Single Cell & Spatial Systems Modeling — Hands-on

Connect single cell and spatial omics data to systems biology models. This module covers concepts of cell state dynamics, trajectories and lineage, spatial context and microenvironments, and how to build simplified models that link single cell views to tissue level behaviors for hypothesis generation and prediction.

Single Cell & Spatial Systems Modeling

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Session Index

Session 1 — Cell States, Trajectories & Lineages Session 2 — Spatial Context, Niches & Microenvironments Session 3 — Linking Single Cell & Spatial Data to Models Session 4 — Mini Capstone: Single Cell plus Spatial Model Sketch

Session 1

Fee: Rs 8800

Cell States, Trajectories & Lineages

Single cell states and phenotypic landscapes

cell state clusters and continua attractors as phenotypes (concept) plasticity and heterogeneity

Pseudotime, trajectories and lineage ideas

trajectory inference concepts branching and fate decisions lineage trees vs state graphs

Dynamic systems views of cell state changes

state space and flows intuition stability and switching concepts links to GRN and signaling motifs

Session 2

Fee: Rs 11800

Spatial Context, Niches & Microenvironments

Basics of spatial omics and tissue maps

spots, pixels and cells idea neighborhood and distance concepts regions of interest in tissues

Cell niches, microenvironments and interactions

paracrine and juxtacrine views immune and stromal neighborhoods gradients and diffusion intuition

Patterns, domains and tissue level organization

spatial domains and boundaries interface and invasion zones links to development and disease

Session 3

Fee: Rs 14800

Linking Single Cell & Spatial Data to Models

From clusters and maps to model ingredients

defining cell types and states estimating densities and compositions summaries as model parameters

Simple models for single cell and spatial dynamics

birth death and transition schemes lattice or grid based sketches linking to PDE or ABM ideas

Model outputs back to data space for checks

marginal distributions and maps patterns and gradients qualitative fit and scenario views

Session 4

Fee: Rs 18800

Mini Capstone: Single Cell plus Spatial Model Sketch

Choose a small single cell plus spatial question

theory plus guided practical

Summarize example data and map to a simple model

cell state and spatial summaries define basic dynamic rules explore a few scenarios

Deliverables: notebook, schematic and short note

Python or R notebook diagram of tissue and states PDF or HTML summary

PDF

Single Cell and Spatial Systems Modeling Training | From Cell States to Tissue Patterns

Single Cell & Spatial Systems Modeling — Hands-on