13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps,โฆ
Builds, inspects, tests, and analyzes bounded process-based discrete-event simulations with SimPy. Use for event scheduling, resource queues, interrupts, monitoring, independent replications, warm-up, and reproducible output analysis.
Claude Code
$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill simpy --agent claude-code
Codex
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Cursor
$ npx skills add K-Dense-AI/scientific-agent-skills --skill simpy -a cursor -y
Gemini CLI
$ npx skills add K-Dense-AI/scientific-agent-skills --skill simpy -a gemini-cli -y
GitHub Copilot
$ npx skills add K-Dense-AI/scientific-agent-skills --skill simpy -a github-copilot -y
OpenCode
$ npx skills add K-Dense-AI/scientific-agent-skills --skill simpy -a opencode -y
Windsurf
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name: simpy description: Builds, inspects, tests, and analyzes bounded process-based discrete-event simulations with SimPy. Use for event scheduling, resource queues, interrupts, monitoring, independent replications, warm-up, and reproducible output analysis. license: MIT compatibility: Upstream SimPy 4.1.2 supports Python 3.8+; bundled CLIs require Python 3.10+, uv, and SimPy 4.1.2. They use only SimPy and the standard library, operate on local bounded inputs, and make no network calls. allowed-tools: Read Write Edit Bash Glob metadata: version: "1.6" last-reviewed: "2026-10-01" skill-author: K-Dense Inc.
Use this skill for process-based discrete-event models where active entities yield events and contend for resources: queues, production systems, logistics, networks, service operations, inventory, and other event-driven systems.
SimPy supplies an event scheduler and modeling primitives. It does **not** choose a scientifically valid conceptual model, input distribution, warm-up, run length, replication count, estimand, or causal interpretation. Treat those as simulation-study methodology, not SimPy API behavior.
Reviewed **2026-10-01** against current official documentation and the released source:
`4.1.2` points to commit `f4381649`.
plus PyPy. SimPy has no runtime dependencies.
Create a reproducible environment:
uv venv --python 3.13
source .venv/bin/activate
uv pip install "simpy==4.1.2"
python -c "import importlib.metadata; print(importlib.metadata.version('simpy'))"Do not silently substitute the `latest` documentation build: it may describe an unreleased development revision. Use the versioned 4.1.2 links in `references/sources.md`.
1. **Define purpose and estimands.** State the decision/question, system boundary, entities, resources, state, outputs, time units, and terminating event or steady-state target. 2. **Write a conceptual model first.** Record assumptions, distributions, routing, priorities, initial conditions, and omitted mechanisms. 3. **Implement generators.** A SimPy process is an event-yielding Python generator. Register the generator object with `env.process(...)`. 4. **Bound execution.** Give every production run explicit time, entity, event, and replication caps. Never call `env.run()` on a model containing an endless process. A time horizon alone cannot stop an endless `yield env.timeout(0)` loop: events keep running at the same simulation time. Add an event-count or no-time-progress guard, and wait on state-change events instead of zero-delay busy polling. 5. **Separate random streams.** Use local RNG instances for logically distinct stochastic sources; retain a seed manifest. 6. **Instrument deliberately.** Observe state after the transition of interest, close time-weighted intervals at the horizon, and test that monitoring does not alter event order. 7. **Verify and validate.** Test deterministic edge cases, conservation identities, traces, queue discipline, and analytical benchmarks; compare against system or expert evidence for the stated purpose. 8. **Run independent replications.** Make intervals from replication-level estimates, not correlated entities within one run. 9. **Report limitations.** Include initialization, unfinished entities, run length, seeds/streams, precision, sensitivity, and validation evidence. Never convert simulation association into a causal claim.
Read `references/simulation-methodology.md` before making inferential claims.
import random
import simpy
HORIZON = 480.0
arrival_rng = random.Random(101)
service_rng = random.Random(202)
env = simpy.Environment()
server = simpy.Resource(env, capacity=2)
completed = []
def customer(arrival):
with server.request() as request:
yield request
wait = env.now - arrival
yield env.timeout(service_rng.expovariate(1 / 6.0))
completed.append((env.now, wait))
def arrivals():
for _ in range(10_000): # Entity cap.
delay = arrival_rng.expovariate(1 / 4.0)
if env.now + delay >= HORIZON:
return
yield env.timeout(delay)
env.process(customer(env.now))
env.process(arrivals())
env.run(until=HORIZON)The numeric horizon is half-open: normal events scheduled exactly at `480.0` are not processed. Report unfinished entities rather than silently treating them as completed observations.
`Environment` is single-threaded. The queue is ordered by simulation time, event priority, then a strictly increasing event ID. Same-time, same-priority events are therefore processed FIFO in scheduling order. Model processes may represent concurrency, but callbacks execute sequentially and deterministically.
This orders the events currently queued. A callback can insert an urgent event at the current time, so a valid processing trace need not have globally increasing priority or event IDs within a timestamp.
`env.run(until=number)` and `env.run(until=event)` are not interchangeable at boundaries:
that exact time.
Other same-time orderi
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