bootstrap-project-context

bootstrap-project-context is a skill for Claude Code, Codex from Rezenders/scientific_writing_agent. It costs 41 tokens per session (1,102 once invoked), scanned A, original, Apache-2.0.

A setup workflow for a scientific-writing project that interviews the author, inspects the manuscript, and fills project context files with approved facts. It prepares information about the paper, terminology, contributions, evidence, claims, and reviewer requests.

In plain words
What is it for?
Use it after installing the scientific-writing workflow and before manuscript writing, claim review, memory setup, or other substantive work.
Why use it?
It gives later writing and review tasks a reliable project-specific foundation instead of generic assumptions. It also avoids inventing missing scientific content.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one. Also seen: mentions CLAUDE.md; installed under .agents/ (shared by several agents); mentions AGENTS.md.

Good fit Use it after installing the scientific-writing workflow and before manuscript writing, claim review, memory setup, or other substantive work.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/rezenders/scientific_writing_agent/bootstrap-project-context
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add Rezenders/scientific_writing_agent --skill bootstrap-project-context
Clone the repo
git clone --depth 1 https://github.com/Rezenders/scientific_writing_agent

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for bootstrap-project-context

README.md
[![agentmods](https://agentmods.dev/badge/skills/rezenders/scientific_writing_agent/bootstrap-project-context/github.svg)](https://agentmods.dev/skills/rezenders/scientific_writing_agent/bootstrap-project-context)
Your own site
<a href="https://agentmods.dev/skills/rezenders/scientific_writing_agent/bootstrap-project-context"><img src="https://agentmods.dev/badge/skills/rezenders/scientific_writing_agent/bootstrap-project-context/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for bootstrap-project-context

Your own site · 80×15
<a href="https://agentmods.dev/skills/rezenders/scientific_writing_agent/bootstrap-project-context"><img src="https://agentmods.dev/badge/skills/rezenders/scientific_writing_agent/bootstrap-project-context.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 41 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,102 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00041 $0.01102
Opus 5.5 $0.00016 $0.00441
Sonnet 5 $0.00008 $0.00220
Haiku 4.5 $0.00004 $0.00110

Measured 2d ago against content hash 12b909c5033c, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-23, from the pricing page.

Security

Grade A, and why

bootstrap-project-context scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.agents/skills/bootstrap-project-context/SKILL.md · 121 lines

How it starts

The opening of the file, as written. The whole thing — 121 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Bootstrap Project Context

Use this skill after scientific_writing_agent.py install and before bootstrap-memory, write-to-intent, or substantive review workflows.

This skill is an interactive setup workflow. Its purpose is to replace generic placeholders in .agents/context/ with author-approved project facts. Do not invent missing scientific content.

Goals

Populate or update these focused context files:

  • .agents/context/manuscript-context.md
  • .agents/context/paper-model.md
  • .agents/context/terminology.md
  • .agents/context/contributions.md
  • .agents/context/evaluation-claims.md
  • .agents/context/claim-ledger.md
  • .agents/context/do-not-say.md
  • .agents/context/reviewer-contracts.md when reviews exist

Leave .agents/context/open-findings.md empty or initialized unless there are known unresolved findings.

Workflow

Phase 1 — Inspect Existing Project Evidence

Before asking questions, inspect the repository for available facts:

  1. Locate the manuscript entry point (<MAIN_TEX>) by checking common names such as main.tex, paper.tex, main-acm.tex, and files containing \documentclass.
  2. Read the entry point and identify \input / \include section files.
  3. Inspect macro/config files when obvious, such as macros.tex, preamble.tex, config/macros.tex, or files included before \begin{document}.
  4. Inspect Makefile, latexmkrc, CI files, or README build instructions for build and lint commands.
  5. Scan the abstract, introduction, conclusion, and evaluation/results sections when available for contribution and evaluation claims.
  6. Check for existing AGENTS.md, CLAUDE.md, reviewer-response files, or project notes.

Report the facts inferred from repository evidence and clearly mark uncertain items.

Phase 2 — Ask a Minimal Questionnaire

Ask only for information not inferable from the repository or requiring author confirmation.

Use this questionnaire, omitting questions already answered by evidence:

Read the full file on GitHub · 121 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2d ago First seen · 121 lines · 41 tokens per session scan A 12b909c5033c

Subscribe to this mod's changes

bootstrap-project-context is a skill published in the GitHub repository Rezenders/scientific_writing_agent (12 stars, last pushed 2d ago), licensed Apache-2.0. It adds 41 tokens to every session and 1,102 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-21.

Related

Other skills, from other repositories

instrument-data-to-allotrope

Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…

anthropics/knowledge-work-plugins · 123 tokens

exploratory-data-analysis

Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain…

K-Dense-AI/scientific-agent-skills · 83 tokens

matlab

Build, review, migrate, and safely plan MATLAB or GNU Octave numerical workflows, including arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.

K-Dense-AI/scientific-agent-skills · 42 tokens

phylogenetics

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.

K-Dense-AI/scientific-agent-skills · 68 tokens

research-engineer

An uncompromising Academic Research Engineer. Operates with absolute scientific rigor, objective criticism, and zero flair. Focuses on theoretical correctness, formal verification, and optimal implementation across any required technology.

davila7/claude-code-templates · 43 tokens

mapping-to-snomed

Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED CT, run an ECL…

maziyarpanahi/openmed · 205 tokens