ai4s-research/open-science

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name: computer-use

description: Use when a task needs an app on the user's own screen — a native desktop application (instrument control software, Origin, GraphPad, ImageJ, a reference manager, a spreadsheet), or a desktop browser window that needs window-level control. Read before the first `computer` call. Covers the observe-act-observe loop, why element indexes go stale, which action to prefer for which control, what "unverified" means and why it must never be reported as success, and the recovery for each error code. Not for page-level web automation (use the browser connector) and not for anything that can be done from the shell.

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name: domain-check

description: Use ONLY when the user asks to check, validate, review or audit analysis code for scientific correctness, or when you are the reviewer agent running its checks. Never run it unprompted as part of ordinary analysis work. Covers physics, earth/geo, biology, chemistry, social science and bioprocess/fermentation. Runs a deterministic domain-correctness gate that catches code which runs but is scientifically wrong (unit/dimension mismatch, Euclidean distance on lat/lon without a CRS, 0-based/1-based coordinate and strand errors, impossible SMILES valence, uncorrected multiple comparisons, averaging a categorical code, unconstrained kinetic-parameter fits, kLa computed from raw DO instead of the driving force, arithmetic mean of raw CFU counts, ANOVA/Tukey with no assumption check, a curvature DOE design fit with a first-order model, an ML model fit across process scales with no correction). Surfaces structured findings; never claims the code is correct.

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name: large-file

description: Use BEFORE reading any data file that could be large (CSV/TSV, Parquet, HDF5, FITS, NetCDF, NDJSON, genomics FASTQ/FASTA/VCF/BAM, GRIB, ROOT, or big text/simulation logs like VASP OUTCAR). Returns a compact memory pointer — header/schema/shape/sample/key numbers — by introspection and sampling in bounded memory, so you never load a file bigger than the context window into the model. Reference data via the pointer; read specific ranges deterministically.

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name: modal-run

description: Use when the user asks to run heavy or GPU work on Modal (the cloud compute platform) — writing a Modal function in the workspace, running it with the user's own `modal` CLI + token, and bringing results back. Data-to-compute for jobs too big for the laptop, without a Slurm cluster.

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name: publication-figures

description: Use whenever you generate or review a chart, plot, table, or paper figure in this workspace, including work delegated by paper-writing, literature-survey, and experiment skills. Applies the Open Science publication style, enforces readable final-size layout for figures and tables, and rejects generic diagram-tool output as a publication figure. Interactive Plotly/HTML may be used for exploration, but paper delivery requires a static publication-ready export.

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name: remote-compute

description: Use when the user asks to run, submit, monitor, or cancel a job on a remote machine over SSH — their own GPU/CPU server, a workstation, or a Slurm cluster ("the cluster", a login node, "my 3090 box", "the compute server"). Picks a saved machine, runs the work directly over SSH (or via Slurm when present), tracks it, and fetches results back into the workspace.

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name: stats-integrity

description: Use whenever you run statistical analysis for the social sciences (regression, hypothesis tests, econometrics) or read Stata (.dta) / SPSS (.sav) data in this workspace. Enforces an execute-don't-interpret boundary (surface estimates, don't volunteer causal claims), checks the analysis against a preregistration plan for HARKing, verifies reproducible seeds, and reproduces .dta/.sav estimates via R. Flags integrity risks; never certifies the analysis is sound.

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name: traceability-review

description: Use when the user asks to review, verify, or audit a report, manuscript, or analysis in the workspace for traceability — resolving citations, flagging numbers with no source, and checking figures against the code that generated them. Emits a structured review block the app renders as reviewer findings. Verifies traceability, never "correctness".