Various computational approaches, model organisms, and their associated developmental processes

Get to know your fellow group members and collaborators.

Various methods employed by the DevoWorm group.

Graphical Analysis of Developmental Trees (AoDT):

Information Isometry (see Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages. bioRxiv, doi:10.1101/062539).

AoDT Github repository link.

Cell Type Alignment:

CAST Alignment (see Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development Via Differentiation Trees of Embryos. Biology, 5(3), 33).

CAST Alignment Demo link.

Machine Learning:

OpenDevoCell repository link.

Digital Bacillaria repository link.

Embryo Networks:

4-dimensional Structure (see Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis). BioSystems, 173, 235-246).

Theoretical Types of Embryo/Developmental Networks link

Embryogenetic Connectome Github repository link.

Dynamical Heterochrony:

Jupyter Notebook and Manuscript link.

Triangular State Machines (TSMs):

Github repository link.

Educational resources for the DevoWorm group


Developmental Data Science link

Tutorials on Pattern Formation link

Dynamical Systems and Development link

Models and Representations link

Microcredentials from Badgelist (OpenWorm Foundation digital badges):

Worm development I: Embryogenesis link

Worm Development II: Larval Development link

Video Lectures:

Digital Biology and Open Science -- the coming revolution, Dr. Stephen Larson (OpenWorm Foundation) at TEDx link

Caenorhabditis elegans: a model organism, Science of Biology link

Online Developmental Biology: Introduction to C. elegans, Dr. Jason Pellettieri at Online Developmental Biology link

Tutorials/Reading List:

Basic biology references and key papers link

Guidelines for Creating Open Datasets link