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Aesthetic guidelines and output-type recipes for scientific figure production. Supports lightweight default-agent use through SKILL.md + one outputType recipe, with optional venue-specific style guides when requested.
Skills for opening and driving agent-controllable visualization components in the Pantheon UI sidebar — interactive viewers the agent can open, control, and read back. Viewers: Vitessce (spatial / single- cell omics), Viv (bioimage / microscopy), volume3d (3D image volumes — MIP/ISO), spatial3d (3D spatial transcriptomics), Mol*, IGV, Gosling, Cytoscape, MSA, RDKit, phylotree, plus agent-generated apps.
Query the Virtual Embryo knowledge graph (mouse/human developmental biology: genes, anatomy, Theiler/Carnegie stages, gene expression, diseases, papers) and its 3D atlas catalog (anatomical OPT/light-sheet volumes + 3D spatial- transcriptomics datasets), and visualise those datasets in 3D with the volume3d / spatial3d live-view viewers. Public read-only HTTP API at https://kg.virtualembryo.ai — no auth, no key needed for reads. Use when the user asks about mouse/human embryo development, where a gene is expressed, an anatomical structure, a developmental stage, or wants to see/visualise the Virtual Embryo atlas or spatial-transcriptomics data.
Skills for rare disease case support: ontology-first normalization/retrieval and the clinical genetics consult report format contract (structure + theme). Load the relevant skill file when performing the matching task.
Scenario router for paper-writing tasks. Use after root triage to select paper submission, journal article, conference paper, grant proposal, lab report, group report, talk/workshop, or revision-response behavior.
Routing and workflow skill family for paper-writing tasks. Covers manuscript drafting, journal and conference papers, grant proposals, lab reports, group-meeting reports, talks, workshop notes, reviewer rebuttals, academic HTML/PDF/LaTeX output with editable-block contracts, citation grounding, evidence checking, and pre-submission quality gates.
Workflow phases for paper-writing tasks: triage, material inventory, research question, literature review, paper outline, data analysis summary, figure storyline, reader testing, and finalize packet. Each phase is a short contract — read the relevant rows for the current task only.
| id | figure_styling_skills_index |
| name | Figure Styling Skills Index |
| description | Aesthetic guidelines and output-type recipes for scientific figure production. Supports lightweight default-agent use through SKILL.md + one outputType recipe, with optional venue-specific style guides when requested. |
General scientific figure styling skill for default agents and graph-generation tasks.
This skill has two layers:
SKILL.md + one recipe file).Lightweight read rule: For normal use, read only this SKILL.md and one outputType recipe. Do not load styles/, quality/, input/, or triage/ unless explicitly needed.
| outputType | Read | Rendering mode | Use for |
|---|---|---|---|
figure | figure.md | code-first | paper figures, data plots, multi-panel figures |
poster | poster.md | mixed | academic posters |
graphical-abstract | graphical-abstract.md | AI-first | graphical abstracts, TOC figures |
presentation | presentation.md | mixed | slide visuals |
flowchart | flowchart.md | AI-first | workflow diagrams, process diagrams |
Read these only when the user explicitly requests a venue/style or a style_id is provided.
If a listed file is not present, continue with the outputType recipe and report the missing file.
| style_id | File | Use for |
|---|---|---|
neurips_diagram | styles/neurips_diagram.md | ML methodology diagrams (NeurIPS / ICML / ICLR / CVPR) |
neurips_plot | styles/neurips_plot.md | ML/statistical plots (NeurIPS / ICML / ICLR / CVPR) |
nature_figure | styles/nature_figure.md | Nature / Cell / Science-style scientific figures |
ieee_figure | styles/ieee_figure.md | IEEE journal / conference figures |
color_palettes | styles/color_palettes.md | Colorblind-safe palette reference (Paul Tol) |
Use concrete visual schemas instead of generic scientific prompts.
Prefer:
Avoid:
Do not assume a fixed scientific domain.
When the user provides a domain, instantiate the visual schema with that domain's concrete entities, structures, labels, and relationships.
Examples (not defaults):
These are domain instantiation examples, not default assumptions.
Additional .md style files may be added to styles/ following the existing file structure. Use the matching style_id when requesting a venue or aesthetic style.