nmrbox.org nmrbox: trd 3 a probabilistic core as a coherent inference engine pine+ core extend...
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nmrbox.org
NMRbox: TRD 3
• A probabilistic core as a coherent inference engine • PINE+ Core
• Extend functionality through the new core• PINE+: Assignment, use of structure data, RNA
• Reproducibility – “revisable executable documentation” • Side-by-side, reproducible, probabilistic and deterministic
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nmrbox.org
Why Bayes?
argmin Etotal = Eempirical + λEexperimentalBayes: Extremizes the log-likelihood. Consistent & extensible determination of parameters
Constrain: NOEs not distances. J’s not dihedrals etc.
Consistency + Extensibility Reproducibility
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nmrbox.org
What is PINE and PINE Core?
• PINE is the probabilistic Bayesian engine for • Data verification (LACS)• Secondary structure determination (PECAN)• Assignment (PISTACHIO)• Peak picking (HIFI)• Bayesian updating (PINE) • Bayesian updating + deterministic constraints (ADAPT-NMR)• RNA assignment (RNA-Pairs)
LACS PECAN PISTACHIO HI FI
LACSPECANPISTACHIO
LACSPECANPISTACHIO
HI FI
ADAPT-NMR
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nmrbox.org
Corollary
• In our view, Pine has been a highly successful probabilistic model. The inference core has proven to be very powerful – an excellent setting for building a structure determination protocol for:
• Repeatability and Reproducibility• Coexistence of probabilistic and deterministic paradigms• Extensibility to support new functions through plugins
• Additionally empowering:• Revisable executable documentation
• Document as you go, execute any time, reuse.
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nmrbox.org
PINE+
• PINE+ is the collection of applications • Containing a core probabilistic engine• The core will support all existing tools
• HIFI, PINE, PECAN, ADAPT-NMR, LACS, RNA-PAIRS
• And, New assignment tools• NOESY, RNA, Structure-based
• PINE+ will support probabilistic and deterministic approaches• PINE+ Will additionally enable reproducible results
• Playback of blocks or the entire project (repeatability)*• Edit & Replay of blocks or the entire project (reproducible)*• Template (reuse)
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nmrbox.org
Key Innovations
• The complete process of structure determination is captured and executed using one language, one environment, one paradigm, in open source form, using open technologies.
• As the user steps through structure determination steps, a living “executable document” is created – repeatability.
• “Blocks” of a structure determination “document” can be modified with new data or process – reproducibility.
• A “document” can be used as a “template”; replacing, or modifying blocks as needed – reuse.
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nmrbox.org
Transition, Transformation, Synergy
Current architecture
TRD 1: Virtual Machine
TRD 1: External applications & built-in applications
TRD 2: NMRSTAR
TRD 2: Workflow & Versions
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nmrbox.org
Impact
• Opportunity for • Enabling repeatable and reproducible structure determination• Empowering other packages with probabilistic functionality• Supporting side-by side deterministic and probabilistic tools• Creating end-to-end open source tools
• Built-in probabilistic functions for• Peak picking, backbone assignment, side-chain assignments,
secondary structure prediction, verification, NOESY assignment, RNA assignment, pipeline/network definition, scientific documentation, capture and replay, edit and execute.
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nmrbox.org
Progress to date
• Things under the hood• Environment • Protocol• Engine
• Demonstration• Interface• Desktop PINE• Executable document
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nmrbox.org
Progress in context
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nmrbox.org
Things under the hood
• Environment• High performance, dynamic, distributed, parallel, scientific computing
• Protocol• JSON for specification and exchange, Pandoc for data transformation
• Engine• Inference-as-a-service using a resource-oriented model• Simple (6 components) relation, learner, predictor, transformer, attribute, schema
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nmrbox.org
Demo
• Show interface and interaction
• Start a PINE job
• Display output of PINE
• Show block idea
• Show repeatability idea