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DevoWorm

The DevoWorm group website is located at devoworm.weebly.com. The website features links to educational, academic, media-related and collaborative opportunities associated with the project. The DevoZoo is located at devoworm.github.io, and features content relevant to community education and engagement. 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. We also have three additional types of initiative which cross-cut the interest areas: theory-building, education, and open science. These initiatives are infused into our interest areas.

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 and theoretical approaches such as Multicell Systems and Braitenberg Vehicles 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)
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)
C-DM Morphozoic (Cellular Automata)
C-DM Multicell Systems
C-DM Braitenberg's Vehicles and Games
Reproduction and Developmental Plasticity (R-DP)
R-DP Experimental Evolution
R-DP Life-history Plasticity
R-DP Dynamical Heterochrony

Repos in DevoWorm Github

Repo Name Description
DevoWorm Basic Secondary C. elegans Embryogenetic Data
Embryo Segmentation Embryo Segmentation Software (GSoC 2017)
Devlopmental XML and Networks Developmental XML and Networks (GSoC 2018)
Semantic Phenotypes Semantic Phenotypes (GSoC 2019)
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
Analysis of Developmental Trees (AoDT) Analysis of Developmental Trees (AoDT)
OW-DW Education OpenWorm-DevoWorm Education (Curriculum-building)
TSMs Triangular State Machine (TSMs)
Zebrafish Embryo Zebrafish Embryo
n-D Visualization n-D Visualization
Drosophila Imaginal Disc Segmentation Drosophila Imaginal Disc Segmentation
Drosophila Embryo (fused cell centroids) Drosophila Embryo (fused cell centroids)
Digital Bacillaria Quantifying Bacillaria (Diatom) Phenotypes
Mouse Embryo (Zygote to Blastocyst) Data from Early Mouse Embryo
DW-ML DevoWormML (interest area for applied Machine Learning)
AoDT Analysis of Developmental Trees
Compositionality Compositionality and Category Theory as Applied to Development
Macro-Mechanisms for Embryogenesis Collective Mechanisms of Morphogenesis in Embryos
Experimental Evolution Experimental Evolution in C. elegans
Triangular State Machines - TSM Theoretical Gene Expression Network Motifs
Theoretical-Types-of-Embryo-Developmental-Networks Graph Theory as Applied to Development
Raising the Worm Brain Functional Developmental Connectomes
Emergent Behavior Behavioral Emergence in Development
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