  the facility uses multiple sequence service centers including CLC and Perkin Elmer.  

Possible new functionality in MiniLIMS

  • GBS database This needs to be re-implemented independant of the existing instance.  if it can be captured within minilims (no longer RDBMS) and samptrack functionality provided, all the better.
  • Display of QC data I think this is a must have 

The SampTrack application reads from and writes to the GBS database. This database could remain, or it could be re-implemented as part of the MiniLIMS semantic database, in which case SampTrack would have to be partially re-coded. The IGD may benefit from the flexibility of the semantic database in the future. yes probably worth pursuing

MiniLIMS could display manually or auto-generated QC data. Users could also execute  scripts and analyses from MiniLIMS and have these results written back to MiniLIMS pages. yes

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