docs(mTNBC): rename tnbc -> mTNBC and update plan.md with full QSP mo…#4
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wjdals011106 wants to merge 9 commits into
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docs(mTNBC): rename tnbc -> mTNBC and update plan.md with full QSP mo…#4wjdals011106 wants to merge 9 commits into
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…del details - Renamed tnbc/ folder to mTNBC/ for clarity - Updated plan.md with detailed equations, parameters, and calibration targets extracted from paper (Arulraj et al., Sci. Adv. 2023) and Data_S1.xlsx - Added key parameter values with units and literature sources - Added KEYNOTE-119 calibration targets and baseline species ranges - Added top predictive biomarkers table from Data_S2.xlsx - Added RECIST v1.1 response evaluation criteria Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Implements Arulraj et al. (2023) mTNBC QSP model: - 01_parameters.R: 737 parameters (cancer growth, T cells, APC, cytokines, macrophages, MDSC, pembrolizumab PK, checkpoint molecules) - 02_model_ode.R: Full ODE system (12 modules - Gompertz growth, T cell trafficking & activation, PD-1/PD-L1 checkpoint, macrophage polarization, MDSC, cytokines, APC maturation, pembrolizumab PK/PD) - 03_events.R: Discrete events (200mg IV q3w dosing, metastatic seeding, surgery) - 04_rules.R: Algebraic rules (tumor volume, RECIST SLD, Shannon index, biomarker fractions) - 05_initial_conditions.R: Initial conditions from Data_S1.xlsx Species sheet - 06_simulation.R: deSolve ODE runner + RECIST v1.1 response evaluation - 07_virtual_patients.R: LHS-based VP generation (127 uncertain parameters) - 08_biomarker_analysis.R: Response probability + RIS computation - 09_visualization.R: Waterfall, spider, tumor growth, biomarker ranking plots - utils.R: Helpers (Shannon index, parallel VP runner, parameter validation) - main.R: Full pipeline (step1-step5 + run_full_pipeline()) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…n pipeline - 02_model_ode.R: fix derivative assembly order to match IC variable order exactly (was causing cross-contamination between antigen-specific T cell compartments) - 05_initial_conditions.R: set quasi-steady-state ICs for all T cell pools (LN activation, central, peripheral, tumor-infiltrating) to resolve stiffness - 01_parameters.R: add ncells_C* defaults for metastatic seeding compartments - 03_events.R: already correct, confirmed working with event-driven dosing - 06_simulation.R: fix atol/rtol (1e-6/1e-4) to prevent vode step collapse - app.R: new Shiny dashboard with 5 tabs — simulation setup, tumor growth, immune response, RECIST assessment, and biomarker visualization - .gitignore: exclude test/debug scripts and output directory Simulation validated: t=0→300 days, BOR=PR, tumor 0.40→0.04 cm (pembrolizumab) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- poster_draft.html: A0 3-column poster with SVG figures, tables, equations Sections: background, model architecture, key equations, parameters (Table 1), tumor dynamics graph (Fig.1), immune cell dynamics graph (Fig.2), biomarker results (Table 2), Shiny app mockup (Fig.3), conclusions Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
This reverts commit 698eaad.
…imulation pipeline" This reverts commit 896edb6.
- 5-tab shinydashboard: 시뮬레이션 설정, 종양 성장, 면역 반응, RECIST 평가, 바이오마커 - Interactive parameter controls: dose, growth rate, immune parameters, metastatic seeding - Tumor diameter plot, SLD waterfall, clone composition, immune cell dynamics - RECIST v1.1 auto-assessment with infoBox summary (BOR, SLD%, responder status) - Biomarker visualization: Shannon diversity, M2/M1 ratio, PD-L1, immune fractions Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- 02_model_ode.R: ODE assembly order fixed to match IC variable order - 05_initial_conditions.R: quasi-SS initial values for all T cell pools - 01_parameters.R: add ncells_C* defaults for metastatic seeding - 03_events.R: event-driven dosing/seeding closure fix - 04_rules.R: RECIST SLD and biomarker computation - 06_simulation.R: atol=1e-6, rtol=1e-4, hmax=1.0 for numerical stability Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- README: 박정민 Shiny App URL 추가 https://wjdals011106.shinyapps.io/tnbc-qsp-simulator/ Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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…del details