Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
Maintain agent-authored investigation memory over Genomi evidence links, reviewed source findings, decisions, contradictions, and unresolved questions.
Install Journal
$ npx skills add exon-research/genomi --skill journal -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install exon-research/genomi journal --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/exon-research/genomi.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/journal .claude/skills/journal && 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 "journal" agent skill from https://github.com/exon-research/genomi/tree/master/skills/journal into .claude/skills/journal/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal", 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/exon-research/genomi/tree/master/skills/journalType 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 exon-research/genomi --skill journal -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install exon-research/genomi journal --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/journal .agents/skills/journal && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "journal" agent skill from https://github.com/exon-research/genomi/tree/master/skills/journal into .agents/skills/journal/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal", 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 exon-research/genomi --skill journal -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install exon-research/genomi journal --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/journal .cursor/skills/journal && 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 "journal" agent skill from https://github.com/exon-research/genomi/tree/master/skills/journal into .cursor/skills/journal/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal", 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/exon-research/genomi.git --path skills/journal--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 exon-research/genomi --skill journal -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install exon-research/genomi journal --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/journal .gemini/skills/journal && 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 "journal" agent skill from https://github.com/exon-research/genomi/tree/master/skills/journal into .gemini/skills/journal/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal", 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 exon-research/genomi journalInstalls 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 exon-research/genomi --skill journal -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/journal .github/skills/journal && 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 "journal" agent skill from https://github.com/exon-research/genomi/tree/master/skills/journal into .github/skills/journal/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal", 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 exon-research/genomi --skill journal -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install exon-research/genomi journal --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/journal .opencode/skills/journal && 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 "journal" agent skill from https://github.com/exon-research/genomi/tree/master/skills/journal into .opencode/skills/journal/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "journal", 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.
Facts
- Skill name
journal- GitHub stars
- 484
- Token cost
- ~1.2k tokens
- SKILL.md length
- 585 words
- Files
- 1
- Skills in repo
- 20
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Maintain agent-authored investigation memory over Genomi evidence links, reviewed source findings, decisions, contradictions, and unresolved questions.
- Research & Science work in your project
- SKILL.md covers Goal, Scopes, Cross-Capability Synthesis and Tools, plus 1 more section
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Journal is an agent skill from exon-research/genomi. Maintain agent-authored investigation memory over Genomi evidence links, reviewed source findings, decisions, contradictions, and unresolved questions.
Its SKILL.md is about 1.2k 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. The repository describes itself as: Local-first, open-source Claude Science alternative, before Claude Science is a thing. Turn your AI agent into personal DNA expert. The licence is Apache-2.0.
When your agent uses it
- Research & Science work in your project
Example prompts
- “/journal”
What it can do on your machine
Read from SKILL.md and the folder at commit 1df4f5b. 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
No URLs in SKILL.md.
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
Journal loads about 1.2k tokens when it runs. Until then it costs about 40 tokens; SKILL.md has 585 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.
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 exon-research/genomi at commit 1df4f5b, republished under its Apache-2.0 licence (© exon-research). 585 words, ~1,235 tokens.
Download SKILL.mdSave it as
.claude/skills/journal/SKILL.md (or your agent's skills folder).- name
- journal
- description
- Maintain agent-authored investigation memory over Genomi evidence links, reviewed source findings, decisions, contradictions, and unresolved questions.
- tools
- journal.append_entry, journal.search_entries, journal.summarize, journal.export_memory, research.list_sources, research.build_target_packet…
- mutating
- true
Journal and Research Memory
Use journal when an investigation spans multiple Genomi tools and the host agent needs to record reasoning, evidence links, or reviewed source findings.
Goal
Record the host agent's observations, hypotheses, decisions, contradictions, plans, summaries, and unresolved questions while preserving traceability to Genomi operations and evidence identifiers.
Journal entries are the append-only notebook. Reviewed research records are source-memory entries in the evidence DB. They live in the same capability because both preserve investigation memory, but they have different roles: journal entries explain what the host agent concluded or still needs to check; reviewed research records store source-backed findings for reuse.
Neither journal entries nor reviewed research records rank candidates by themselves. Candidate ranking still belongs to the relevant evidence tools, with reviewed source records passed only when a tool explicitly accepts them.
Scopes
session: current chat/session notebook. It may link private/sample evidence only after scoped Active Genome Index access is approved for this session.project: current workspace notebook. It is public/target-scoped and rejects private/sample evidence links.
Cross-Capability Synthesis
A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.
Tools
journal.append_entry
Append a new journal entry, or append evidence links and/or an amendment to an existing entry.
Use when: Record an observation, hypothesis, decision, contradiction, plan, summary, unresolved question, or append evidence/amendment to an existing entry.
Why necessary: Multi-tool investigations need one append-only write path for notes, evidence links, and corrections so agents do not sequence separate journal mutations.
Not for: Not source evidence and not a candidate-ranking input by itself.
Example prompts: Record this supported Genomi finding with evidence links.
Result semantics: With no entry_id, creates a new entry. With entry_id, adds evidence_links and/or stores content as an append-only amendment; original entry text is preserved.
journal.export_memory
Return a MemOS-shaped JSON memory artifact from journal entries without requiring or writing to MemOS.
Use when: The user or host agent explicitly wants the journal exported for ingestion by another memory system.
Why necessary: External memory systems need a shaped export without requiring Genomi to write to that system.
Result semantics: Exports journal memory records only; private evidence links are omitted unless explicitly requested and approved.
Show full SKILL.md (202 more words)Show less
journal.search_entries
Token-search session and project journal entries by scope, target, tag, entry type, and text.
Use when: The host agent needs to recover recorded investigation state before continuing a multi-tool Genomi analysis.
Why necessary: Agents need to recover prior investigation state without treating chat memory as authoritative evidence.
Result semantics: Returns agent-authored notes and traceability links; journal entries are not source evidence.
journal.summarize
Summarize journal state into observations, decisions, contradictions, unresolved questions, and commonly linked evidence sources.
Use when: The host agent needs a compact state of an ongoing Genomi investigation before deciding next evidence steps.
Why necessary: Long investigations need compact journal state before the agent chooses the next evidence step.
Result semantics: Summarizes journaled reasoning only; evidence authority remains in the linked Genomi outputs and public sources.
Operating Checks
- Link evidence for traceability, but treat linked Genomi outputs and public sources as the authority.
- When a downstream tool needs
source_records, provide reviewed research or tool-returned source records that satisfy that tool's verified source-record input contract. - Use
journal.append_entrywithentry_idfor corrections; do not silently overwrite entries. - Omit private evidence links from memory exports unless the user explicitly requests them and scoped Active Genome Index access is approved for the session.
© exon-research, Apache-2.0. 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/journal of exon-research/genomi.
Open the folder on GitHubat commit 1df4f5b
Compare with similar skills
Journal 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 |
|---|---|---|---|---|---|---|
| Journal this skillexon-research/genomi | 484 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Hypothesis Generationspacering-net/codeg | 3.8k | 15 repos | ~3.6k | Automated safety check: Notes | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 83k | 5 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 46k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Read arXiv Paperkarpathy/nanochat | 58k | 2 repos | ~494 | Automated safety check: Pass | MIT | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT |
Similar skills
GitHub Deep Research
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
Nature Paper Card
Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
Read arXiv Paper
karpathy/nanochat
Fetches the TeX source of an arXiv paper from its URL, reads it and writes a markdown summary tied to the nanochat project.
Content Research Writer
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
Peer Review
spacering-net/codeg
Structured manuscript/grant review with checklist-based evaluation.
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Related
Categories
Questions about Journal
What does Journal do?
Maintain agent-authored investigation memory over Genomi evidence links, reviewed source findings, decisions, contradictions, and unresolved questions. Journal is an agent skill from exon-research/genomi. Maintain agent-authored investigation memory over Genomi evidence links, reviewed source findings, decisions, contradictions, and unresolved questions.
When should I use Journal?
Journal fits situations like: research & Science work in your project.
How do I install Journal in Claude Code?
Run `npx skills add exon-research/genomi --skill journal -a claude-code`. Or copy the skill folder (skills/journal in exon-research/genomi) into .claude/skills/journal in your project. Claude Code loads it when a task matches its description.
How do I install Journal in Codex?
Run `npx skills add exon-research/genomi --skill journal -a codex`. Or copy the skill folder (skills/journal in exon-research/genomi) into .agents/skills/journal in your project. Codex loads it when a task matches its description.
Can I use Journal 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 exon-research/genomi --skill journal -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/journal, .gemini/skills/journal, .github/skills/journal and .opencode/skills/journal in your project.
What does Journal need to run?
SKILL.md names no scripts, command-line tools or credentials: Journal is instructions for the agent only.
Does Journal access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Journal 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 Journal use?
Journal is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Journal use?
About 1.2k tokens (SKILL.md is roughly 4.9k 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 Journal?
Skills that share tags, products or a category with Journal: Hypothesis Generation (spacering-net/codeg, 3.8k stars), GitHub Deep Research (bytedance/deer-flow, 83k stars), Nature Paper Card (Yuan1z0825/nature-skills, 46k stars) and Read arXiv Paper (karpathy/nanochat, 58k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Journal?
exon-research (a GitHub organization) maintains it in exon-research/genomi, which has 484 GitHub stars. The repository holds 20 skills in this directory. The repository was last updated on August 31, 2026.
Source: exon-research/genomi on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.