Cognisom

World's first multi-scale cellular simulator with molecular sequence tracking—from DNA mutations to tissue dynamics

Production ReadyGPU ComputingCancer ResearchImmunotherapyCUDASystems BiologyPrecision MedicineOpen Source

Production-Ready Platform

Cognisom is fully functional with GUI, API, and cloud deployment capabilities. Currently running at 100+ cells, seeking GPU credits to scale to 100,000+ cells for organ-scale cancer simulations.

~6,000 lines of code62 docs (15K+ lines)MIT License

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See Cognisom in Action

Multi-scale cellular simulation with molecular sequence tracking

Watch real-time cellular simulation showing multi-scale biological processes from molecular interactions to tissue dynamics

Key Innovation

World's First Multi-Scale Cellular Simulator with Molecular Sequence Tracking

Unlike existing simulators that use abstract molecular counts, cognisom tracks actual DNA/RNA sequences (ATCG/AUCG bases) with real mutations, enabling unprecedented mechanistic insight into cancer development, immune response, and treatment resistance.

Real DNA/RNA sequences with known oncogenic mutations (KRAS G12D, TP53 R175H, BRAF V600E)

Exosome-mediated molecular transfer between cells (cancer transmission mechanism)

Detailed immune system (T cells, NK cells, macrophages with recognition mechanisms)

Multi-system tissue architecture (vascular, lymphatic, immune, spatial)

Circadian clock integration (chronotherapy optimization)

Morphogen gradients and spatial patterning

Epigenetic regulation (DNA methylation, histone modifications)

Real-time 3D interactive visualization

9 Integrated Biological Modules

Cognisom is the ONLY platform with all these features integrated into a single, cohesive system.

Molecular

DNA/RNA sequences, gene expression, mutations, exosomes

Cellular

Cell cycle, metabolism, division, death, transformation

Immune

T cells, NK cells, macrophages, surveillance, killing

Vascular

Capillary networks, oxygen/nutrient delivery, angiogenesis

Lymphatic

Drainage, immune trafficking, metastasis pathways

Spatial

3D positioning, diffusion fields, gradient formation

Epigenetic

DNA methylation, chromatin states, gene silencing

Circadian

24-hour clocks, timing effects, chronotherapy

Morphogen

Gradient sensing, positional information, cell fate

Event-Driven Architecture

• 243,000+ events/second - High-performance event bus

• Modular plugin system - Easy extension and customization

• Real-time control - Parameter adjustment on-the-fly

• ~500KB memory - Efficient for 25 cells + 16 immune cells

Vision

To simulate and visualize full organ somatic tissue communication and messaging at the cellular level, creating the world's most comprehensive platform for understanding how organs function as integrated systems.

Our initial focus is prostate cancer—modeling initiation, progression, immune evasion, and metastasis to enable precision medicine through digital organ simulation.

Platform Demo

Watch cellular simulation in action

Real-time cellular simulation showing multi-scale biological processes from molecular interactions to tissue dynamics

Current Performance

100+

Cells Simulated

19.9

Steps/Second

Active Modules

Real-time

3D Visualization

GPU Acceleration Roadmap

Phase 1: Months 1-2

GPU Integration

• Port core modules to CUDA

• GPU spatial indexing

• Memory optimization

Target: 10,000 cells

Phase 2: Months 3-4

Multi-GPU

• Distributed computing

• Domain decomposition

• Load balancing

Target: 100,000 cells

Phase 3: Months 5-12

Production Scale

• Million-cell simulations

• Real-time organ modeling

• Clinical deployment

Target: 1,000,000+ cells

Research Applications

Cancer Biology

• Model tumor growth and microenvironment

• Simulate immune surveillance and evasion

• Track metastatic pathways

• Predict treatment resistance mechanisms

Immunotherapy

• Simulate checkpoint blockade (anti-PD-1/PD-L1)

• Model CAR-T therapy efficacy

• Optimize combination therapies

• Chronotherapy timing optimization

Drug Development

• Virtual compound screening in silico

• Optimize dosing schedules

• Discover predictive biomarkers

• Enable patient stratification

Precision Medicine

• Build patient-specific models

• Forecast treatment response

• Predict clinical outcomes

• Guide treatment decisions

Clinical Focus: Prostate Cancer

Why Prostate Cancer?

Prevalence

Most common cancer in men (1 in 8)

Mortality

35,000+ deaths/year in US

Clinical Need

Metastatic disease is incurable

Data Availability

Well-characterized biology and genomics

Specific Goals

• Model primary tumor growth and microenvironment

• Simulate immune surveillance and evasion mechanisms

• Track metastatic pathways (lymphatic → bone)

• Predict treatment response and resistance

• Optimize chronotherapy timing for enhanced efficacy

• Enable patient-specific simulations for precision medicine

Demonstrated Capabilities

Working demos prove the platform's ability to model complex biological phenomena

Cancer Transmission via Exosomes

Result: 3/4 normal cells transformed in 5 hours

Mechanism: Oncogenic mRNA transfer (KRAS G12D)

First simulator to model molecular cancer transmission

Immune Surveillance

Result: 5 cancer cells killed by T/NK cells

Mechanism: MHC-I recognition and cytotoxic killing

Detailed immune cell recognition mechanisms

Tissue Architecture

Components: 100 epithelial + 33 immune cells

Systems: 8 capillaries + 4 lymphatic vessels

Size: 200 × 200 × 100 μm tissue volume

Real-Time Visualization

Interface: 9-panel dashboard with 3D tissue view

Features: Live statistics and monitoring

Control: Interactive parameter adjustment

Multiple User Interfaces

Desktop GUI Control Panel

• Interactive Tkinter-based interface

• Real-time simulation control

• Parameter adjustment on-the-fly

• Live statistics and monitoring

Web Dashboard

• Browser-based interface

• REST API backend (Flask)

• Multi-panel visualization

• Data export (CSV, JSON, HTML, LaTeX)

Command-Line Interface

• Interactive menu system

• Scenario library

• Batch processing

• Scripting support

Programmatic API

from core import SimulationEngine
engine = SimulationEngine()
engine.register_module('cellular')
engine.run(duration=24.0)

Competitive Position

Cognisom vs. Existing Platforms

Cognisom is the ONLY platform with all these features integrated

Feature	PhysiCell	VCell	CompuCell3D	cognisom
Molecular sequences	❌	❌	❌	✅
Exosome transfer	❌	❌	❌	✅
Detailed immune	❌	❌	❌	✅
Circadian clocks	❌	❌	❌	✅
Real-time GUI	❌	❌	❌	✅
Open source	✅	✅	✅	✅