launch elixir be 2017
TRANSCRIPT
FROM LOCAL MANAGEMENT TOGLOBAL DISSEMINATION
UNLOCKING THE POTENTIAL OF CELL MIGRATION DATA
http://uproxx.com/hitfix/4-important-lessons-a-child-learns-from-the-lion-king/
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Local management and analysis of cell migration data
Community-driven standards as a mean to discover, share and re-use data
Minimum reporting requirements and controlled vocabularies: an example
CC BY-SA 4.0
Local management and analysis of cell migration data
Community-driven standards as a mean to discover, share and re-use data
Minimum reporting requirements and controlled vocabularies: an example
CC BY-SA 4.0
A typical cell migration experimental workflow is composed of diverse steps
Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0
sample preparation
image acquisition
image processing
data analysis
CC BY-SA 4.0
These steps produce rich data sets represented in various file formats
sample preparation
image acquisition
image processing
data analysis
• paper laboratory notebooks
• electronic laboratory notebooks
• spreadsheets• text files• protocols• papers...
• raw files• XML files• proprietary
microscope or acquisition software files ND2 for Nikon, LIF for Leica, OIB or OIF for Olympus, LSM or ZVI for Zeiss
• image files with pixel values and metadata
• png, jpeg, tiff, avi• text files
describing processing algorithms
• text files describing extracted features
• graphs, plots• analysis pipelines• text files
describing computational algorithms...
Servier Medical Art, CC-BY 3.0; Cell Image Library, CC-BY 3.0
CC BY-SA 4.0
Our open-source and free solutions for cell migration data management and analysis
Cell migrationexperiment setup
• technical and biological replicates
• metadata annotation• experimental settings
export and import
Masuzzo, Bioinformatics, 2013, Masuzzo, Scientific Reports, 2017, Naji, in preparation
CC BY-SA 4.0
Experiment
sample preparation
image acquisition
Our open-source and free solutions for cell migration data management and analysis
Cell migrationexperiment setup
• technical and biological replicates
• metadata annotation• experimental settings
export and import
Masuzzo, Bioinformatics, 2013, Masuzzo, Scientific Reports, 2017, Naji, in preparation
CC BY-SA 4.0
Experiment
sample preparation
image acquisition
Our open-source and free solutions for cell migration data management and analysis
Cell migrationexperiment setup
• technical and biological replicates
• metadata annotation• experimental settings
export and import
Masuzzo, Bioinformatics, 2013, Masuzzo, Scientific Reports, 2017, Naji, in preparation
Image analysis
• pre-processing, segmentation & tracking
• multiple algorithms• interactive GUI
CC BY-SA 4.0
Experiment
sample preparation
image acquisition
Our open-source and free solutions for cell migration data management and analysis
Cell migrationexperiment setup
• technical and biological replicates
• metadata annotation• experimental settings
export and import
Image analysis
• pre-processing, segmentation & tracking
• multiple algorithms• interactive GUI
Cell migrationdata import
• modules for collective and single-cell migration
• drag and drop files• formats: TSV, CSV, XLS
Masuzzo, Bioinformatics, 2013, Masuzzo, Scientific Reports, 2017, Naji, in preparation
CC BY-SA 4.0
Experiment
sample preparation
image acquisition
Our open-source and free solutions for cell migration data management and analysis
Cell migrationexperiment setup
• technical and biological replicates
• metadata annotation• experimental settings
export and import
Image analysis
• pre-processing, segmentation & tracking
• multiple algorithms• interactive GUI
Cell migrationdata import
• modules for collective and single-cell migration
• drag and drop files• formats: TSV, CSV, XLS
Masuzzo, Bioinformatics, 2013, Masuzzo, Scientific Reports, 2017, Naji, in preparation
CC BY-SA 4.0
Experiment
sample preparation
image acquisition
Our open-source and free solutions for cell migration data management and analysis
Cell migrationexperiment setup
• technical and biological replicates
• metadata annotation• experimental settings
export and import
Image analysis
• pre-processing, segmentation & tracking
• multiple algorithms• interactive GUI
Cell migrationdata import
• modules for collective and single-cell migration
• drag and drop files• formats: TSV, CSV, XLS
Collective and single-cell migrationdata inspection and analysis
• single-cell trajectories visualization
• trajectory-centric & step-centric parameters
• cell-covered area or cell-free area analysis
• intra- and inter-replicates quality control
• two-criterion filtering and quality control
• statistical comparison across condition
• regression on area• statistical
comparison across conditions
• robust z*-scores• plate heat-map
• dedicated module for dose-response analysis
• statistics
Masuzzo, Bioinformatics, 2013, Masuzzo, Scientific Reports, 2017, Naji, in preparation
CC BY-SA 4.0
Automation and provenance trackingare essential for reproducibility
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Metadata annotation is crucial fordata interpretation
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Once in a database, data and metadata are easily manageable and accessible
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Like a wet-lab protocol, a data processing pipeline needs full annotation
CC BY-SA 4.0
Like a wet-lab protocol, a data processing pipeline needs full annotation
CC BY-SA 4.0
Like a wet-lab protocol, a data processing pipeline needs full annotation
CC BY-SA 4.0
Local management and analysis of cell migration data
Community-driven standards as a mean to discover, share and re-use data
Minimum reporting requirements and controlled vocabularies: an example
CC BY-SA 4.0
We are creating a cell migration data exchange ecosystem
https://multimot.org/ Masuzzo, Trends in Cell Biology, 2016
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Community-driven standardization efforts are crucial in this process
https://cmso.science/Masuzzo, Trends in Cell Biology, 2016
CC BY-SA 4.0
Different information units require specific standardization tasks
raw data & metadata
set up experiment: annotate
investigation, study, assay
convert processed and derived data
into standard formats
process raw data
convert raw data & metadata into
standard formats
analyzedata
experiment
CC BY-SA 4.0
The goal of these tasks is to maximizedata use
raw data & metadata
set up experiment: annotate
investigation, study, assay
convert processed and derived data
into standard formats
process raw data
convert raw data & metadata into
standard formats
analyzedata
experiment
data re-analysis
data re-use
data re-purpose
CC BY-SA 4.0
A lot of standards are already availablefor the life sciences
https://biosharing.org/
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And these can certainly be used, expanded and built upon
Image adapted from Josh Moore, CMSO workshop 2017
ISA OME data_pkg
Data deposition
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Minimum reporting requirements and CVs improve data verification and accessibility
Image adapted from Josh Moore, CMSO workshop 2017
ISA OME data_pkg
Data deposition
MIA
CME
CV
CC BY-SA 4.0
Local management and analysis of cell migration data
Community-driven standards as a mean to discover, share and re-use data
Minimum reporting requirements and controlled vocabularies: an example
CC BY-SA 4.0
What is the level of detail to report when describing cell migration experiments?
MIACME v0.2https://github.com/CellMigStandOrg/MIACME
CC BY-SA 4.0
Minimum metadata annotations are agreat starting point
Experimental setup• Cell type
H1299 human lung cancer cells
• Interference Fibronectin concentration ROCK inhibitor Y-27632 Rho-activator Calpeptin
• Microenvironment: substrate Fibronectin
• Assay Single-cell migration
Lock et al., PLOSONE 2015
CC BY-SA 4.0
But data discovery and re-use cannot happen efficiently without CVs
Lock et al., PLOSONE 2015
CLO:0007986
FMA:67311CHEBI:75393CHEBI:3330
FMA:67311
Experimental setup• Cell type
H1299 human lung cancer cells
• Interference Fibronectin concentration ROCK inhibitor Y-27632 Rho-activator Calpeptin
• Microenvironment: substrate Fibronectin
• Assay Single-cell migration
CC BY-SA 4.0
CVs facilitate knowledge discovery through associations and relationships
Lock et al., PLOSONE 2015
CLO:0007986
FMA:67311CHEBI:75393CHEBI:3330
FMA:67311
Experimental setup• Cell type
H1299 human lung cancer cells
• Interference Fibronectin concentration ROCK inhibitor Y-27632 Rho-activator Calpeptin
• Microenvironment: substrate Fibronectin
• Assay Single-cell migration
CC BY-SA 4.0
Domain-specific entities sometimes require the definition of new terms
Lock et al., PLOSONE 2015
CLO:0007986
FMA:67311CHEBI:75393CHEBI:3330
FMA:67311
Experimental setup• Cell type
H1299 human lung cancer cells
• Interference Fibronectin concentration ROCK inhibitor Y-27632 Rho-activator Calpeptin
• Microenvironment: substrate Fibronectin
• Assay Single-cell migration
a quantitative test that enables the study of the migratory behavior of
individual cells
CC BY-SA 4.0
www.compomics.com