Data and Dissemination Core 1. Overview and EFI Website – Heidi Imker, UIUC 2. EFI LabDB LIMS – Wladek Minor, UVA 3. SFLD – Patsy Babbitt, UCSF (post lunch) Enzyme Function Initiative (EFI) Advisory Committee Meeting November 30, 2011

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 SFLD 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) Structure/Function Context for EFI Targets using the Structure-Function Linkage Database Experimental Data Management using the Laboratory Information Management System (LIMS) LabDB EFI Data and Dissemination

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

EFI Website - Initial

EFI Website - Revamped

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

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

EFI Website as a Data Portal

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

EFI Website Stats

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

Data and Dissemination Core 1. Overview and EFI Website – Heidi Imker, UIUC 2. EFI LabDB LIMS – Wladek Minor, UVA 3. SFLD – Patsy Babbitt, UCSF (post lunch) Enzyme Function Initiative (EFI) Advisory Committee Meeting November 30, 2011

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

10 Oct 2011Charlottesville, VA 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

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

LabDB: the private interface to the LIMS

LabDB: shipment

LabDB: export as Comma Separated Values CSV

LabDB: Kinetic assays

EFI-DB: Public

EFI-DB: Target

EFI-DB: Status of the Target

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

Plate design and set-up (Mosquito)

Many drops

Many drops + control

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.

Deposition -> Publication (SG)

Electronic Structure Description (minipaper)

EFI-DB: mini-paper