grammar_samples - v2.0.1

Minor bug fixes and addition of data analysis script. See v2.0.0 for more details.

- Jupyter Notebook
Published by drbergman 7 months ago

grammar_samples - v2.0.0 - sync with PhysiCell 1.14.1

This release contains the models and associated scripts used in Digitize your Biology! Modeling multicellular systems through interpretable cell behavior as of February 20, 2025. All examples were developed using PhysiCell 1.14.1.

Refinements and Upgrades:

• Model 1: Modeling the progression of hypoxia in a metastatic tumor (link). This model represents oxygen-dependent tumor growth, incorporating mechano-feedback mechanisms and hypoxia-induced cell migration. Sensitivity analysis was performed on this example.
• Model 2: Fibroblast-mediated invasion of neoplastic cells (link) This model represents the interactions between neoplastic cancer cells and fibroblasts in the context of cancer invasion. Two scenarios are considered:
  • Coculture experiment
  • Patient-derived samples
• Model 3: Base tumor-immune example (link) This model represents the basic interactions between the tumor and the immune system, incorporating immune responses such as macrophage polarization and CD8 T cell cytotoxicity. Sensitivity analysis was performed on this example.
• Model 4: Extended tumor-immune example (link) This model extends the base tumor-immune model by including distinct macrophage states and naive CD8 T cells that can become activated.
• Model 6: PDAC immunotherapy example (link) This model represents tumor-immune interactions in pancreatic ductal adenocarcinoma (PDAC), incorporating the effects of immunotherapies. Initial conditions represent 16 different samples, each treated with one of eight therapies, considering combinations of GVAX (GVAX), nivolumab (ICI), and urelumab (URU).

New examples:

• Model 5: Tumor-associated macrophage and EGFR signaling example (link) This model represents interactions between tumor cells and tumor-associated macrophages (TAMs), incorporating the effects of EGFR signaling on tumor growth and motility. Three hypotheses are tested:
  • EGFR signaling increases tumor growth.
  • EGFR signaling increases tumor motility.
  • EGFR signaling increases both tumor growth and motility.
• Model 7: Neurodevelopment example (link) This model represents the formation of the laminar structure of the cortex, incorporating asymmetric division of a progenitor layer and neuronal migration to form cortical layers. Two configuration files represent different cortical regions:
  • SOM: Somatosensory cortex
  • AUD: Auditory cortex

- Jupyter Notebook
Published by heberlr about 1 year ago

grammar_samples - Version 1.0.0

This version is compatible with version 1 of the manuscript: Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.

- Jupyter Notebook
Published by heberlr over 1 year ago