data and dissemination core overview and efi website – heidi imker, uiuc
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
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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
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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
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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
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EFI Website - Initial
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EFI Website - Revamped
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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
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EFI Website as a Data Portal
Streamlined Navigation
1-Click AccessHOMOLOGUE SEARCH
RESOURCES
RESOURCES
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EFI Website as a Data Portal
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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
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EFI Website Stats
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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
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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
![Page 13: Data and Dissemination Core Overview and EFI Website – Heidi Imker, UIUC](https://reader036.vdocuments.mx/reader036/viewer/2022081520/56815009550346895dbde2c6/html5/thumbnails/13.jpg)
EFI-DB
LabDBPrivate (EFI)
Public (Biologist)
TargetDB/PepCDB
TargetTrack
PDB
Every 60 minutes
Real-time
Once weekly
Real-time
Experimental Data Management Architecture
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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
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chemicals,solutions
clones,expressions,purifications
crystallizationdiffraction,structures
Equipment
InterfacesXtaldb
LabDB database
HKL-3000LabDB mobile LabDB web
LabDB: automated/semi-automated import from hardware (Private)
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LabDB: the private interface to the LIMS
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LabDB: shipment
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LabDB: export as Comma Separated Values CSV
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LabDB: Kinetic assays
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EFI-DB: Public
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EFI-DB: Target
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EFI-DB: Status of the Target
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Flu
ore
scen
ce
Temperature [C]
Experimental design and plate preparation
+ SYPRO Orange
+ protein
Experiment
Data analysis
EFI-DB: Automatic data harvesting
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Plate design and set-up (Mosquito)
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Many drops
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Many drops + control
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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.
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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
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Electronic Structure Description (minipaper)
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EFI-DB: mini-paper