Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research.
$ npx skills add K-Dense-AI/scientific-agent-skills --skill marine-carbonate-chemistry -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install K-Dense-AI/scientific-agent-skills marine-carbonate-chemistry --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/marine-carbonate-chemistry .claude/skills/marine-carbonate-chemistry && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "marine-carbonate-chemistry" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/marine-carbonate-chemistry into .claude/skills/marine-carbonate-chemistry/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marine-carbonate-chemistry", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/marine-carbonate-chemistryType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add K-Dense-AI/scientific-agent-skills --skill marine-carbonate-chemistry -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install K-Dense-AI/scientific-agent-skills marine-carbonate-chemistry --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/marine-carbonate-chemistry .agents/skills/marine-carbonate-chemistry && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "marine-carbonate-chemistry" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/marine-carbonate-chemistry into .agents/skills/marine-carbonate-chemistry/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marine-carbonate-chemistry", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add K-Dense-AI/scientific-agent-skills --skill marine-carbonate-chemistry -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install K-Dense-AI/scientific-agent-skills marine-carbonate-chemistry --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/marine-carbonate-chemistry .cursor/skills/marine-carbonate-chemistry && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "marine-carbonate-chemistry" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/marine-carbonate-chemistry into .cursor/skills/marine-carbonate-chemistry/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marine-carbonate-chemistry", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/K-Dense-AI/scientific-agent-skills.git --path skills/marine-carbonate-chemistry--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add K-Dense-AI/scientific-agent-skills --skill marine-carbonate-chemistry -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install K-Dense-AI/scientific-agent-skills marine-carbonate-chemistry --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/marine-carbonate-chemistry .gemini/skills/marine-carbonate-chemistry && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "marine-carbonate-chemistry" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/marine-carbonate-chemistry into .gemini/skills/marine-carbonate-chemistry/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marine-carbonate-chemistry", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install K-Dense-AI/scientific-agent-skills marine-carbonate-chemistryInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add K-Dense-AI/scientific-agent-skills --skill marine-carbonate-chemistry -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/marine-carbonate-chemistry .github/skills/marine-carbonate-chemistry && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "marine-carbonate-chemistry" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/marine-carbonate-chemistry into .github/skills/marine-carbonate-chemistry/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marine-carbonate-chemistry", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add K-Dense-AI/scientific-agent-skills --skill marine-carbonate-chemistry -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install K-Dense-AI/scientific-agent-skills marine-carbonate-chemistry --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/marine-carbonate-chemistry .opencode/skills/marine-carbonate-chemistry && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "marine-carbonate-chemistry" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/marine-carbonate-chemistry into .opencode/skills/marine-carbonate-chemistry/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "marine-carbonate-chemistry", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
marine-carbonate-chemistrySolves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research.
Marine Carbonate Chemistry is an agent skill from K-Dense-AI/scientific-agent-skills. Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research. Use for paired total alkalinity, dissolved inorganic carbon, pH, or seawater pCO2/fCO2 measurements; carbonate speciation; aragonite and calcite saturation; Revelle factors; lab-to-in-situ temperature and pressure corrections; and measurement uncertainty propagation. Applies to carbonate-system calculations, not general aqueous speciation or air-sea gas-flux estimation.
Its SKILL.md is about 2.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts and reference files (for example `references/chemistry-decisions.md`, `references/input-and-results.md` and `scripts/solve_carbonate.py`). Compatibility notes: Requires Python 3.13 with PyCO2SYS 1.8.3.4 and NumPy. Network access is needed only to install packages or obtain external data; bundled calculations run…
It sits in Research & Science, covering Physical and earth sciences and Drug discovery and cheminformatics. The repository describes itself as: Turn any AI agent into an AI Scientist. The 1 Agent Skills library for science, used by 250,000+ scientists worldwide. 177 ready-to-use validated skills plus 100+ scientific… The licence is MIT.
5 steps, taken from the first numbered list in SKILL.md.
Read from SKILL.md and the folder at commit 92ace75. It shows what the files ask for, not the result of running them.
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
uvpythonFrom the folder's file list and the shell code blocks in SKILL.md.
Links to these hosts (documentation or services it may open):
pyco2sys.readthedocs.iomvdh.xyzgithub.comdoi.orgFrom URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Requires Python 3.13 with PyCO2SYS 1.8.3.4 and NumPy. Network access is needed only to install packages or obtain external data; bundled calculations run locally without credentials.
From compatibility in the SKILL.md frontmatter.
Marine Carbonate Chemistry loads about 2.4k tokens when it runs, and up to ~5.2k if it reads all its reference files. Until then it costs about 133 tokens; SKILL.md has 1,000 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
The full file from K-Dense-AI/scientific-agent-skills at commit 92ace75, republished under its MIT licence (© K-Dense-AI). 1,000 words, ~2,387 tokens.
.claude/skills/marine-carbonate-chemistry/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.Turn two independent seawater carbonate measurements into a reproducible speciation table, mineral saturation estimates, and a record of the calculation assumptions. Targets PyCO2SYS 1.8.3.4, tested with Python 3.13 and NumPy 2.5.3. As reviewed on 2026-10-01, this remains the stable PyPI release. The v2 documentation is for a beta with breaking changes; use the v1 documentation for this pin.
This workflow concerns seawater carbonate equilibria. Freshwater, porewaters with substantial uncharacterized alkalinity, brines outside the selected calibration range, and reaction/transport models require additional chemistry and validation. Do not infer an air-sea flux or atmospheric carbon removal from a carbonate equilibrium alone.
Before running a solver, identify the two measured variables, their units, quality flags, and their temperature/pressure basis. Retain a separate source table containing station, depth, timestamps, methods, reference materials, and original QC codes, joined by sample ID. Do not turn missing values or rejected measurements into zero.
| Quantity | Required convention |
|---|---|
| Total alkalinity (TA), DIC, nutrients | micromol per kg seawater, not per litre or kg water |
| Salinity | Practical Salinity, not Absolute Salinity in g/kg |
| Temperature | In-situ/measurement temperature in degrees Celsius, not potential or Conservative Temperature |
| Pressure | Sea pressure in dbar; surface sample is 0, not 1 atmosphere |
| pH | Declared total, seawater, free, or NBS scale, at the declared measurement conditions |
| pCO2 / fCO2 | Seawater partial pressure / fugacity in microatm; these are distinct quantities |
TA and DIC remain constant during the solver's temperature/pressure conversion for a
closed sample. pH and gas parameters change. Two inputs measured at different conditions
cannot simply share one temperature value. Establish a consistent measurement basis
first. Temperature correction does not repair sample changes caused by gas exchange,
biology, evaporation, or mineral dissolution/precipitation.
Use two independent carbonate parameters. pCO2 plus fCO2 is not an independent pair. Three or more measurements enable an overdetermination check: solve independent pairs and compare predicted versus measured third parameters, including their uncertainty. Do not average inconsistent solutions to hide a calibration or scale mismatch.
Create a dedicated environment in the user's working directory:
uv venv --python 3.13 .venv
uv pip install --python .venv/bin/python "PyCO2SYS==1.8.3.4" "numpy==2.5.3"On Windows the environment's interpreter is .venv/Scripts/python.exe. The commands
below use the POSIX interpreter path. Set the shell variable SKILL_DIR to this installed
skill's directory. Keep inputs and generated outputs in the working directory.
scripts/solve_carbonate.py. It validates the full input table, solves
the pair, checks finite outputs and DIC species balance, then writes carbonate.csv
and provenance.json into a new output directory._out describe the supplied
output temperature/pressure. Unsuffixed results describe input conditions. Gas results
retain the helper's uncorrected hydrostatic gas convention (see below). Include
parameter pair, pH scale, units, constants, nutrient assumptions, uncertainty scope,
software versions, and excluded/flagged samples with the result table.The following values are synthetic, not field observations. Save this as samples.csv
in a working directory. The two samples differ only in DIC; the second represents a
fixed-alkalinity CO2-addition comparison. Their measurements are at 25 C and 0 dbar;
results are also requested at 10 C and 1000 dbar.
sample_id,par1,par2,salinity,temperature,pressure,total_phosphate,total_silicate,temperature_out,pressure_out,u_par1,u_par2
baseline,2300,2000,35,25,0,0,0,10,1000,2,2
added_co2,2300,2100,35,25,0,0,0,10,1000,2,2Run from that working directory:
.venv/bin/python "$SKILL_DIR/scripts/solve_carbonate.py" samples.csv \
--par1-type alkalinity --par2-type dic --k-carbonic 10 \
--output-dir carbonate-resultsFor the baseline, the tested version gives input-condition total pH 8.045886,
pCO2 396.958 microatm, and aragonite saturation 3.386201. At the specified output
conditions, total pH is 8.241241 and aragonite saturation 2.605691. These rounded
values are regression checks for this exact setup, not universal seawater benchmarks.
With independent 2 micromol/kg uncertainties in TA and DIC only, u_pH_total is about
0.004580. This excludes equilibrium-constant and other input uncertainty.
Both rows carry gas_pressure_correction_disabled_output: the output pH and mineral
saturation include pressure effects, but the reported pCO2/fCO2 do not include the
hydrostatic corrections to CO2 solubility and fugacity. Do not compare those gas values
directly with a pressure-corrected subsurface sensor measurement.
For TA + measured pH, use --par2-type ph --ph-scale total only if the source explicitly
identifies total-scale pH; replace par2 and u_par2 with the measured pH and its absolute
standard uncertainty. A column named merely pH is insufficient to establish its scale.
Optional u_ input columns contain absolute one-standard-deviation uncertainties.
They propagate to total pH, pCO2, and aragonite saturation at each requested condition.
The helper assumes independent errors and treats unlisted inputs/constants as exact.
For covariance, constants uncertainty, or strongly nonlinear uncertainty, follow the
decision guide and validate a tailored propagation instead of calling these outputs a
complete uncertainty budget.
Omega < 1 indicates thermodynamic undersaturation with respect to the named mineral. It does not establish a dissolution rate or an organism's response. A lower pH across unmatched samples is not by itself evidence of an anthropogenic acidification trend.
Repository tests exercise the pinned solver, independent-pair round trips, carbon balance,
pH-scale equivalence, condition correction, Revelle-factor derivatives, gas-pressure
conventions, uncertainty quadrature, CSV errors, and the worked example. The helper calls
the local pyco2.sys Python API; it has no HTTP endpoints or authentication. Tests establish
software behavior, not independent field-data validation; upstream's validation page also
contains historical examples, including a removed pyco2.test interface.
© K-Dense-AI, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
SKILL.md and 3 other files (scripts, references) in skills/marine-carbonate-chemistry of K-Dense-AI/scientific-agent-skills.
Open the folder on GitHubat commit 92ace75
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in K-Dense-AI/scientific-agent-skills, which our catalogue first saw on October 7, 2026.
Marine Carbonate Chemistry next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Marine Carbonate Chemistry this skillK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.4k | Automated safety check: Pass | MIT | |
| Antechamberjinzhezenggroup/computational-chemistry-agent-skills | 148 | — | ~3.2k | Automated safety check: Pass | LGPL-3.0-or-later | |
| Chem Solution Mdlearningmatter-mit/AtomisticSkills | 176 | — | ~1.9k | Automated safety check: Pass | MIT | |
| Chemgraphargonne-lcf/ChemGraph | 162 | — | ~2.7k | Automated safety check: Pass | Apache-2.0 | |
| AstropyzLanqing/codex-claude-academic-skills | 4.7k | 13 repos | ~2.9k | Automated safety check: Pass | BSD-3-Clause | |
| MolecodeAtomFlow-AI/MoleCode | 306 | — | ~1.9k | Automated safety check: Pass | MIT |
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Categories
Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research. Marine Carbonate Chemistry is an agent skill from K-Dense-AI/scientific-agent-skills. Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research.
Marine Carbonate Chemistry fits situations like: paired total alkalinity; dissolved inorganic carbon; seawater pCO2/fCO2 measurements; carbonate speciation.
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill marine-carbonate-chemistry -a claude-code`. Or copy the skill folder (skills/marine-carbonate-chemistry in K-Dense-AI/scientific-agent-skills) into .claude/skills/marine-carbonate-chemistry in your project. Claude Code loads it when a task matches its description.
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill marine-carbonate-chemistry -a codex`. Or copy the skill folder (skills/marine-carbonate-chemistry in K-Dense-AI/scientific-agent-skills) into .agents/skills/marine-carbonate-chemistry in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add K-Dense-AI/scientific-agent-skills --skill marine-carbonate-chemistry -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/marine-carbonate-chemistry, .gemini/skills/marine-carbonate-chemistry, .github/skills/marine-carbonate-chemistry and .opencode/skills/marine-carbonate-chemistry in your project.
Going by SKILL.md and its folder, Marine Carbonate Chemistry needs Python for the scripts in its folder and the command-line tools its instructions call (uv and python). Our summary lists: Python 3. Compatibility (from SKILL.md): Requires Python 3.13 with PyCO2SYS 1.8.3.4 and NumPy. Network access is needed only to install packages or obtain external data; bundled calculations run locally without credentials..
SKILL.md names 4 domains. As links in the text: pyco2sys.readthedocs.io, mvdh.xyz, github.com and doi.org. This is read from the text; nothing was executed.
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
Marine Carbonate Chemistry is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.4k tokens (SKILL.md is roughly 9.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 2.8k tokens, read only when the agent opens those files.
Skills that share tags, products or a category with Marine Carbonate Chemistry: Antechamber (jinzhezenggroup/computational-chemistry-agent-skills, 148 stars), Chem Solution Md (learningmatter-mit/AtomisticSkills, 176 stars), Chemgraph (argonne-lcf/ChemGraph, 162 stars) and Astropy (zLanqing/codex-claude-academic-skills, 4.7k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
K-Dense-AI (a GitHub organization) maintains it in K-Dense-AI/scientific-agent-skills, which has 48,215 GitHub stars. The repository holds 153 skills in this directory. The repository was last updated on October 5, 2026.
Source: K-Dense-AI/scientific-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.
