1 / 12

NMRbox: TRD 3

NMRbox: TRD 3. A probabilistic core as a coherent inference engine PINE+ Core E xtend functionality through the new core PINE+: Assignment, use of structure data, RNA Reproducibility – “revisable executable documentation” Side-by-side, reproducible, probabilistic and deterministic.

hugh
Download Presentation

NMRbox: TRD 3

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. 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

  2. Why Bayes? Bayes: Extremizes the log-likelihood. Consistent & extensible determination of parameters argmin Etotal = Eempirical + λEexperimental Constrain: NOEs not distances. J’s not dihedralsetc. Consistency + Extensibility Reproducibility

  3. 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 ADAPT-NMR HI FI PISTACHIO PISTACHIO PECAN PECAN LACS LACS

  4. 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.

  5. 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)

  6. 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.

  7. Transition, Transformation, Synergy TRD 2: NMRSTAR TRD 1: Virtual Machine TRD 2: Workflow & Versions TRD 1: External applications & built-in applications Current architecture

  8. 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.

  9. Progress to date • Things under the hood • Environment • Protocol • Engine • Demonstration • Interface • Desktop PINE • Executable document

  10. Progress in context

  11. 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

  12. Demo • Show interface and interaction • Start a PINE job • Display output of PINE • Show block idea • Show repeatability idea

More Related