Perturbation Experiments, Design & Model Fitting — Hands-on

Learn how to design perturbation experiments and link them to dynamic models for mechanistic insight. This module covers planning drug or genetic perturbations, collecting and curating time course and dose response data, and fitting and validating models against these experiments for quantitative systems biology.

Perturbation Experiments, Design & Model Fitting

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Session Index

Session 1 — Principles of Perturbation Experiments Session 2 — Time Course, Dose Response & Data Quality Session 3 — Model Fitting to Perturbation Data Session 4 — Mini Capstone: Design & Fit a Perturbation Study

Session 1

Fee: Rs 8800

Principles of Perturbation Experiments

Perturbation types and readouts

drug and small molecule perturbations CRISPR or RNAi style concepts signal, phenotype and omics readouts

Experimental design and controls

replicates and blocking ideas negative and positive controls baseline and vehicle conditions

Design for model identifiability and insight

choice of stimuli and schedules which species to measure linking design to model questions

Session 2

Fee: Rs 11800

Time Course, Dose Response & Data Quality

Time course and dose response basics

sampling schedules and resolution dose ranges and spacing single versus multiple hits

Data QC and normalization concepts

baseline correction ideas outlier checks and flags batch and plate effects overview

Summarizing perturbation responses for modeling

mean and variability signals simple effect size views data formats for model fitting tools

Session 3

Fee: Rs 14800

Model Fitting to Perturbation Data

Choosing model structures and observables

simple ODE motifs for responses link functions to measurements handling measurement noise conceptually

Parameter estimation and fit diagnostics

cost functions and residuals goodness of fit summaries overfitting and parsimony awareness

Using perturbation data to refine models

accept or reject model structures updating assumptions and parameters planning follow up experiments

Session 4

Fee: Rs 18800

Mini Capstone: Design & Fit a Perturbation Study

Define a small perturbation based systems question

theory plus guided practical

Work through design, data mock up and model fitting

time points and doses plan synthetic or provided datasets fit model and inspect diagnostics

Deliverables: notebook, design sheet and short report

Python or R notebook design summary in table form PDF or HTML project summary

PDF

Perturbation Experiments, Design & Model Fitting Training | Link Experiments & Dynamic Models

Perturbation Experiments, Design & Model Fitting — Hands-on