The EFI/TCCS Ignition System Overview of Toyota EFI/TCCS Ignition ...
Data and Dissemination Core 1. Overview and EFI Website – Heidi Imker, UIUC 2. EFI LabDB LIMS –...
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Transcript of Data and Dissemination Core 1. Overview and EFI Website – Heidi Imker, UIUC 2. EFI LabDB LIMS –...
Data and Dissemination Core
1. Overview and EFI Website – Heidi Imker, UIUC2. 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 Targetsusing the
Structure-Function Linkage Database
Experimental Data Managementusing 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
SFLDLabDB
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 AccessHOMOLOGUE SEARCH
RESOURCES
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 (1st 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, UIUC2. EFI LabDB LIMS – Wladek Minor, UVA3. SFLD – Patsy Babbitt, UCSF (post lunch)
Enzyme Function Initiative (EFI)Advisory Committee Meeting
November 30, 2011
EFI-DB
LabDBPrivate (EFI)
Public (Biologist)
TargetDB/PepCDB
TargetTrack
PDB
Every 60 minutes
Real-time
Once weekly
Real-time
Experimental Data Management Architecture
10 Oct 2011 Charlottesville, 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
crystallizationdiffraction,structures
Equipment
InterfacesXtaldb
LabDB database
HKL-3000LabDB 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
Flu
ore
scen
ce
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)
Time between deposition and publication
0%
5%
10%
15%
20%
25%
6 12 18 24 30 36 42 48 54 60 66 72 78 84 90 96
Time (months)
fraction of papers
Electronic Structure Description (minipaper)
EFI-DB: mini-paper