13c-metabolic-flux SKILL.md skillA
13c-metabolic-flux from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/13c-metabolic-flux@v1.2Pins v1.2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/13c-metabolic-flux/SKILL.md- Versions recorded
- 3
- Latest version
- v1.2, committed Oct 1, 2026
- First version recorded
- Sep 29, 2026
- Size
- 12,711 bytes
- Repository stars
- 53,159
- License
- MIT
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile diagnostics. Use for 13C-MFA, carbon tracing, mass isotopomer distributions (MDVs/MIDs), positional isotopomers, parallel tracer experiments, and determining whether labeling data constrain a pathway flux. Distinguishes measured-label inference from COBRA flux balance analysis and flags…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Carbon-13 metabolic flux inference Turn reviewed carbon maps, explicit tracer mixtures, and corrected labeling measurements into feasible flux estimates and evidence about which fluxes the experiment constrains. Use the bundled solver rather than reconstructing isotope balances or fitting each reaction independently. It runs mfapy's EMU forward simulator and fits fluxes in the mass-balanced feasible space with SciPy. It does not use an FBA objective. ## Scope and required evidence This implementation supports **metabolic and isotopic steady state**, a single shared flux state across one or more tracer experiments, nonnegative one-way reaction fluxes, and carbon-subset mass distributions. Reversible reactions are two separately mapped directions. Measurement error is Gaussian with a supplied covariance or a disclosed diagonal approximation. Before fitting, obtain: - The carbon network and the source of each atom assignment. Stoichiometry alone does not specify where labeled atoms go. Record compartments as separate metabolite IDs. - Evidence for both steady-state assumptions. Stable metabolite abundance does not …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/13c-metabolic-flux@sha256:8318b1c785cc80bfThe line at the top of this page pins the label v1.2, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_4h5t5sqwefawceqc)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Sep 29, 2026 and Oct 1, 2026, more than one a day.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.2 latest | 2026-10-01 | a92663a | 12,711 B | A | view · diff |
| v1.1 | 2026-09-30 | ce9e6e9 | 12,271 B | A | view · diff |
| v1.0 | 2026-09-29 | 65d6e78 | 12,107 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (12711 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 53,159 stars · license MIT · pushed 2026-10-19 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_4h5t5sqwefawceqc GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/13c-metabolic-flux GET https://markdownregistry.com/api/v1/blob/8318b1c785cc80bf095b8667a96061cd5f4b0b9c4e5fa77fd7f57fd8403f2c0f
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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