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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.
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.
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 | paper_writing_scenarios |
| name | Paper Writing Scenario Router |
| description | 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. |
| tags | ["paper_writing","scenarios","routing"] |
Scenario files decide the task shape. They do not write prose directly; they select workflow, format, theme, and quality gates.
| Scenario | File | Use when |
|---|---|---|
paper_submission | paper_submission.md | User asks for a manuscript or general paper submission |
journal_article | journal_article.md | User targets a journal or article type |
conference_paper | conference_paper.md | User targets a conference/workshop paper |
grant_proposal | grant_proposal.md | User asks for grant/proposal/funding application |
lab_report | lab_report.md | User asks for experiment/lab report |
group_report | group_report.md | User asks for group meeting, weekly report, progress report |
conference_talk | conference_talk.md | User asks for talk, speech, slides narrative, speaker notes |
workshop_share | workshop_share.md | User asks for workshop sharing, tutorial, reproducible notes |
revision_response | revision_response.md | User provides reviewer/editor comments or asks for rebuttal |
For every scenario, write the chosen IDs into triage.md before drafting.
