13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps,β¦
Builds, simulates, transpiles, and executes quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Estimator primitives, target-aware transpilation, local or noisy simulation, IBM QPU execution, Runtime sessions or batches,
Claude Code
$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill qiskit --agent claude-code
Codex
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qiskit -a codex -y
Cursor
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qiskit -a cursor -y
Gemini CLI
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qiskit -a gemini-cli -y
GitHub Copilot
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qiskit -a github-copilot -y
OpenCode
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qiskit -a opencode -y
Windsurf
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qiskit -a windsurf -y
name: qiskit description: Builds, simulates, transpiles, and executes quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Estimator primitives, target-aware transpilation, local or noisy simulation, IBM QPU execution, Runtime sessions or batches, error mitigation, and Qiskit ecosystem packages. license: Apache-2.0 compatibility: Python 3.10+ on a supported 64-bit platform. Local SDK workflows need qiskit; noisy simulation needs qiskit-aer; IBM QPU access needs qiskit-ibm-runtime, network access, an IBM Quantum Platform account, and an API key. metadata: version: "2.3" last-reviewed: "2026-10-01" skill-author: K-Dense Inc.
Use current Qiskit 2.x APIs to build circuits, prepare hardware-compatible instruction set architecture (ISA) circuits, and execute them through V2 primitives.
Reviewed **2026-10-01** with local tests on `qiskit==2.5.2`, `qiskit-ibm-runtime==0.50.0`, and `qiskit-aer==0.17.2`. IBM account, QPU, session, and batch examples are illustrative and documentation/source-checked; no remote workloads were submitted. See [references/sources.md](references/sources.md) for the verification boundary.
Runtime 0.50 deprecates the top-level `SamplerV2`/`EstimatorV2` implementations. New code imports `Sampler` from `qiskit_ibm_runtime.executor_sampler` and `Estimator` from `qiskit_ibm_runtime.executor_estimator`. These still implement the V2 PUB interface, using client-side processing and `Executor`. Use option models from `qiskit_ibm_runtime.options_models`.
| Goal | Recommended interface | |---|---| | Ideal evolution with finite-shot sampling | `qiskit.primitives.StatevectorSampler` | | Exact local expectation values | `qiskit.primitives.StatevectorEstimator` | | High-performance or noisy simulation | Qiskit Aer | | IBM QPU sampling | `qiskit_ibm_runtime.executor_sampler.Sampler` | | IBM QPU expectation values and mitigation | `qiskit_ibm_runtime.executor_estimator.Estimator` | | Backend without native primitives | `BackendSamplerV2` or `BackendEstimatorV2` | | Open-system or master-equation dynamics | Prefer QuTiP | | Differentiable quantum machine learning | Prefer PennyLane unless Qiskit integration is required |
Create an isolated environment and install only the components needed:
uv venv --python 3.13 source .venv/bin/activate # Core SDK plus plotting support uv pip install "qiskit[visualization]==2.5.2" # Add only when needed uv pip install "qiskit-ibm-runtime==0.50.0" uv pip install "qiskit-aer==0.17.2"
Do not install `qiskit-terra`; it was superseded by the `qiskit` distribution. Qiskit Runtime, Aer, Nature, Machine Learning, Optimization, and Algorithms are separate distributions.
For IBM account setup, CI-safe credential handling, optional packages, and environment repair, read [references/setup.md](references/setup.md).
Follow this sequence for every hardware-oriented workload:
1. **Map** the problem to a circuit and, for Estimator, one or more observables. 2. **Optimize** the parameterized circuit once for the selected backend. 3. **Apply the layout** to every observable. 4. **Execute** ISA circuits through a V2 primitive using Primitive Unified Blocs (PUBs). 5. **Analyze** register-aware results, metadata, uncertainty, and resource usage.
Do not bind and retranspile a parameterized circuit inside every optimizer iteration. Transpile the parameterized circuit once, then pass parameter arrays in PUBs.
from qiskit import QuantumCircuit from qiskit.primitives import StatevectorSampler circuit = QuantumCircuit(2) circuit.h(0) circuit.cx(0, 1) circuit.measure_all() # creates the classical register named "meas" sampler = StatevectorSampler(seed=7) pub_result = sampler.run([circuit], shots=1024).result()[0] counts = pub_result.data.meas.get_counts() print(counts)
Sampler V2 preserves shots and classical-register structure. Access the register by its actual name; `measure_all()` uses `meas`.
For circuits with multiple classical registers, each registerβs counts are a marginal distribution. Preserve shot alignment when computing cross-register correlations; multiplying marginal frequencies destroys those correlations. Use `SamplerPubResult.join_data` with an explicit register order for joint bitstrings and record that order in the result labels. Qiskit 2.5.2 puts the first joined `BitArray` register in the least-significant bits, contrary to the current docstring; verify with an asymmetric state. See [references/primitives.md](references/primitives.md).
import numpy as np
from qiskit import QuantumCircuit
from qiskit.circuit import Parameter
from qiskit.primitives import StatevectorEstimator
from qiskit.quantum_info import SparsePauliOp
theta = Parameter("theta")
circuit = QuantumCircuit(2)
circuit.ry(theta, 0)
circuit.cx(0, 1)
observable = SparsePauliOp.from_list([("ZZ", 1.0), ("XX", 0.5)])
parameter_values = [[0.0], [np.pi / 4], [np.pi / 2]]
estimator = StatevectorEstimator(seed=7)
pub = (circuit, observable, parameter_values)
pub_result = estimator.run([pub]).result()[0]
print(pub_result.data.evs)Estimator circuits should not contain final measurements. PUB arrays broadcast; verify circuit parameter order before constructing large sweeps.
This example assumes credentials were saved securely as described in [references/setup.md](references/setup.md). It never embeds or prints an API key.
from qiskit import QuantumCircuit
from qiskit.transpiler import generate_preset_pass_manager
from qiskit_ibm_runtime import QiskitRuntimeService
from qiskit_ibm_runtime.executor_sampler import Sampler
service = QiskitRuntimeService()
backend = service.least_busy(
operational=True,
simulator=False,
min_num_qubits=2,
)
circuit = QuantumCircuit(2)
circuit.h(0)
circuit.cx(0, 1)
circuit.measure_all(π Claude Scientific Skills is now Scientific Agent Skills. Same skills, broader compatibility β now works with any AI agent that supports the open Agent Skills standard, not just Claude.
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