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05/01/2023
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TOWARDS A (UNITED) FEDERATION OF BIOINFORMATICS RESOURCES
Matthew Vaughn @mattdotvaughnDirector, Life Sciences Computing, TACC | Co-PI Cyverse, Araport, Jetstream
Interoperability and Federation Across Bioinformatic Platforms and Resources
Jan 14, 2017
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WHY FEDERATE?
Because you can’t do it all or be it all. And would you even want to?
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WHY FEDERATE?There’s always some existing or emergent
• Data Set • Database • Visualization Technology • Software Algorithm or Library • Physical Capacity or Capability • Source of funding and support
not in scope for you to directly provide or avail yourself of
Federated infrastructures are TEAM-BUILT
Increase the resiliency of your informatics ecosystem
Leverage all the other brains who have different views of your problem
WHY DON’T WE FEDERATE BY DEFAULT?
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Federation requires three things:
• Components confirming to “standardized" schemas, protocols for interaction and usage
• Stably-operated frameworks to handle yeoman’s work of integrating components
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WHY DON’T WE FEDERATE BY DEFAULT?
Hey wait.. I said there were three things we needed for federation:
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WHY DON’T WE FEDERATE BY DEFAULT?
Hey wait.. I said there were three things we needed for federation:
Planning & Specific Effort
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Lab-Born Software
• Immediately responsive• Limited R&D• Resources on hand• Sustainability? What’s
that?
Centrally-Planned Software
• Mindfully built• Better chance for R&D• Dedicated resources• Sustainability? What’s
that?
WHY DON’T WE FEDERATE BY DEFAULT?
Some of the most interesting work is done at the edges of our infrastructure. Their adopting federated access patterns post-hoc means assuming substantial technical debt.
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Science applications
Domain-specific services
Establishedsoftware and CI
Physical resources
Federated Storage National CI Virtualization Job
SchedulingSingle
Sign-on
Ease
of U
se
Ease
of R
e-us
e
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HOW CAN WE MAKE FEDERATION EASIER?Deeply understand the capabilities of existing integration platforms
• Avoid Not-Invented-Here by adopting the 80% rule• Contribute enhancements, either via active feedback or by coding them• Build on our platforms and make sure they get credit for their role
Identify and adopt existing standards. Contribute where they fall short of our needs• OpenAPI for web service definitions• ISA Framework for experimental metadata• Oauth2 for authorization
Provide tooling and documentation for users with diverse technical backgrounds
• GUI, Forms, Web Services. But also language libraries and SDKs.• Make sure we understand the motivations and constraints of those users• Write cookbooks, not just shopping lists
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Jetstream GUI
Agave API Developer Portal
DesignSafe.CI Workbench
Araport Web Services
MAKING FEDERATION WORK REQUIRES THAT WE INCREASE EVERYONE’S
PRODUCTIVITY
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@mattdotvaughn www.slideshare.net/mattdotvaughn [email protected]
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