Preparing for the Hackathon

Preparing for DaSH

The purpose of DaSH is to have implementers work to integrate a toolset with the various NGS systems and analysis software packages currently in use. For this to be a success, participants should prepare ahead of time by reading the documentation of the available tools (see sidebar), and having an idea of what they want to accomplish. There will not be any formal presentations on the tools themselves (MIRING, HML, GL Service, etc) so please prepare by reading the documentation on this wiki and prepare your questions ahead of time.

An AWS computing environment with tools and sample data will be available. Participants are encouraged to bring their own sample data, and workflow issues and questions. You should bring your own laptops with your own development tools and ssh and sftp clients to connect to the servers. Although there will be a short presentation explaining this environment at the beginning of the hackathon, we recommend that you prepare ahead of time by reading and understanding the Tool Access page on this wiki.

While you don't need a github account to download and use the resources from DaSH, we encourage you to create an account so that you can submit issues & code, and make changes to the wiki. Documentation for how to use github and the wiki can be found on Github Help.

Groups with common interests will be formed. Possible topics include:

• for Developers

  • Pipeline - going from raw reads to HML
  • Parsing/consuming HML
  • Using external references in HML
    • GL Service
    • NCBI Genetic Testing Registry (GTR)
    • Sequence Read Archive (SRA) like resources for raw reads
  • Validation tools
    • Syntactic - schema
    • Semantic
      • Does the message make sense?
      • Operational - what's required/acceptable by the organization
      • MIRING compliance
      • Working with external references
        • Value domains (e.g., HUGO gene families, IMGT/HLA)
        • Data (e.g., SSA & raw reads, methodologies in the GTR )

• for Discussion

  • How to represent novel polymorphisms
  • How to represent unreferenced sequences
  • Date formats - XDS vs ISO8601 (dealing with colons and dashes)
  • Operational issues
    • security
    • communications
      • transport mechanism
      • acknowledgements
      • error reporting
    • data storage/staging

If you have any topics that you think we should add to this list please email mwright@nmdp.org and I can add it, unless you wish to edit the page immediately.