DevoWorm
Developmental and computational biology centered on C. elegans and other model organisms
DevoWorm is a working group studying the development of the nematode Caenorhabditis elegans and other model organisms through simulation, network analysis, and visualization. Founded in 2014 and led by Dr. Bradly Alicea, the group brings together biologists, computer scientists, and educators to map how cells, tissues, and behavior emerge during embryogenesis — and how those processes can be represented as computable data.
The group works across multiple model systems including C. elegans, Drosophila melanogaster, diatoms (Bacillaria), and broader comparative development. Active research lines include differentiation waves, connectome emergence, machine-learning analysis of embryo images, and theoretical frameworks for morphogenesis and the origin of life.
DevoWorm is hosted by the OpenWorm Foundation and Orthogonal Research and Education Laboratory (OREL), and serves as a sister group to the Representational Brains and Phenotypes working group.
Further Information
- For software, datasets, tutorials, and the full publication record, see the DevoWorm site
- For extended Google Summer of Code information, view the GSoC Historical Archive
Active Research Lines
- Embryogenesis and differentiation waves in C. elegans and comparative model organisms
- Developmental connectome emergence and neural-activity onset
- Diatom and Bacillaria motility analysis with deep learning (Digital Diatom)
- DevoLearn — open-source machine-learning models and education for developmental biology
- Cellular automata, hypergraphs, and theoretical morphogenesis
- Origin of life and ensemble approaches to early evolution
Training and Community
DevoWorm has supported Google Summer of Code scholars since 2018 through its OpenWorm Foundation affiliation, alongside the DevoWormML interest group, the DevoZoo educational resource, and an ongoing seminar series.
Projects
D-GNNs: DevoGraph for Computational Developmental Biology
Graph neural networks for modeling developmental biological processes
D-GNNs: developing DevoGraph for computational developmental biology
DevoTG: Dynamic Graph Neural Networks for Modeling C. elegans Development
Dynamic graph neural networks for modeling the temporal development of the C. elegans embryo.
NDP-HNN: Modelling Neural Developmental Programs of C. elegans Using Growing Hypergraph Neural Networks
Growing hypergraph neural networks for modeling the neural developmental programs of C. elegans.
Digital Microsphere
Building the Digital Microsphere for modeling early embryonic development.
GNNs as Developmental Networks
Treating graph neural networks as models of biological developmental networks.
Modeling Axolotl Embryos
Computational modeling of axolotl embryo development within the Digital Microsphere effort.
Improving DevoLearn
Extending and improving the DevoLearn library for computational developmental biology.
OpenDevoCell Integration
Integrating and extending the OpenDevoCell platform for cell-level developmental analysis.
Pre-trained Models for Developmental Neuroscience
Developing pre-trained machine learning models for developmental neuroscience tasks.
Semantic Segmentation of the Embryogenetic Process
Semantic segmentation of microscopy data capturing the embryogenetic process.
Developmental Networks and XML Frameworks for the C. elegans Embryo
Developmental network models and XML data frameworks for the C. elegans embryo.
Image Processing with ImageJ (Segmentation of High-Resolution Images)
ImageJ-based processing and segmentation of high-resolution developmental microscopy images.
Publications
An Ensemble Approach to the Origin of Life
Origin of Life via Archaea, Chapter 8
The Molecular Basis of Differentiation Wave Activity in Embryogenesis
BioSystems, 105272
Embodied Cognitive Morphogenesis as a Route to Intelligent Systems
Royal Society Interface Focus, 20220067
Hypergraphs Demonstrate Anastomoses During Divergent Integration
arXiv:2311.17067
Updates from the OpenWorm Project: Incorporating NeuroPAL Data and ASH Neuron Electrophysiological Recordings
International C. elegans Conference, Glasgow, Scotland
The Psychophysical World of the Motile Diatom Bacillaria Paradoxa
Mathematics and Biology of Diatoms, Chapter 9
DevoLearn: Machine Learning Models and Education that Enable Computational Developmental Biology
INCF / DevoLearn
Game Theory of Developmental Processes
Dynamics Days 2022, Atlanta, GA
Game Theory of Developmental Processes
ResearchGate
Mathematics of DevoWorm
Find Your Inner Modeler V, University of Illinois–Chicago
Data-theoretical Synthesis of the Early Developmental Process
Neuroinformatics
Neuromorphogenetic Patterns and the Theory of Deep Learning
NetNeuro Satellite, Networks Conference
The OpenWorm Project: Progress Update, Available Resources and Future Plans
International C. elegans Conference (Virtual)
Periodicity in the Embryo: Emergence of Order in Space, Diffusion of Order in Time
BioSystems, 204, 104405
Towards a Digital Diatom: Image Processing and Deep Learning Analysis of Bacillaria paradoxa Dynamic Morphology
Diatom Gliding Motility
Elementary Morphogenetic Cellular Automata for Modeling Developmental Phenotypes
ResearchGate
Raising the Connectome: The Emergence of Neuronal Activity and Behavior in C. elegans
Frontiers in Cellular Neuroscience
A New Kind of Developmental Biology
Find Your Inner Modeler III, University of Alabama–Birmingham
Cell Differentiation Processes as Spatial Networks: Identifying Four-dimensional Structure in Embryogenesis
BioSystems, 173, 235–246
Data Repository for "Morphogenetic Processes as Data: Quantitative Structure in the Drosophila Eye Imaginal Disc"
Open Science Framework
Embryo Networks and Connectomes in Caenorhabditis elegans
Open Science Framework
Morphogenetic Processes as Data: Quantitative Structure in the Drosophila Eye Imaginal Disc
BioSystems, 173, 256–265
OpenWorm: Overview and Recent Advances in Integrative Biological Simulation of Caenorhabditis elegans
Philosophical Transactions of the Royal Society B, 373, 20170382
The Emergent Connectome in Caenorhabditis elegans Embryogenesis
BioSystems, 173, 247–255
Morphognosis: The Shape of Knowledge in Space and Time
arXiv:1701.02272
Data from: Evolution in Eggs and Phases
Dryad
Evolution in Eggs and Phases: Experimental Evolution of Fecundity and Reproductive Timing in Caenorhabditis elegans
Royal Society Open Science, 3, 160496
Genotype-specific Developmental Plasticity Shapes the Timing and Robustness of Reproductive Capacity in Caenorhabditis elegans
bioRxiv
Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages
bioRxiv
Morphozoic: Cellular Automata with Nested Neighborhoods as a Metamorphic Representation of Morphogenesis
Multi-Agent Based Simulations Applied to Biological and Environmental Systems, Chapter 3
Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development via Differentiation Trees of Embryos
Biology, 5(3), 33
DevoWorm: Raising the Worm on Datapoints, Trees, and Matrices
20th International C. elegans Conference, Los Angeles, CA
Network Architecture of Embryo Developmental Regulation
Network Frontiers Workshop, Northwestern University
DevoWorm: Differentiation Waves and Computation in C. elegans Embryogenesis
bioRxiv