12 Sep 2014
They say it takes a village to raise a child. In this case, the village is raising… A WORM!. OpenWorm’s main focus recently has been to emulate the whole C. elegans worm, with a focus on the nervous system in an adult worm’s body. However, a new subgroup is opening up within the project called DevoWorm, which seeks to simulate the cell-by-cell divisions and growth that leads to the adult. C. elegans is the optimal candidate system to study this process on a cell-by-cell basis because every cell in every developmental lineage is known and labelled.
The ultimate goal of the DevoWorm project is to create a simulation of highly-specified organismal development, where virtual variations can be introduced at various stages of development.
Presenting DevoWorm is Dr. Bradly Alicea. He has a Masters degree from the University of Florida and a PhD from Michigan State University. He has published in multiple academic fields, and in venues including Nature Reviews Neuroscience, Stem Cells and Development, and Proceedings of Artificial Life. He will be joined by Dr. Richard Gordon, Director & Theoretical Biologist at the Embryogenesis Center, Gulf Specimen Marine Laboratory, Inc., and one of the founders of the DevoWorm project.
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ABSTRACT
From synthetic biology to software development, collaborative efforts have allowed us to "hack at" incredibly complex systems. When hackathon efforts are done at scale, we can produce sparsely represented emulations of these systems. While these efforts might yield immediate (albeit small-scale) rewards, the broader implications are typically not a part of such efforts. As OpenWorm is an attempt to emulate the whole organism (C. elegans), DevoWorm is an attempt to emulate developmental processes that lead to the adult C. elegans. Such a meta-emulation is useful in a number of ways, from providing crucial information about development itself to providing a combinatorial source of developmental outcomes for evaluating phenotypic mutants. Therefore, we will discuss not only how emulation of C. elegans development can proceed, but also how this is relevant to a broader developmental perspective. We will primarily focus on the embryogenetic aspects of mosaic development, and how using a differentiation tree approach can provide multi-axis resolution to the process of cell division and identity. Information on the use of multiple datatypes such as gene expression, microscopy, and semantic metadata will also be featured. In conclusion, we will consider the limitations of developmental simulations and how they can be useful heuristics for enabling better cell, molecular, and computational biology.
The ultimate goal of the DevoWorm project is to create a simulation of highly-specified organismal development, where virtual variations can be introduced at various stages of development.
Presenting DevoWorm is Dr. Bradly Alicea. He has a Masters degree from the University of Florida and a PhD from Michigan State University. He has published in multiple academic fields, and in venues including Nature Reviews Neuroscience, Stem Cells and Development, and Proceedings of Artificial Life. He will be joined by Dr. Richard Gordon, Director & Theoretical Biologist at the Embryogenesis Center, Gulf Specimen Marine Laboratory, Inc., and one of the founders of the DevoWorm project.
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ABSTRACT
From synthetic biology to software development, collaborative efforts have allowed us to "hack at" incredibly complex systems. When hackathon efforts are done at scale, we can produce sparsely represented emulations of these systems. While these efforts might yield immediate (albeit small-scale) rewards, the broader implications are typically not a part of such efforts. As OpenWorm is an attempt to emulate the whole organism (C. elegans), DevoWorm is an attempt to emulate developmental processes that lead to the adult C. elegans. Such a meta-emulation is useful in a number of ways, from providing crucial information about development itself to providing a combinatorial source of developmental outcomes for evaluating phenotypic mutants. Therefore, we will discuss not only how emulation of C. elegans development can proceed, but also how this is relevant to a broader developmental perspective. We will primarily focus on the embryogenetic aspects of mosaic development, and how using a differentiation tree approach can provide multi-axis resolution to the process of cell division and identity. Information on the use of multiple datatypes such as gene expression, microscopy, and semantic metadata will also be featured. In conclusion, we will consider the limitations of developmental simulations and how they can be useful heuristics for enabling better cell, molecular, and computational biology.
- 5 participants
- 1:18 hours
