Signaling Pathways — Boolean & Rule-Based Modeling (Hands-on)

Learn two powerful paradigms for signaling: discrete logical models (Boolean/multi-valued) for large-scale pathway reasoning and rule-based models for site-specific biochemical interactions without reaction explosion. You will curate networks, encode logic/rules, simulate dynamics (steady states, attractors, perturbations) , and package models with community standards (SBGN-PD, SBML-qual, SED-ML) .

Signaling Pathways — Boolean & Rule-Based Modeling

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Session Index

Session 1 — Pathway Curation & Logical Modeling Basics Session 2 — Boolean/Multi-Valued Dynamics & Perturbations Session 3 — Rule-Based Modeling (BioNetGen/Kappa/PySB) Session 4 — Mini Capstone: Logic ↔ Rules Integration

Session 1

Fee: Rs 8800

Pathway Curation & Logical Modeling Basics

From biology to logic: nodes, edges, update rules

activation/inhibition logic gates & truth tables multi-valued states

Toolchain & standards

GINsim / CellNOpt / PyBoolNet MaBoSS (probabilistic Boolean) SBGN-PD / SBML-qual

Curation inputs & mapping

KEGG/Reactome to logic text-mined edges evidence tagging

Session 2

Fee: Rs 11800

Boolean/Multi-Valued Dynamics & Perturbations

Dynamics & attractors

synchronous vs. asynchronous updates state transition graphs trap spaces & basins

Perturbations & control

knockouts/overexpression drug/mock interventions attractor control targets

Calibration & validation

CellNOpt with phospho-proteomics MaBoSS parameter scans logic → SBML-qual export

Session 3

Fee: Rs 14800

Rule-Based Modeling (BioNetGen/Kappa/PySB)

From reactions to rules: sites, states, bonds, patterns

combinatorial complexity rule application & matching observable definitions

Tools & simulation modes

BioNetGen (BNGL) Kappa (KaSim) PySB (Python API)

Parameterization & analysis

GSA/sensitivity parameter scans export to SBML/SED-ML

Session 4

Fee: Rs 18800

Mini Capstone: Logic ↔ Rules Integration

Case study: receptor → TF cascade (logic prototype → rule-based refinement)

Theory + Practical

Calibration, scenarios & packaging

drug perturbations dose–response & robustness SBML-qual/SBML + SED-ML bundle

Deliverables

PDF/HTML report .gin/.bnet/.cfg (logic) & .bngl/.ka/.py (rules) environment.yml/requirements.txt

PDF

Signaling Pathways — Boolean & Rule-Based Modeling Training | GINsim, MaBoSS, BioNetGen/Kappa

Signaling Pathways — Boolean & Rule-Based Modeling (Hands-on)