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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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slide1

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
slide2

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

slide3

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

slide6

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

slide7

EFI Website as a Data Portal

Streamlined Navigation

HOMOLOGUE SEARCH

1-Click Access

RESOURCES

RESOURCES

slide9

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
slide11

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
slide12

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
slide13

Experimental Data Management Architecture

Once weekly

TargetDB/PepCDB

Real-time

TargetTrack

EFI-DB

PDB

Public (Biologist)

Every 60 minutes

Private (EFI)

LabDB

Real-time

the labdb lims
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

slide15

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

slide23

EFI-DB: Automatic data harvesting

+ SYPRO Orange

Data analysis

+ protein

Experimental design

and plate preparation

Experiment

Fluorescence

Temperature [C]

how to measure success
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.