DevoWorm: raising the (Open)Worm
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.