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Agent skill

Scientific Schematics

by jaechang-hits in jaechang-hits/SciAgent-Skills

Designing scientific schematics, diagrams, and graphical abstracts.

CC-BY-4.0Auto-check passedResearch & Science

Install Scientific Schematics

skills CLI
$ npx skills add jaechang-hits/SciAgent-Skills --skill scientific-schematics -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install jaechang-hits/SciAgent-Skills scientific-schematics --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/scientific-writing/scientific-schematics .claude/skills/scientific-schematics && rm -rf skills-src

Use ~/.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/

Facts

Skill name
scientific-schematics
GitHub stars
374
Token cost
~3.8k tokens
SKILL.md length
1,696 words
Files
1
Skills in repo
169
Repo updated
First seen
Licence
CC-BY-4.0

At a glance

Designing scientific schematics, diagrams, and graphical abstracts.

  • Works in 4 steps: Schematic Types and Their Purpose → Tool Comparison → Color Usage in Biological Schematics → …
  • Creating illustrative (not data-driven) scientific figures
  • SKILL.md covers Overview, Key Concepts, Decision Framework and Best Practices, plus 5 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Scientific Schematics is an agent skill from jaechang-hits/SciAgent-Skills. Designing scientific schematics, diagrams, and graphical abstracts. Covers tool selection (BioRender, Inkscape, Affinity, PowerPoint), design principles for pathway diagrams, mechanism schematics, experimental workflows, and journal graphical abstracts. Includes composition, icon sourcing, color for biological entities, and accessibility. Use when creating illustrative (not data-driven) scientific figures.

Its SKILL.md is about 3.8k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Data visualization and Diagrams. It works with Microsoft PowerPoint. The repository describes itself as: 197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon. The licence is CC-BY-4.0.

When your agent uses it

  • Creating illustrative (not data-driven) scientific figures
  • Tasks that involve Data visualization
  • Tasks that involve Diagrams

Example prompts

  • “/scientific-schematics”

Workflow steps

4 steps, taken from the step headings in SKILL.md.

  1. Schematic Types and Their Purpose
  2. Tool Comparison
  3. Color Usage in Biological Schematics
  4. Composition and Layout Principles

What it can do on your machine

Read from SKILL.md and the folder at commit 82c862c. It shows what the files ask for, not the result of running them.

  • Tool permissions

    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.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • biorender.com
    • clauswilke.com
    • bioicons.com
    • reactome.org
    • ncbi.nlm.nih.gov
    • doi.org

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Scientific Schematics loads about 3.8k tokens when it runs. Until then it costs about 108 tokens; SKILL.md has 1,696 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~108
When it runs · the whole SKILL.md, loaded when a task matches
~3.8k

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.

Safety

Auto-check passed

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); files beside SKILL.md are not scanned.

SKILL.md

The full file from jaechang-hits/SciAgent-Skills at commit 82c862c, republished under its CC-BY-4.0 licence (© jaechang-hits). 1,696 words, ~3,785 tokens.

Download SKILL.mdSave it as .claude/skills/scientific-schematics/SKILL.md (or your agent's skills folder).
name
scientific-schematics
description
Designing scientific schematics, diagrams, and graphical abstracts. Covers tool selection (BioRender, Inkscape, Affinity, PowerPoint), design principles for pathway diagrams, mechanism schematics, experimental workflows, and journal graphical abstracts. Includes composition, icon sourcing, color for biological entities, and accessibility. Use when creating illustrative (not data-driven) scientific figures.
license
CC-BY-4.0

Scientific Schematics

Overview

Scientific schematics are illustrative figures that communicate biological mechanisms, experimental designs, or conceptual frameworks — as distinct from data-driven figures (graphs, heatmaps). A well-designed schematic makes a manuscript's key concept immediately comprehensible to a broad scientific audience, while a poorly designed one confuses reviewers and reduces the paper's impact. This guide covers the design decisions, tool selection, composition principles, and accessibility standards specific to biological schematics in peer-reviewed publications.

Key Concepts

1. Schematic Types and Their Purpose

Not all schematics serve the same function. Choosing the wrong type leads to overloaded or underspecified figures.

TypePurposeKey ElementsExamples
Mechanism diagramShow step-by-step molecular eventsProteins, DNA, membranes, arrows indicating causalityCRISPR cleavage, signaling cascade, transcription factor binding
Pathway diagramShow relationships in a networkNodes (proteins/metabolites), edges (activation/inhibition), directionMAPK signaling, metabolic flux, gene regulatory network
Experimental workflowShow experimental protocol as a figureNumbered steps, icons for equipment/samples, time arrowsSingle-cell sequencing pipeline, drug treatment protocol
Graphical abstract1-panel summary of entire paper2–4 key findings, minimal text, journal-specified dimensionsCell, Nature, PNAS graphical abstracts
Structural diagramShow molecular structure/conformationRibbon structure, surface representation, active siteProtein domain schematic, ligand binding pocket

Decision rule: If the reader needs to understand what happened step-by-step, use a workflow. If they need to understand why (cause and effect), use a mechanism/pathway diagram. If they need a 30-second paper summary, use a graphical abstract.

2. Tool Comparison
ToolBest ForLearning CurveCostFile Output
BioRenderQuick biological schematics; built-in icon libraryLowSubscription (~$99/month academic; free for draft)PNG, SVG, PDF (license required for publication)
InkscapeFull vector editing; open-sourceMedium–HighFreeSVG, PDF, PNG, EMF
Affinity DesignerProfessional vector + raster hybridMedium~$55 one-timeSVG, PDF, AFDESIGN
Adobe IllustratorIndustry standard; full featuresHigh~$55/monthSVG, PDF, AI, EPS
PowerPoint / KeynoteQuick drafts; non-scientistsLowIncluded in MS/ApplePNG (low resolution), PDF
draw.io / LucidchartFlowcharts, pathway diagramsLowFree/subscriptionSVG, PNG, XML
ChimeraX / PyMOLMolecular structure rendersMediumFree (academic)PNG, TIFF, movie

Key difference: BioRender provides curated biological icons (cells, proteins, instruments) that are publication-quality and royalty-free under the publication license. For complex custom graphics, Inkscape (free) or Affinity Designer (paid) offer more flexibility.

3. Color Usage in Biological Schematics

Color in biological schematics carries semantic meaning and must be used consistently.

Conventional biological color assignments:

  • DNA: double helix colored in blue/navy or gray
  • mRNA: orange or yellow
  • Protein: varying; use consistent color per protein family across all figures in a paper
  • Cell nucleus: light gray or blue fill
  • Cell membrane: tan/beige bilayer
  • Mitochondria: orange
  • Lysosomes: red/purple

Signal direction conventions:

  • Arrows: activation (→ solid arrowhead), inhibition (⊣ flat bar), indirect (- - →)
  • Color coding arrows: green = activating, red = inhibiting, gray = neutral/context

Accessibility:

  • Never use red–green encoding alone; add shape cues (✓/✗, solid/dashed)
  • Test with CVD simulator before submission
  • Use at least 3:1 contrast ratio for text on colored backgrounds
4. Composition and Layout Principles

Visual hierarchy: The most important element should be the largest and most central. Support elements (labels, arrows, scale bars) should be visually subordinate.

Element spacing: Maintain consistent padding between grouped elements. Crowded diagrams cause readers to misread association between elements.

Arrow semantics: Every arrow must convey exactly one relationship. Do not use arrows interchangeably for "leads to," "causes," "physically binds," and "is required for" — use distinct arrow styles for each.

Text minimalism: Labels should be noun phrases only (not full sentences). Move explanatory text to the figure caption, not into the diagram itself.

Decision Framework

What is this schematic trying to communicate?
│
├── A sequence of experimental steps
│   └── → Workflow diagram
│       ├── Numbered panels or numbered arrows
│       ├── Icons for equipment (instrument, pipette, plate, animal)
│       └── Time axis or step axis
│
├── How a molecule works mechanistically
│   └── → Mechanism diagram
│       ├── Protein shapes (surface or cartoon)
│       ├── Conformational change arrows
│       └── Before/after state panels
│
├── How multiple components interact in a network
│   └── → Pathway diagram
│       ├── Nodes = proteins/metabolites (circles, rectangles)
│       ├── Edges = arrows (activation = →, inhibition = ⊣)
│       └── Compartment boxes (nucleus, cytoplasm, extracellular)
│
├── A single-panel paper summary
│   └── → Graphical abstract
│       ├── Check journal specifications (size, text policy)
│       ├── Show: question → approach → key finding → implication
│       └── Minimal text; max 3–4 panels
│
└── A 3D molecular structure
    └── → Structural diagram
        ├── Use ChimeraX, PyMOL, or RCSB PDB viewer for render
        ├── Annotate active site/binding pocket
        └── Add scale bar (Å or nm)
ScenarioToolFormatKey Consideration
First-author manuscript, fast turnaroundBioRenderPDF/SVGRequires publication license for final submission
Lab with ongoing schematic needsInkscape + master templateSVGReusable elements; free; no vendor lock-in
Graphical abstract for Cell/NatureBioRender or IllustratorPNG at journal specCheck exact pixel dimensions and text policy
Molecular mechanism with protein structureChimeraX + InkscapePNG render + SVG annotationUse PDB structure; annotate key residues
Pathway diagram with many nodesdraw.io / CytoscapeSVG/PDFAuto-layout for networks with >20 nodes

Best Practices

  1. Start with a sketch before opening any tool: Draw the schematic on paper first. Determine what elements are needed, their hierarchy, and the spatial relationships. Opening software first leads to layout decisions driven by tool constraints, not by communication goals.

  2. Define a consistent visual vocabulary before drawing the first panel: Assign colors, shapes, and arrow styles to each biological entity type at the project level. Document these assignments in a legend or lab style guide. Inconsistency across figures in a paper signals carelessness and confuses reviewers.

  3. Use the journal's graphical abstract template: Every high-impact journal (Cell, Nature, PNAS, PLOS) publishes exact dimensions, resolution requirements, and font rules for graphical abstracts. Download the template before starting — resizing after the fact destroys aspect ratios and makes text too small.

  4. Export at publication resolution from the vector source: Always export final figures from the original vector file (SVG, AI, AFDESIGN) at the target DPI, never by screenshot or screen capture. Screenshots are raster at screen resolution (~72 dpi); journals require 300–600 dpi.

  5. Label arrows and connections in captions, not in the diagram: Arrow labels ("activates," "phosphorylates," "recruits") add clutter and reduce diagram readability. Move these relationships to the figure caption using panel reference labels (A, B, C). The diagram should be self-explanatory to someone who reads the caption.

  6. Group related elements visually using proximity, enclosure, and color: Elements that belong together conceptually should be spatially close, share a background color, or be enclosed in a bounding box. Do not use arbitrary spatial arrangements — viewers interpret proximity as association.

  7. Version-control your source files: Store original editable source files (.svg, .afdesign, .ai, .brd) in version-controlled storage alongside the manuscript. Journals frequently request revised figures during revision, and re-creating from a PNG is extremely time-consuming.

Show full SKILL.md (740 more words)Show less

Common Pitfalls

  1. Using inconsistent arrow styles across a figure

    • What goes wrong: Solid arrows and dashed arrows mixed arbitrarily make readers unsure whether dashed means "indirect," "hypothetical," or merely a stylistic choice.
    • How to avoid: Define an arrow legend: solid arrow = direct activation, dashed = indirect, flat bar = inhibition. Use this consistently in every panel of every figure in the paper.

  2. Overloading a single panel with too many elements

    • What goes wrong: Pathway diagrams with 20+ nodes and 30+ arrows cannot be read in a journal figure at 170 mm width. Reviewers ask for simplification; revisions are time-consuming.
    • How to avoid: Limit mechanism panels to ≤8 elements. Move complex pathway context to supplementary figures. Focus the main-text schematic on the core novel finding.

  3. Using BioRender without purchasing the publication license

    • What goes wrong: BioRender figures created under the free or draft license cannot be published. Submitting without proper licensing violates BioRender's terms of service and risks manuscript rejection.
    • How to avoid: Purchase the publication license before creating the final figure version. BioRender generates a citation string that must be included in the figure legend.

  4. Text inside the schematic at 6 pt or smaller at print size

    • What goes wrong: Labels inside pathway nodes or protein icons become illegible at publication dimensions (85 mm single-column). Reviewers flag this; revision requires recreating the entire figure.
    • How to avoid: Work at print size from the start. In Inkscape: set canvas to 85 mm × target height. Minimum label size: 7 pt at 100% print scale.

  5. Red–green arrow encoding for activation–inhibition without shape cues

    • What goes wrong: ~8% of male readers have red–green color vision deficiency and cannot distinguish activation (green) from inhibition (red) arrows.
    • How to avoid: Use distinct arrow shapes: → for activation, ⊣ for inhibition. Color is redundant encoding, not the only cue.

  6. Copying schematic elements from published papers without redrawing

    • What goes wrong: Reproducing figures from published papers without permission violates copyright. This applies to diagrams and icons, not just photographs.
    • How to avoid: Use BioRender's licensed icon library, Reactome's freely licensed pathway diagrams (CC-BY), or Bioicons (free, open icons). Always redraw; never screenshot.

  7. Missing scale bars in structural diagrams

    • What goes wrong: Protein structure renderings without scale bars prevent readers from assessing relative sizes of domains, ligands, or interfaces.
    • How to avoid: Add a scale bar (e.g., "10 Å" or "2 nm") using ChimeraX's scalebar command or annotate in Inkscape after export.

Workflow

  1. Define the message — write one sentence stating what the schematic must communicate
  2. Sketch on paper — rough layout, element list, arrow types
  3. Choose tool — BioRender for icon-heavy biology; Inkscape for custom vectors; ChimeraX for structures
  4. Set canvas to print dimensions — match journal column width before placing any element
  5. Build in layers — background → structural elements (membranes, organelles) → protein/molecule icons → arrows → labels
  6. Apply visual vocabulary — consistent colors, arrow styles, fonts per lab style guide
  7. Run accessibility check — CVD simulation; test grayscale version
  8. Export from vector source — PDF or TIFF at target DPI (≥300 dpi raster, vector for line art)
  9. Archive source file — commit .svg/.afdesign/.brd to version control alongside manuscript

Protocol Guidelines

  1. BioRender publication workflow: Create figure → File → Publish Figure → Generate Attribution → copy citation string into figure legend. The attribution reads: "Created with BioRender.com" with a unique agreement ID. Without this, the figure cannot be legally published.
  2. Inkscape CMYK-safe workflow: Inkscape does not natively support CMYK. For CMYK journals: design in RGB → export to PDF → convert using Ghostscript (gs -sDEVICE=pdfwrite -dUseCIEColor). Verify colors after conversion.
  3. ChimeraX protein structure render: open 6YYT → graphics silhouettes true → lighting soft → saveimage figure.png width 2400 height 2400 → annotate in Inkscape.
  4. Multi-panel figure assembly in Inkscape: Use Inkscape extensions → Grids → set column guides at journal column widths. Import each panel as a linked SVG to enable per-panel updates without recreating the composite.

Further Reading

  • scientific-visualization — data-driven figures (graphs, heatmaps) as distinct from illustrative schematics
  • scientific-manuscript-writing — figure legend writing and integration of schematics into papers
  • latex-research-posters — assembling schematics into poster layouts

© jaechang-hits, CC-BY-4.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/scientific-writing/scientific-schematics of jaechang-hits/SciAgent-Skills.

Open the folder on GitHubat commit 82c862c

Compare with similar skills

Scientific Schematics 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.

Scientific Schematics compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Scientific Schematics this skilljaechang-hits/SciAgent-Skills374—~3.8kAutomated safety check: PassCC-BY-4.0
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Figure Legend Writeraipoch/medical-research-skills1.9k—~1.5kAutomated safety check: PassMIT
Academic Figure SkillTingxiYu/academic-figure-skill4831 repos~7kAutomated safety check: PassApache-2.0
Astra Figure WorkflowIamJerryXu/AstraDraw148—~1.9kAutomated safety check: PassNone
Plotting AgentAr9av/PaperOrchestra6791 repos~2.3kAutomated safety check: PassCustom licence

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Works with

Categories

Questions about Scientific Schematics

What does Scientific Schematics do?

Designing scientific schematics, diagrams, and graphical abstracts. Scientific Schematics is an agent skill from jaechang-hits/SciAgent-Skills. Designing scientific schematics, diagrams, and graphical abstracts.

When should I use Scientific Schematics?

Scientific Schematics fits situations like: creating illustrative (not data-driven) scientific figures; tasks that involve Data visualization; tasks that involve Diagrams.

How do I install Scientific Schematics in Claude Code?

Run `npx skills add jaechang-hits/SciAgent-Skills --skill scientific-schematics -a claude-code`. Or copy the skill folder (skills/scientific-writing/scientific-schematics in jaechang-hits/SciAgent-Skills) into .claude/skills/scientific-schematics in your project. Claude Code loads it when a task matches its description.

How do I install Scientific Schematics in Codex?

Run `npx skills add jaechang-hits/SciAgent-Skills --skill scientific-schematics -a codex`. Or copy the skill folder (skills/scientific-writing/scientific-schematics in jaechang-hits/SciAgent-Skills) into .agents/skills/scientific-schematics in your project. Codex loads it when a task matches its description.

Can I use Scientific Schematics in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add jaechang-hits/SciAgent-Skills --skill scientific-schematics -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/scientific-schematics, .gemini/skills/scientific-schematics, .github/skills/scientific-schematics and .opencode/skills/scientific-schematics in your project.

What does Scientific Schematics need to run?

SKILL.md names no scripts, command-line tools or credentials: Scientific Schematics is instructions for the agent only.

Does Scientific Schematics access the network?

SKILL.md names 6 domains. As links in the text: biorender.com, clauswilke.com, bioicons.com, reactome.org, ncbi.nlm.nih.gov and doi.org. This is read from the text; nothing was executed.

Is Scientific Schematics safe to install?

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. Review the folder before installing.

What licence does Scientific Schematics use?

Scientific Schematics is published under the CC-BY-4.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Scientific Schematics use?

About 3.8k tokens (SKILL.md is roughly 15k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Scientific Schematics?

Skills that share tags, products or a category with Scientific Schematics: Engineering Figure Agent (heyu-233/engineering-figure-agent, 307 stars), Figure Legend Writer (aipoch/medical-research-skills, 1.9k stars), Academic Figure Skill (TingxiYu/academic-figure-skill, 483 stars) and Astra Figure Workflow (IamJerryXu/AstraDraw, 148 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Scientific Schematics?

jaechang-hits (a GitHub user) maintains it in jaechang-hits/SciAgent-Skills, which has 374 GitHub stars. The repository holds 169 skills in this directory. The repository was last updated on September 29, 2026.

Source: jaechang-hits/SciAgent-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.