{
  "title": "Reproducible Literature Synthesis with infrastructure/search and infrastructure/reference",
  "version": "0.1",
  "doi": "10.5281/zenodo.21298895",
  "doi_url": "https://doi.org/10.5281/zenodo.21298895",
  "zenodo_record": "https://zenodo.org/records/21298894",
  "record_id": "21298895",
  "publication_date": "2026",
  "resource_type": {
    "title": "Journal article",
    "type": "publication",
    "subtype": "article"
  },
  "creators": [
    {
      "name": "Daniel Ari Friedman",
      "affiliation": "Active Inference Institute",
      "orcid": "0000-0001-6232-9096"
    }
  ],
  "description": "This paper documents template_search_project, the literature-search exemplar shipped with the Research Project Template (https://github.com/docxology/template). The project demonstrates two configurable, reproducible pipelines sharing the same configuration file and the same infrastructure/search/ + infrastructure/reference/ modules. The standard pipeline (scripts/run_search_pipeline.py) handles a single SearchQuery end-to-end. The deep-search pipeline (scripts/run_deep_search.py, see ) fans out across a list of keywords (each capped at 100 papers per keyword from deep_search.max_results_per_keyword in manuscript/config.yaml), fully enriches every paper with its abstract and PDF fulltext, and (optionally) uses the local LLM to write a multi-section reading note for every paper. When a deep-search aggregate exists, the latest run covered 3 keyword(s) with unique paper(s) after cross-keyword deduplication. Both turn a free-text topic into: 1. a deduplicated, year-filtered set of papers drawn from arXiv, Crossref, optional local corpora, and (opt-in) Paperclip (https://paperclip.gxl.ai/); 2. a Pandoc-compatible references.bib byte-identical in style to the canonical exemplar in template_code_project (../../template_code_project/manuscript/references.bib) (file manuscript/references.bib); 3. cached abstracts and (optionally) extracted PDF full text, written to disk under stable per-paper identifiers; and 4. an LLM-synthesised reading report assembled from per-paper analyses and a cross-corpus thematic synthesis, all produced by a local Ollama model with pinned seed and temperature. All discovery logic lives in infrastructure/search/literature/ (source on GitHub (https://github.com/docxology/template/tree/main/infrastructure/search/literature)); all export logic lives in infrastructure/reference/citation/ (source on GitHub (https://github.com/docxology/template/tree/main/infrastructure/reference/citation)); LLM synthesis reuses the existing infrastructure/llm/ (source on GitHub (https://github.com/docxology/template/tree/main/infrastructure/llm)) bridge. The project itself contains only thin orchestration, manuscript prose, and a test suite — perfectly mirroring the two-layer architecture the template enforces. The motivating concern is reproducibility: a query at time $t_0$ should produce the same results at time $t_1$ unless the cache is explicitly invalidated. This is achieved by deterministic search caching keyed on canonical query identity, on-disk caching of every fetched abstract / PDF, and pinned LLM seeds. The same manuscript/config.yaml that drives the pipeline is also the only configuration any reviewer needs. Run snapshot. With the bundled manuscript/config.yaml, the most recent pipeline execution evaluated the query \"reproducible research optimization\" against local, returned 6 deduplicated paper(s) (4 carrying a DOI, 6 carrying an abstract), and recorded backend errors: none. Resolve `{{…}} tokens by running scripts/z_generate_manuscript_variables.py after run_search_pipeline.py; the script writes output/data/manuscript_variables.json and resolved markdown under output/manuscript/`, which the PDF-rendering stage prefers when present. Keywords: literature search, BibTeX automation, reproducible research, local LLM synthesis, scientific infrastructure",
  "keywords": [
    "literature search",
    "automated reference management",
    "BibTeX",
    "reproducible research",
    "local LLM synthesis"
  ],
  "files": [
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      "name": "Friedman_2026_Reproducible_003aed0d.pdf",
      "size_bytes": 843313,
      "checksum": "md5:2164816cb48414072020a2eb240dabd9",
      "download_url": "https://zenodo.org/api/records/21298895/files/Friedman_2026_Reproducible_003aed0d.pdf/content"
    }
  ],
  "related_resources": [],
  "github_repo": "",
  "source": "zenodo-only",
  "checked_at": "2026-07-10T19:31:12Z"
}