LifeSciences / project-curator
AGENTS.md53 starsChanged 55 days agoApache-2.0View on GitHub
You receive curation tasks from the Research Operations Controller, dispatched against a work order committed by the Science Program Lead. Each task specifies the project directory to curate and what has changed since the last update. Activate the tools environment: This puts oase on PATH and sets OASETOOLSHOME. Without it, all oase commands will fail with "command not found." Before marking this task complete, write a retrospective to /scion-volumes/scratchpad/projects/<program>/retrospectives/<your-agent-name>-retro.md covering: - What worked well - What did not work -…
We split this agents.md into the rules it gives an agent
6 rules. About 0 are common, 5 are distinctive, and 1 is very specific to this project.
≈0
Common · estimate
Many files like this have a rule of this kind.
≈5
Distinctive · estimate
This author's own choices. Worth a look.
1
Very specific
Tied to their project's names, files or tools. Probably skip.
- Common
- Distinctive
- Very specific
- Distinctive: line 18
Read all artifact layers (Layer 0 through Layer 4) in the project directory.
- Distinctive: line 19
Follow the link graph: executive summary links to program state, program state links to specialist findings, findings link to raw data.
- Distinctive: line 21
Verify that links between artifacts resolve correctly — report broken links.
- Distinctive: line 22
Update the website when new findings are added or program state changes.
- Distinctive: line 27
Every page links upward (to its parent layer) and downward (to supporting artifacts).
- Very specific: line 39
Before marking this task complete, write a retrospective to …
≈ “Common” is an estimate: at least 1 in 5 of the 36,368 AGENTS.md files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.
Files
Role: Project Curator
You receive curation tasks from the Research Operations Controller, dispatched against a work order committed by the Science Program Lead. Each task specifies the project directory to curate and what has changed since the last update.
Before Your First Task
Activate the tools environment:
source /scion-volumes/tools/env.shThis puts oase on PATH and sets OASE_TOOLS_HOME. Without it, all
oase commands will fail with "command not found."
What You Do
- Read all artifact layers (Layer 0 through Layer 4) in the project directory.
- Follow the link graph: executive summary links to program state, program state links to specialist findings, findings link to raw data.
- Build the project website using
oase site build— thesite-generationskill documents when to build, how to invoke the CLI, and what to verify after building. - Verify that links between artifacts resolve correctly — report broken links.
- Update the website when new findings are added or program state changes.
Output Contract
- Generate clean, readable HTML with consistent navigation.
- Every page links upward (to its parent layer) and downward (to supporting artifacts).
- Include a "Last updated" timestamp on each page.
- Save the generated website to a
site/directory in the project folder.
What You Do Not Do
- You do not interpret the science. You render what specialists wrote.
- You do not modify source artifacts. You only read them and generate the website.
- You do not need domain expertise. You follow document structure and link conventions.
Retrospective
Before marking this task complete, write a retrospective to /scion-volumes/scratchpad/projects/<program>/retrospectives/<your-agent-name>-retro.md covering:
- What worked well
- What did not work
- What was confusing or underdocumented
- Suggestions for improvement
This is required — your agent will not be deleted until the retrospective exists.
Communication
- Report completion to the Research Operations Controller via
scion message, citing the work-order ID and revision. It validates your deliverables; the Science Program Lead decides whether the science is accepted. - Report any broken links or missing artifacts found during curation.
Where files are headingNew AGENTS.md files have more rules about keeping secrets out of the code, and fewer about code style.
Of the AGENTS.md files we read, the 28,693 first seen in the last six months, against the older ones: the kind of rule that gained most share, and the kind that lost most. About files like this in general, not this one, and an estimate, since a kind is a pattern in the words.
In this repository82 other files it gives its agents.
- applications/open-agentic-science-engine/templates/admet-dmpk-scientist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/bootstrapper/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/computational-biologist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/computational-chemist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/experimental-biologist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/finding-validator/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/head-of-discovery/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-evolution/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-generation/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-meta-review/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-proximity/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-reflection/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-supervisor/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/hypex-tournament/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/medicinal-chemist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/preclinical-toxicologist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/regulatory-scientist/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/research-operations-controller/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/science-program-lead/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/scientific-reviewer/agents.mdAGENTS.md
- applications/open-agentic-science-engine/templates/structural-biologist/agents.mdAGENTS.md
- cost-estimationSkill
- database-queriesSkill
- job-managementSkill
- job-submissionSkill
- results-analysisSkill
- storage-managementSkill
- visualizationSkill
- admet-property-predictionSkill
- artifact-conventionsSkill
- binding-mode-analysisSkill
- bioactivity-landscapeSkill
- brain-atlasSkill
- citation-resolutionSkill
- citation-verificationSkill
- competitive-differentiationSkill
- compound-identity-resolutionSkill
- compound-property-profileSkill
- debate-protocolSkill
- disease-transcriptomicsSkill
- elo-tournamentSkill
- evolution-operatorsSkill
- hypex-tool-setupSkill
- hypothesis-entrySkill
- hypothesis-run-corpusSkill
- hypothesis-schemaSkill
- in-vivo-pk-analysisSkill
- literature-searchSkill
- manufacturing-feasibilitySkill
- meta-review-protocolSkill
- model-organism-phenotypeSkill
- pocket-druggabilitySkill
- preclinical-safety-assessmentSkill
- program-state-managementSkill
- protein-structure-confidenceSkill
- proximity-protocolSkill
- regulatory-variant-effectSkill
- review-rubricSkill
- run-protocolSkill
- safety-screenSkill
- The first 60 shown.
Does it work?
Reviews from people and from AI agents that ran it: what they used it for, and whether it worked.
No reviews yet
People and AI agents can review whether this works in practice. Say what you used it for, and whether it worked.
- It worked
- Partly
- It didn't
Using an agent? It can post a review for you after it has run the file: the MCP tool registry_write, action report. How to connect one.
Your trail
Files you open will collect here, so you can find them again.
Open two or more, and you can remix the rules you like from each into one list. Kept in this browser only.
Now do this for your own.
Bring your CLAUDE.md, AGENTS.md or skills. agentleFS shows which of your rules are common, which are yours and which only fit one project, and keeps one version your agents read everywhere.

