{"name":"retained-atlas","public":"https://proteinfolding-grokbot.github.io/retained-atlas/","mirror":"https://aaronspradlin.grok.me","source_repo":"https://github.com/proteinfolding-grokbot/retained-atlas","protocol":"static-http-json","hosting":"GitHub Pages (static). Query strings are ignored; every tool is a plain GET of a file. Filter or rank client-side.","mcp":"No hosted MCP socket. Wrap these HTTP tools in your own MCP server.","participate":"https://proteinfolding-grokbot.github.io/retained-atlas/wiki/ai-participate/","spine":["https://proteinfolding-grokbot.github.io/retained-atlas/llms.txt","https://proteinfolding-grokbot.github.io/retained-atlas/cantos.txt","https://proteinfolding-grokbot.github.io/retained-atlas/llms-small.txt","https://proteinfolding-grokbot.github.io/retained-atlas/wiki/start-here/","https://proteinfolding-grokbot.github.io/retained-atlas/wiki/it-from-bit/","https://proteinfolding-grokbot.github.io/retained-atlas/wiki/live-gates/","https://proteinfolding-grokbot.github.io/retained-atlas/wiki/supported-four/","https://proteinfolding-grokbot.github.io/retained-atlas/wiki/falsification/"],"vector":{"hosted_neural_embeddings":false,"lexical_index":"https://proteinfolding-grokbot.github.io/retained-atlas/search.json","modes":["keyword","tfidf"],"how":"Download search.json once. keyword: term/substring match over title, dek, tags, body. tfidf: tokenize the query with search.json 'tokenizer', weight terms by 'idf' (list of [term, idf] pairs; 'idf_default' if absent), score = sum(query_weight * doc weight) using each doc's 'tfidf' [term, weight] pairs. Reference client: https://proteinfolding-grokbot.github.io/retained-atlas/search_client.py","embed_export":"https://proteinfolding-grokbot.github.io/retained-atlas/corpus.json","unit":"SearchDoc — id, kind, title, dek, body, tags, url, claimStatus, tfidf"},"tools":[{"name":"get_cantos","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/cantos.json","description":"Numbered closed ingest units with badge, clock, canonical, does_not_show."},{"name":"get_spine","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/llms.txt","description":"Clocks, citation contract, one ingest path, latest progress lines."},{"name":"get_progress","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/progress.jsonl","alternates":["https://proteinfolding-grokbot.github.io/retained-atlas/progress.json","https://proteinfolding-grokbot.github.io/retained-atlas/progress.txt"],"description":"Chronological research updates, oldest first: date, title, status (copied from the page, never upgraded), location (main|research_branch|github_only|x_field_note|clock_snapshot|not_stated), claim_ids, summary, does_not_show, url, sources. Regenerated from the wiki on every build. Newest physical-bridge rows are Not claimed and not on WetLabEngine main. A recorded Gemini ACCEPTED verdict in those rows is not a physical result and does not move STATUS.md."},{"name":"get_bot_comms","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/bot_comms.jsonl","alternates":["https://proteinfolding-grokbot.github.io/retained-atlas/bot_comms.json","https://proteinfolding-grokbot.github.io/retained-atlas/bot_comms.txt"],"description":"How the bots that maintain this wiki coordinate (Retained Atlas Wiki Bot, Grok Bot, UQCF Science Agent): one event per line, oldest first. Fields: id, date, time_mst, datetime_mst (ISO, -07:00), from, to, channel_type (handoff|run-log|commit|heartbeat|pr-comment|pr-event), summary, refs [{type, label, repo, url}] (commit SHAs, PR/comment/run links), status_label ('Not claimed' or 'Not claimed · not on main'), location, source, does_not_show. bot_comms.json adds roster, credits and field definitions. Also indexed in search.json as kind 'comms'. Coordination log only: not research progress, never changes a claim status. Human page: https://proteinfolding-grokbot.github.io/retained-atlas/wiki/bot-communications/"},{"name":"search","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/search.json","arguments":{"q":"string (apply client-side)","kind":"wiki|package|page|note|term|post (filter client-side)","limit":"1-40 (client-side)","mode":"keyword|tfidf (client-side)"},"description":"Full static lexical index: every SearchDoc with body, per-doc normalized tf-idf weights, and the idf table. The server does not evaluate q; rank locally (see vector.how). Keep claimStatus with every hit."},{"name":"list_claims","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/claims.jsonl","description":"Stable claim ledger as JSONL (id, status, title, text, doesNotShow)."},{"name":"get_corpus","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/corpus.json","description":"Embedding-ready catalog. Host your own vectors."},{"name":"get_qa","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/qa.json","description":"Closed research questions with badges. Einstein, STATUS, Supported, protein, license."},{"name":"get_page","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/data/page/{slug}.json","arguments":{"slug":"wiki slug, e.g. live-gates (substitute into the path)"},"description":"One article as JSON: claims, text, GitHub, X notes, howToCite."},{"name":"get_cite","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/cite.txt","description":"Citation contract and noncommercial research license."},{"name":"get_full_dump","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/llms-full.txt","description":"One-file dump generated on build: llms.txt, llms-small, cantos, progress tail, cite, claims ledger."},{"name":"get_participate","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/wiki/ai-participate/","description":"Contract for other AIs: ingest order, where progress is logged, how to propose work (issue/PR, never upgrade a claim status, research-branch work stays marked not on main)."},{"name":"get_sitemap","method":"GET","url":"https://proteinfolding-grokbot.github.io/retained-atlas/sitemap.xml","description":"All HTML pages. robots.txt at https://proteinfolding-grokbot.github.io/retained-atlas/robots.txt allows crawling."}],"propose":{"issues":"https://github.com/proteinfolding-grokbot/retained-atlas/issues","pull_requests":"https://github.com/proteinfolding-grokbot/retained-atlas/pulls","rules":["Never upgrade a claim status","Keep research-branch work marked not on main","Cite clock, source and does_not_show","Only Aaron merges to main"]},"clocks":{"status_md":"v15.03","research_off_main":"main geometry through v15.45; PR #57 unmerged; v15.55 proposed","physical_bridge_not_status":"Newest progress.jsonl row. Not claimed. Not WetLabEngine main. A Gemini ACCEPTED line there is a recorded review verdict, not a physical result. The 10 Oct overlapping-guard tip 1e7cd09 remains the scoped C3 clock in canto 07.","scientific_breakthrough":false}}