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DevoWorm

The DevoWorm website is located at devoworm.weebly.com. The website features links to educational, academic, media-related and collaborative opportunities associated with the project. DevoWorm is affiliated with the OpenWorm Foundation and the Orthogonal Research Laboratory. We engage in Open Science, an encourage the use of Jupyter Notebooks, short video descriptions of research, and demos.

Roadmap

DevoWorm is currently divided into three loosely-knit interest areas: developmental dynamics, cybernetics and digital morphogenesis, and reproduction and developmental plasticity. While our main interest is in the nematode Caenorhabditis elegans, we are also interested in cross-species comparative work.

Developmental Dynamics currently involves using secondary data collected from embryos along with bioinformatic and data science techniques to answer questions regarding the process of early embryogenesis and the timing of later morphogenesis. To address these problems, we have used number of innovative approaches.

Cybernetics and Digital Morphogenesis has involved using platforms such as Morphozoic (Cellular Automata) or CompuCell3D (Cellular Potts Model) to better understand physical interactions during embryogenesis and morphogenesis. We have also explored the use of cybernetic models and concepts to better understand the general process of embryogenesis.

Reproduction and Developmental Plasticity involves utilizing an evo-devo approach to understand Caenorhabditis elegans more generally. Our existing datasets and papers include a focus on larval development and life-history processes. This area of the project also features primary empirical data, based on formal experimental design.

Objective Examples
Developmental Dynamics (DD) Comparative Quantitative Embryogenesis
DD Differentiation Trees and Maps
DD Embryo Networks and Developmental Connectomes
DD Time-series of Terminal Differentiation
Cybernetics and Digital Morphogenesis (C-DM) Morphozoic (Cellular Automata)
C-DM Cybernetic Embryo
C-DM CompuCell 3D
Reproduction and Developmental Plasticity (R-DP) Experimental Evolution
R-DP Life-history Plasticity

Repos in DevoWorm Github

Repo Name Description
Google Summer of Code 2017 GSoC Activities for 2017
CC3D CompuCell 3D Models
Embryogenetic Connectome Embryogenetic Connectome Analysis
Assorted Notebooks Project-related Jupyter Notebooks
Graphical Visualization Code for Graph Creation
Datasets and Analysis Tools for Developmental Data Science
Morphozoic Morphozoic Models