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One of the greatest challenges of biology is to create a
generic model of multicellular development, in order to
unify what Darwin called nature's "endless forms most
beautiful", and construe them as variants
around a common theme. The variants are the unique
genetic (and epigenetic) information of each species; the
common theme is the developmental dynamics that this
information guides and parametrizes.
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While the "modern synthesis" of genetics and evolution focused most of
the attention on selection, it is only during the past decade
that analyzing and understanding variation by comparing
the developmental processes of different species, at both
embryonic and genomic levels, became a major concern of
evolutionary development, or "evo-devo".
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From cell behavior to tissue deformation: A platform for the computational
modeling and simulation of animal early embryogenesis
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Drawing from real data measured on microscopy imaging,
my PhD student Julien Delile, under the co-supervision of
Nadine Peyriéras (CNRS, Gif-sur-Yvette),
designed a realistic model of animal embryogenesis. It is construed
as the collective behavior of a myriad of individual cells implemented in an
agent-based simulation centered on the mechanic-chemical coupling
between cellular and genetic dynamics. The MecaGen platform can run both on a GPGPU array or on
a cluster or computing grid.
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The aim of the MecaGen
platform is to provide a computational modeling and simulation environment
for the multiscale dynamics of the early stages of biological morphogenesis.
This virtual reconstruction is done under the control of experimental
and quantitative reconstructions coming from live imaging (see
below).
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An integrative biology platform allowing the exhaustive detection and measurement
of multicellular dynamics from in vivo observations
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Since 2007, I have been contributing to the scientific and technical
direction of a team working on European (FP6/7) and French (ANR)
projects about animal morphogenesis, including
Embryomics (ended 2009) and
BioEmergences (continued).
These initiatives were launched by
Nadine Peyriéras (CNRS) and Paul Bourgine
(Ecole Polytechnique), and have pioneered the design of methods
and algorithms for reconstructing the complete dynamics of
multicellular development observed by microscopy. The workflow
runs on a computing grid, partly via the OpenMOLE platform developed at ISC-PIF.
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The BioEmergences platform allows biologists to produce and
annotate time-lapse shots of organism development, while
mathematicians and computer scientists process these images
to "reconstruct" and model collective cell dynamics.
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Translating the principles of biological morphogenesis into a stack of formal programming languages
compiled and implemented in a (virtual or real) synthetic biological substrate or "bioware"
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The SynBioTIC project, whose WP1 I lead with my collaborator
Taras Kowaliw and
postdoc Jonathan Pascalie, proposes to design
and develop tools to literally "compile" (as in programming
languages) the overall behavior of a population of cells (bacteria)
into processes local to each entity (one bacterium).
The motivation is to exploit the collective properties
of a cellular population to create artificial biosystems that
can meet various needs in the fields of health care,
nanotechnology, energy and chemistry.
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Synthetic biology is an emerging scientific discipline that promotes a
standardized design and manufacturing of biological system
components without natural equivalents (Endy 2005). It is
currently in search of design principles to achieve a reliable
and secure level of functionality from reusable biological parts
(e.g. BioBricks, Knight 2003).
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iscpif.fr
