Synthetic Ecology & Consortia Design (In Silico) — Hands-on

Engineer synthetic microbial consortia using rigorously validated in silico methods. This hands-on module covers generalized Lotka–Volterra (gLV) and genome-scale, constraint-based community modeling to predict interactions, cross-feeding, growth, and productivity. You will use COBRApy/MICOM/SMETANA/COMETS and design strategies (OptKnock/OptCouple/OptAux) to optimize media, fluxes, and stability, culminating in a reproducible design dossier ready for bench testing.

Synthetic Ecology & Consortia Design (In Silico)

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Session Index

Session 1 — Interaction Models: gLV & Data Fitting Session 2 — GEMs & Community FBA (COBRA/MICOM) Session 3 — Cross-Feeding, Media & Design Algorithms Session 4 — Dynamics, Robustness & Design Dossier

Session 1

Fee: Rs 8800

Interaction Models: gLV & Data Fitting

Pairwise & multispecies gLV models

competition, mutualism, parasitism stability & equilibria parameter identifiability

Fitting to time-series/absolute abundance

regularization & cross-validation compositional→absolute via refs forecasting & uncertainty

Perturbation & control concepts

invasibility & resilience feedback & set-point shifts designable attractors

Session 2

Fee: Rs 11800

GEMs & Community FBA (COBRA/MICOM)

Genome-scale metabolic models (GEMs)

ModelSEED/KBase drafts gapfilling & curation exchange/bounds setup

Community FBA & coupling

MICOM/SMETANA/OptCom Pareto fronts & trade-offs secretion/uptake constraints

dFBA & spatial simulations (overview)

COMETS-style dynamics batch vs chemostat bioreactor heuristics

Session 3

Fee: Rs 14800

Cross-Feeding, Media & Design Algorithms

Metabolite exchange & niches

SMETANA scores auxotrophies & complementarity syntrophy vs competition

Media & intervention optimization

OptKnock/OptCouple/OptAux feed strategies & supplements target metabolite yield

Safety & constraints

containment objectives antagonists/kill-switch proxies off-target metabolite limits

Session 4

Fee: Rs 18800

Dynamics, Robustness & Reproducible Design Dossier

Dynamic & spatial scenarios

dFBA chemostat/batch biofilm/plug-flow heuristics shock & invasion tests

Sensitivity & robustness

Morris/variance-based SA parameter/posterior sweeps fail-safe criteria

Design dossier & deliverables

Quarto report + model cards SBML/JSON models & env files SOPs & testable hypotheses

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Synthetic Ecology & Consortia Design (In Silico) Training | gLV, COBRA/MICOM, Cross-Feeding & Robustness

Synthetic Ecology & Consortia Design (In Silico) — Hands-on