13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps,โฆ
Solves and validates single-, multi-, and many-objective optimization with pymoo, including NSGA-II, NSGA-III, MOEA/D, constraints, Pareto approximations, reference directions, and ZDT/DTLZ benchmarks for engineering and research problems.
Claude Code
$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill pymoo --agent claude-code
Codex
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pymoo -a codex -y
Cursor
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pymoo -a cursor -y
Gemini CLI
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pymoo -a gemini-cli -y
GitHub Copilot
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pymoo -a github-copilot -y
OpenCode
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pymoo -a opencode -y
Windsurf
$ npx skills add K-Dense-AI/scientific-agent-skills --skill pymoo -a windsurf -y
name: pymoo description: Solves and validates single-, multi-, and many-objective optimization with pymoo, including NSGA-II, NSGA-III, MOEA/D, constraints, Pareto approximations, reference directions, and ZDT/DTLZ benchmarks for engineering and research problems. license: Apache-2.0 license allowed-tools: Read Write Edit Bash compatibility: Requires Python 3.10+ and pymoo 0.6.2 with its NumPy, SciPy, matplotlib and autograd dependencies. Optional joblib for parallel runners, optuna for its algorithm wrapper, and dill for checkpoints. Network needed for installation only. metadata: version: "1.6" last-reviewed: "2026-10-01" upstream-version: "0.6.2" skill-author: K-Dense Inc.
Pymoo is a comprehensive Python framework for optimization with emphasis on multi-objective problems. Solve single and multi-objective optimization using state-of-the-art algorithms (NSGA-II/III, MOEA/D, SPEA2), benchmark problems (ZDT, DTLZ), customizable genetic operators, and multi-criteria decision making methods. Excels at finding trade-off solutions (Pareto fronts) for problems with conflicting objectives. Targets stable **pymoo 0.6.2**, reviewed 2026-10-01 against current official docs and native toy runs.
uv pip install "pymoo==0.6.2"
For reproducible environments, pin a version: `uv pip install "pymoo==0.6.2"`.
**Dependencies:** The released 0.6.2 wheel requires NumPy, SciPy, moocore, autograd, cma, matplotlib, alive_progress, and Deprecated. NumPy 2.x is supported. The current installation prose describes some dependencies as optional; the released package metadata governs installation. Joblib, Optuna and dill are separate dependencies for the corresponding recipes.
**Documentation:** https://pymoo.org/ โ LLM-friendly index: https://pymoo.org/llms.txt
This skill should be used when:
Pymoo uses a consistent `minimize()` function for all optimization tasks:
from pymoo.optimize import minimize
result = minimize(
problem, # What to optimize
algorithm, # How to optimize
termination, # When to stop
seed=1,
verbose=True
)**Result object contains:**
**Check feasibility before plotting or selecting:** If no feasible solution was found, `result.X` and `result.F` can be `None`. With `return_least_infeasible=True`, a returned candidate can still violate constraints; report its `CV` and residuals instead of calling it feasible. Re-evaluate chosen candidates against the original physical constraints after any normalization or repair. See the [result contract](https://pymoo.org/interface/result.html).
Pymoo supports three problem definition styles:
**Single-objective:** One objective to minimize; negate a maximization objective and record the conversion **Multi-objective:** 2-3 conflicting objectives โ Pareto front **Many-objective:** 4+ objectives โ High-dimensional Pareto front **Constrained:** Objectives + inequality/equality constraints **Mixed-variable:** Continuous, integer, binary, and categorical variables in one problem **Dynamic:** Time-varying objectives or constraints
Nine workflows and context-dependent adaptation snippets are in [references/quick_start_workflows.md](references/quick_start_workflows.md):
| # | Workflow | Use when | | --- | --- | --- | | 1 | Single-objective optimization | one objective, GA or DE | | 2 | Multi-objective (2-3 objectives) | NSGA-II and a Pareto front | | 3 | Many-objective (4+ objectives) | NSGA-III or reference-direction methods | | 4 | Custom problem definition | subclassing `Problem` / `ElementwiseProblem` | | 5 | Constraint handling | inequality and equality constraints | | 6 | Decision making from a Pareto front | scalarization and MCDM selection | | 7 | Visualization | scatter, PCP, radviz, and heatmap views | | 8 | Parallel evaluation | threads or joblib for expensive objectives | | 9 | Mixed-variable optimization | integer, binary, and categorical variables |
| Algorithm | Best For | Key Features | |-----------|----------|--------------| | **GA** | General-purpose | Flexible, customizable operators | | **DE** | Continuous optimization | Good global search | | **PSO** | Smooth landscapes | Fast convergence | | **CMA-ES** | Difficult/noisy problems | Self-adapting |
| Algorithm | Best For | Key Features | |-----------|----------|--------------| | **NSGA-II** | Standard benchmark | Fast, reliable, well-tested | | **SPEA2** | Strength/density survival | Strength-based
๐ Claude Scientific Skills is now Scientific Agent Skills. Same skills, broader compatibility โ now works with any AI agent that supports the open Agent Skills standard, not just Claude.
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