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JAX BioConnect Quartermaster: JBQ CLI Tool

Vision statement

When computational research scientists or scientific software engineers work with BioConnect data sets, they should be able to flow - within their compute environment and with limited interruptions and minimal transitions - as they interrogate multidimensional data from new angles. JBQ is the command line interface that provides users with access to BioConnect data directly from their terminal. Just as a quartermaster is the military officer responsible for supervising stores and distributing supplies to soldiers, the JAX BioConnect Quartermaster or JBQ serves as a source of provisions for novel biomedical exploration and research. JAX scientists, bioinformaticians, and engineers can use JBQ to:

  • review ISA-formatted metadata,
  • filter datasets by relevant research characteristics,
  • identify tools in BioConnect relevant to a selected data set,
  • download datasets locally or on virtual servers (ex. HPC environment),
  • upload RO-Crates for derived datasets with new processes and workflows, ยง connect external systems (ex. glue) with BioConnect, and
  • share an RO-Crate with another researcher or engineer.

With these capabilities, we hope JBQ CLI will significantly reduce the friction surrounding JAX data analyses, exploration, and collaborative research.

Methods

From the command-line and within a folder where the JBQ_package is downloaded, you can use the methods listed below to interact with BioConnect.

login

  • Authenticate yourself as a valid JAX user and gain access to your unique user space.
  • Command: python3 jbq.py login

logout

  • Remove authentication from your machine to reduce risk of an illegitimate masquerader using your legitimate account.
  • Command: python3 jbq.py logout

explore

  • Review metadata of the RO-Crates in your user space with a text-user-interface (TUI).
  • Command: python3 jbq.py contents

focus

  • Reduce the list of RO-Crates in the TUI to a specific subset that share a particular research-relevant characteristic (ex. assays based on a specific tissue type).
  • Command: python3 jbq.py filter

mobilize

  • With a given RO-Crate selected in exploration mode, view the tools in BioConnect that may be relevant to analyzing or working with that data set.
  • Command: click within the TUI

deploy

  • Download an RO-Crate for use elsewhere.
  • Command: python3 jbq.py download

garrison

  • Having completed a transformation upon a previously deployed dataset, upload a derived-dataset into a new RO-Crate in BioConnect, identifying the lineage and ensuring reproducibility.
  • Command: python3 jbq.py upload
  • Variant: from within external systems (ex. glue) we may provide ways to directly repatriate your data into BioConnect through JBQ

share

  • Send an RO-Crate to an email address. Note: future versions may involve passing a link to JBQ that does not require JAX authentication for login.
  • Command: python3 jbq.py email