emen2 steve ludtke ncmi baylor college of medicine ncrr
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EMEN2Steve Ludtke
NCMIBaylor College of Medicine
NCRR
Current EMEN Database
• Diverse data requirements:
purification data collection reconstruction • OODB (Zope based)• Direct equipment interface• 290 users from dozens of labs• ~7 Tb image data• 2-3 Tb/year of image data • 385,000 total records
LIMS
• Centralized databases (PDB, EBI, etc.) vs. in-house archives with detailed information
• Scientific Database vs. Electronic Notebook
Film/Frame Id
Defocus MagTotal Dose
ExpTime
ccd_20040314193633 #1
0.8 um 138.44k 20.0 1.0 s
ccd_20040314193634 #2
2.5 um 138.44k 20.0 1.0 s
ccd_20040314194642 #1
0.8 um 138.44k 20.0 1.0 s
ccd_20040314194643 #2
2.5 um 138.44k 20.0 1.0 s
ccd_20040314194917 #1
0.8 um 138.44k 20.0 1.0 s
ccd_20040314194918 #2
2.5 um 138.44k 20.0 1.0 s
ccd_20040314195514 #1
0.8 um 138.44k 20.0 1.0 s
ccd_20040314195515 #2
2.5 um 138.44k 20.0 1.0 s
ccd_search1 #1
0.8 um 138.44k 20.0 1.0 s
ccd_search2 #2
2.5 um 138.44k 20.0 1.0 s
ccd_search3 #1
0.8 um 138.44k 20.0 1.0 s
ccd_search4 #2
2.5 um 138.44k 20.0 1.0 s
ccd_search5 #1
0.8 um 138.44k 20.0 1.0 s
ccd_search6 #2
2.5 um 138.44k 20.0 1.0 s
• Excellent mineability• Limited flexibility• Good for centralized databases (standards)
Excellent flexibilityRich information contentLimited mineability
Goals
• BOTH flexibility and mineability
• KISS
• Database should think like the scientist, not the other way around
• Archive detailed experimental protocols
• Association of databases
New Concepts
• Object Oriented Databases (OODB)
• Web Ontologies (semantic web)
• Evolving collaborative environment (wikipedia)
• XML
• Peer to Peer Networking
• Blogging
Experimental Protocol
Experimental Parameter
Record
DescriptiveText
Experimental ParameterExperimental
ParameterExperimental Parameter
Experimental Parameter
Experimental Parameter
Temperature
Parameter Ontology
Ambient_Conditions
Ambient_Temperature Ambient_Pressure
Ambient_RelativeHumidity
Specimen_Temperature
Grid_Temperature
Grid_Temperature_Imaging
Grid_Temperature_Previtrification
grid
negative_stain_gridvitrified_grid
manually_vitrified_grid vitrobot_vitrified_grid
manually_vitrified_grid_flash_photolysis
TEM_specimen
holey_carbon_grid
quantifoil_grid
Protocol Ontology
manually_vitrified_grid
A preprepared #grid was placed in a pair of forceps and loaded into the plunger. $cryogen was preprepared below the plunger (ethane and other cryogens which may become solid are reliquefied using a room temperature copper rod immediately prior to plunging). $grid_volume of specimen was deposited on the front of the grid using a pipette. The grid was then blotted on $grid_blot_side using $filter_paper_type and the plunger was triggered after a $grid_plunge_delay to rapidly submerse the grid in the cryogen. The forceps were then released from the guillotine and the grid was placed in $grid_storage_id in $grid_storage_slot. The grid storage button was then placed in $cryofreezer_id for storage until imaging.
EMEN2
• Ease of use (new protocols without DBA)• Protocol archival• Protocol and Parameter Ontologies (P2P)• ‘Blogging’• Traceability• Workflow• Dissemination (mirroring)• Data Mining
plot bfactor vs truedefocus where truedefocus is between 0.1 and 5.0 and bfactor is between 1 and 1000
Microscopy Session
CCD FrameMicrograph
Scan
Particles
Project Microscope
Particles
plot bfactor vs truedefocus where truedefocus is between 0.1 and 5.0 and bfactor is between 1 and 1000
split by protocol
plot bfactor vs truedefocus where truedefocus is between 0.1 and 5.0 and bfactor is between 1 and 1000
split by creator
plot bfactor vs truedefocus where truedefocus is between 0.1 and 5.0 and bfactor is between 1 and 1000
split by microscope
Microscopy Session
CCD FrameMicrograph
Scan
Particles
Project Microscope
Particles
EMEN2 Status
• Core library functional– BerkeleyDB + Python
• All EMEN data EMEN2• Begun work on Web-based front-end
– Apache + Cheetah
• P2P incorporated into design, but implementation incomplete
• Formal XML interfaces (OWL for exchange incomplete)
Acknowledgements
Thanks to:National Center for Research ResourcesAgouron Institute
• Haili Tu• Runsun Pan
Relational vs. OODB
Tables
Tabular Storage
Fixed Records
No Table-mixing
Classes
Hierarchical Storage
Flexible Records
Mixed Class Reports
0
1000
2000
3000
4000
5000
6000
7000
Scanned Micrographs
CCD Frames
EMEN Goals
• Project Management• Data Archival• Data Mining• Automation• Flexibility• Communication with Collaborators• Dissemination• Portability
plot intendeddefocus vs truedefocus where truedefocus>0 and intendeddefocus>0
Group Address Affiliations City Contact Email Contact Name Fax # Group Name Institution Phone # State Support Sources Website URL Zip Code
Microscope CCD Camera Type CCD Model # CCD Serial # CCD Size X CCD Size Y CC CS Microscope Serial # Pole Piece Sensitivity Title Voltage
Project Axis Codes Bio-hazard Codes Biomedical Properties Biophysical Properties Biochemical Properties Genetic Characterization Goals of Project Height (of specimen) Keywords for Project Length (of specimen) Mass (of specimen) Particle Diameter Project Description Project Title Sequence Specimen Storage Location (Data) Symmetry (of specimen)
User Address Degrees Department Email First Name Institution Last Name Login Name Phone
Aliquot Buffer Concentration Date Received Identifiers Received By Storage Loc. Volume
Freezing Session Aliquots Used Apparatus Blotting Concentration Frozen By Grid Batch Grids Used Grid Type Hole Size Mesh Size Number of Grids Post Freezing Pre-Treatment Storage Loc. Substrate Substrate Prep. Freezing Tech. Vitrobot Parm.
Purification Buffer Concentration Description Purification Meth. Spec. Stability Storage Condn.
Labnotebook Links (web) Notebook Text
Structure Factor From Whom Processed Source
Reference Comments
CCD Anti Blooming Astigmatism Parm. Beam Diameter B Factor Binning Camera Camera Length Camera Units Dose Drift Parm. Energy Filter Exposure # Exposure Time Frame ID Ice Comments Ice Thickness Identifier Intended Defocus Lens Current Magnification Peak S/N Ratio Screen Current Screen Magnification Tilt Angle True Defocus True Magnification (X,Y) Coordinates Zoom Factor
Micrograph Amplitude Cont. Astig. Parm. Beam Diameter B Factor Camera Length Camera Units Contamination Dose Drift Parm. Energy Filter Exposure # Exposure Time Film ID Ice Comments Ice Thickness Illum. Angle Intended Defocus Lens Current Magnification Maximum Res. Micrograph Qual. Peak S/N Ratio Screen Current Screen Mag. Tilt Angle True Defocus True Mag. (X,Y) Coordinates
Microscopy Sess. Apertures Camera Length Camera Units Condenser CS Develop Time Film Type Freezing Session Magnification Microscope Room Humidity Room Temp. Specimen Temp. Spot Size Voltage Scan
Averaging Fac. Brightness Contrast Exposure Time Parameters Scanned By Scanner Used Scan Step
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