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Data and Dissemination Core Overview and EFI Website – Heidi Imker, UIUC

Data and Dissemination Core Overview and EFI Website – Heidi Imker, UIUC EFI LabDB LIMS – Wladek Minor, UVA SFLD – Patsy Babbitt, UCSF (post lunch) Enzyme Function Initiative (EFI) Advisory Committee Meeting November 30, 2011. EFI Data and Dissemination.

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Data and Dissemination Core Overview and EFI Website – Heidi Imker, UIUC

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  1. Data and Dissemination Core • Overview and EFI Website – Heidi Imker, UIUC • EFI LabDB LIMS – Wladek Minor, UVA • SFLD – Patsy Babbitt, UCSF (post lunch) • Enzyme Function Initiative (EFI) • Advisory Committee Meeting • November 30, 2011

  2. EFI Data and Dissemination The EFI’s goal is to develop and disseminate an integrated sequence/structure‑based strategy that incorporates a spectrum of essential expertise, including high‑throughput bioinformatics, computation and structural biology that will enable focused experimental enzymology, genetics, and metabolomics. • Superfamily/Genome Core • complete curated sequence archive for • EFI superfamilies • “tools” for sequence analysis (including • sequence/structure similarity networks) • portal for external bioinformatic data • (including genomic contexts) • Computational Core • - computational models • computational docking • virtual screening libraries • Protein Core • cloning, expression and purification • Structure Core • screening and crystallization • ligand binding (Thermofluor) • Microbiology Core • - phenotypic analysis (Biolog) • - metabolomics (MS based) • Bridging Projects • - assay data (5 distinct superfamilies) LabDB Structure/Function Context for EFI Targets using the Structure-Function Linkage Database Experimental Data Management using the Laboratory Information Management System (LIMS) SFLD

  3. EFI Dissemination Flow General Information and Data Portal EFI Website Data Deposition Structure/Function Context Experimental LabDB TargetDB cross-linking SFLD EFI Experiment DB PDB PepCDB Annotation Transfer PSI-MR Protein Core

  4. EFI Website - Initial

  5. EFI Website - Revamped

  6. EFI Website as a Reference • New layout • Rotating content • Figures from recent publications • Images from recent structures • Frequently used external link access UIUC Web Developer Gabriel Horton

  7. EFI Website as a Data Portal Streamlined Navigation HOMOLOGUE SEARCH 1-Click Access RESOURCES RESOURCES

  8. EFI Website as a Data Portal

  9. Tutorials • EFI-QuickHelps • Find a specific target in the experimental database (EFI-DB) • Find a specific enzyme in the bioinformatic database (SFLD • Change memory for large networks (Cytoscape) • Searching in networks (Cytoscape) • View network at more stringent E-values (Cytoscape) • Add node attribute file to network (Cytoscape) • Full Guides and Tutorials • EFI-DB Guide • SFLD Guide • Cytoscape Wiki • Cytoscape Tutorial • Chimera Tutorial

  10. EFI Website Stats

  11. Outreach • Current • Journal Publications (13) • Collaborations (2 proposed) • Talks/Seminars (4+) • Posters (1st EFI Session today) • Meeting Workshops (ASBMB 2013) • EFI Wikipedia Page • Planned • (Public) Newsletters • Mini-Papers • Instructional Webinars/Videos • Intensive Workshops

  12. Data and Dissemination Core • Overview and EFI Website – Heidi Imker, UIUC • EFI LabDB LIMS – Wladek Minor, UVA • SFLD – Patsy Babbitt, UCSF (post lunch) • Enzyme Function Initiative (EFI) • Advisory Committee Meeting • November 30, 2011

  13. Experimental Data Management Architecture Once weekly TargetDB/PepCDB Real-time TargetTrack EFI-DB PDB Public (Biologist) Every 60 minutes Private (EFI) LabDB Real-time

  14. The LabDB LIMS Tracks all experiments in the pipeline from cloning to structure solution Chemicals / stock solutions Protein production: cloning / expression / purification Crystallization / crystal harvesting X-ray diffraction experiments / structures Access control Login required to view data Users divided into research groups Different users/groups have varying permissions to access data Designed to extract as much information directly from the laboratory hardware as possible 10 Oct 2011 Charlottesville, VA

  15. LabDB: automated/semi-automated import from hardware (Private) Equipment LabDB database clones, expressions, purifications diffraction, structures chemicals, solutions crystallization LabDB mobile LabDB web Xtaldb HKL-3000 Interfaces

  16. LabDB: the private interface to the LIMS

  17. LabDB: shipment

  18. LabDB: export as Comma Separated Values CSV

  19. LabDB: Kinetic assays

  20. EFI-DB: Public

  21. EFI-DB: Target

  22. EFI-DB: Status of the Target

  23. EFI-DB: Automatic data harvesting + SYPRO Orange Data analysis + protein Experimental design and plate preparation Experiment Fluorescence Temperature [C]

  24. Plate design and set-up (Mosquito)

  25. Many drops

  26. Many drops + control

  27. How to measure success? • High Throughput ? • High Output ? • High Impact • SG - 10% structures are published • EFI is an investment for enabling the biological community to accomplish functional assignments in their “favorite” families and superfamilies.

  28. Deposition -> Publication (SG)

  29. Electronic Structure Description (minipaper)

  30. EFI-DB: mini-paper

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