open worm public hangout 10-08-11
DESCRIPTION
Introduction to the Open Worm project, progress for release 1, plans for release 2.TRANSCRIPT
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What I cannot create I do not understand
Richard Feynman’s last board
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A multi-scale data problem
Scale
Whole brain data (20 um
microscopic MRI)
Mosiac LM images (1 GB+)
Conventional LM images
Individual cell morphologies
EM volumes & reconstructions
Solved molecular structures
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Reverse-engineering?
A system whose mechanisms are obscured
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What is reverse-engineering?
System whose mechanisms are obscured
Individual components andan explanation of how they fit together
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What is reverse-engineering?
Provide a framework of parts ready to be snapped together
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Put the parts back together
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A multi-scale synthesis problem
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Simulation-based research Challenging intuition via predictive models Construction of models requires deep
organization of understanding of a system Forces you to fill in gaps Observing unexpected behaviors produced
by the models Able to look across multiple variables at the
same time Can do experiments that would otherwise
be impossible to do in a real biological system
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Enter the worm: c. elegans
What’s up, baby?
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Virtual physical organisms in a computer simulation
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In search of nature’s design principles via simulation
• How can a humble worm regulate itself?– Reproduces– Avoids predators– Survives in different chemical and temperature
environments– Seeks and finds food sources in an ever
changing landscape– Distributes nutrients across its own cells– Manages waste and eliminates it
– If we can’t understand genes to behavior here, why would we expect to understand it anywhere?
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Enter the worm: c. elegans
I’ve only got 1000 cells in
my whole body… please simulate me!
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A complete simulation of the worm’s brain, body and environment
SimulatedWorld
Detailed simulation of worm body
Detailed simulation of cellular activity
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The goal: understanding a faithfully simulated organism end to end
Extracting mathematical principles from biological systems is necessary if we are going to understand and reconstruct the much larger system of the human.
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Outreach: put the model online and let the world play with it
•Sex: Hermaphrodite•Interested in: Escaping my worm Matrix•Relationship status: Its complicated.
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Worm biology ~1000 cells / 95 muscles Neuroscience:
302 neurons 15k synapses
Shares cellular and molecular structures with higher organisms Membrane bound organelles; DNA complexed into chromatin and organized into discreet chromosomes Control pathways
Genome size: (9.7 x 107 base pairs or 97 Megabases), vs human: 3 billion base pairs (3 X 109 bp or 3000 Megabases).
C. elegans homologues identified for 60-80% of human genes (Kaletta & Hangartner, 2006)
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C. Elegans disease models
Kaletta & Hengartner, 2006
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Can present drugs
Kaletta & Hengartner, 2006
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Entire cell lineage mapped
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Entire cell lineage mapped
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Entire cell lineage mapped
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Entire cell lineage mapped
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Full connectome
Varshney, Chen, Paniaqua, Hall and Chklovskii, 2011
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P. Sauvage et al. / Journal of Biomechanics 2011
Biomechanics
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Interrogation of Behavior
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Core platform: Open Worm project
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One core hooks together multiple simulation engines addressing diverse biological behavior
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Estimates of computational complexity Mechanical model
~5 Tflops Muscle / Neuronal
conductance model~240 Gflops
One Amazon GPU cluster provides 2 Tflops Source: http://csgillespie.wordpress.com/2011/01/25/cpu-and-gpu-trends-over-time/
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Mechanical model
Palayanov, Khayrulin, Dibert (submitted)
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3D body plan
Christian Grove, Wormbase
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Team – A brief history
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Collaboration technologies used
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Jan – Sept 2011
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Architecture
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Neuronal model
GPU Performance Testing: 302 Hodgkin-Huxley neurons for 140 ms (dt = 0.01ms)
Architecture proof of concept using Hodgkin-Huxley neurons
ms
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Worm Browser
http://www.youtube.com/watch?v=nAd9rMey-_0
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Physics: SPH
Smoothed particle hydrodynamics (SPH) algorithm for soft-body / liquid finite element interactions
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Soft-body & fluid mechanics
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Finite element modeling
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C.elegans neuron models in NeuroML
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Mendeley group has 234 references
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Presented poster at Neuroinformatics 2011
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OpenWorm links:
Project page: http://code.google.com/p/openworm/
Twitter: @openworm
Mailing List: http://groups.google.com/group/openworm
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Sept 2011 – March 2012
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Muscle cell with “arms”
Cell Body
5 arms, 10 compartments
each, passive currents
Cell body, 1 compartment, active
currents
Boyle & Cohen, 2007
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Case study: locomotion
Gao et al, 2011
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Conductance model of c. elegans muscle cell
Boyle & Cohen, 2007
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Cell
Body
Cell
Body
Cell
Body
Cell
Body
Cell
Body
Cell
Body
Cell
Body
Cell
Body
Cell
Body
Cell
Body
Cell
Body
Cell
Body
Quadrant 1 Quadrant 2
Quadrants of muscle cells
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Genetic Algorithms and Parameter optimization
Achard, De Schutter, 2006
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Gaming and crowdfunding