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  • 32cc6bcbf2 Revert "Add a new Image Data Commons tool, plus Wikidata skill coverage" #606 feature/close-life-sciences-skill-gaps Shanghua Gao 2026-09-18 09:38:38 -04:00
  • a90693c29c Add a new Image Data Commons tool, plus Wikidata skill coverage Shanghua Gao 2026-09-18 09:33:26 -04:00
  • 3b5474eaf5 Merge: drop redundant manual catalog fix, bot already applied it Shanghua Gao 2026-09-18 05:24:17 -04:00
  • ab04e6d63e Regenerate API key catalog for PROTOCOLS_IO_API_KEY Shanghua Gao 2026-09-18 05:23:24 -04:00
  • 9e98744546 chore: sync API key catalog [skip ci] github-actions[bot] 2026-09-18 09:21:50 +00:00
  • eebcb851bc Add a brand-new protocols.io tool, plus 5 more skill revisions Shanghua Gao 2026-09-18 05:21:38 -04:00
  • 7891022512 Close 4 gaps surfaced by an adversarial self-review of this campaign Shanghua Gao 2026-09-17 22:22:48 -04:00
  • c0368a3a13 Update the CLI subcommand count in the setup skill #607 docs/setup-skill-stale-counts Shanghua Gao 2026-09-17 20:25:00 -04:00
  • f1ab115b2e Update stale counts in the setup skill Shanghua Gao 2026-09-17 19:39:12 -04:00
  • c89713fde8 Revise 31 skills for remaining biomedical straggler tool families Shanghua Gao 2026-09-17 10:20:40 -04:00
  • e12ae37d06 Revise 12 skill clusters for previously-unwrapped tool families (long tail) Shanghua Gao 2026-09-17 09:31:04 -04:00
  • ddbf72e346 Revise 8 more skills and add 1 more for previously-unwrapped tool families Shanghua Gao 2026-09-17 07:47:09 -04:00
  • a15e4ed993 Revise 9 more skills for previously-unwrapped tool families Shanghua Gao 2026-09-17 07:35:56 -04:00
  • 750437115e Revise 8 more skills for previously-unwrapped tool families Shanghua Gao 2026-09-17 07:27:36 -04:00
  • ebaf62c2d1 Revise 3 more skills for previously-unwrapped tool families Shanghua Gao 2026-09-17 06:32:36 -04:00
  • bdbcff76ab Revise 4 skills and add 1 more for previously-unwrapped tool families Shanghua Gao 2026-09-17 06:25:38 -04:00
  • ba68074982 Add 3 more skills for previously-unwrapped tool families Shanghua Gao 2026-09-17 06:19:20 -04:00
  • a1b028dc21 Add 5 skills closing gaps vs. Claude for Life Sciences marketplace Shanghua Gao 2026-09-17 05:43:42 -04:00
  • 2128ff571b Retry the publish verification before calling it a mismatch (#605) main Shanghua Gao 2026-09-17 04:15:15 -04:00
  • f075c2a75e Publish the .mcpb from CI instead of by hand (#604) Shanghua Gao 2026-09-17 00:10:04 -04:00
  • e69495f01e Start the built .mcpb in CI instead of only inspecting it (#603) Shanghua Gao 2026-09-16 23:45:57 -04:00
  • 2cb460dfe3 Release v1.5.1 v1.5.1 github-actions[bot] 2026-09-17 03:24:55 +00:00
  • 47d43871b0 chore: sync server.json version to 1.5.0 [skip ci] v1.5.0 v1.5.0 GitHub Action 2026-09-16 22:08:19 +00:00
  • 3145efb822 Merge pull request #601 from mims-harvard/release/1.5.0 Shanghua Gao 2026-09-17 06:07:12 +08:00
  • 6936c33113 Merge pull request #602 from mims-harvard/fix/http-client-positional-args Shanghua Gao 2026-09-17 06:06:24 +08:00
  • 9778b89588 Fix: accept positional arguments in ToolUniverseClient #602 fix/http-client-positional-args Shanghua Gao 2026-09-16 17:53:13 -04:00
  • 1f3ff54204 Release tooluniverse 1.5.0 #601 release/1.5.0 Shanghua Gao 2026-09-16 17:33:58 -04:00
  • e8313460c0 Drop --no-sync: the Claude Desktop bundle on main never starts (#600) Shanghua Gao 2026-09-16 23:16:02 +08:00
  • f7aeb281cc Fix Claude Desktop MCPB requirements and dependency setup (#591) mcpb Shanghua Gao 2026-09-16 22:12:39 +08:00
  • 20f9b51e3a Fix MCPB requirements and prepare UV dependencies before launch #591 fix/mcpb-python-314 Shanghua 2026-09-16 09:57:36 -04:00
  • 9e29bc8fce Retry openFDA rate limits in the FDA label tools (#599) Shanghua Gao 2026-09-16 21:54:17 +08:00
  • c8ae1f1542 fix: paginate Cellosaurus search with Solr rows/start (#596) zhv50 2026-09-16 05:02:47 -05:00
  • 0ccfa4aba2 fix: reject blank Cellosaurus search queries (#595) zhv50 2026-09-16 05:02:42 -05:00
  • 6d0ed9779b fix: link Europe PMC guideline results through the PMC route (#594) zhv50 2026-09-16 05:02:34 -05:00
  • 314491cd52 Merge pull request #597 from mims-harvard/fix/duplicate-tool-names Shanghua Gao 2026-09-16 17:25:30 +08:00
  • 2885fefc1d Fix duplicate tool-name collisions: OpenMeteo_get_air_quality, UniProt_get_proteome #597 fix/duplicate-tool-names Shanghua Gao 2026-09-16 05:12:17 -04:00
  • e2e76b0e88 Merge pull request #593 from mims-harvard/docs/skill-sweep-round2 Shanghua Gao 2026-09-16 15:11:08 +08:00
  • 8fc703fa56 Fill remaining skill gaps: DHS Program, EBI sequence tools, DeepSpotM, MolGlueDB #593 docs/skill-sweep-round2 Shanghua Gao 2026-09-16 02:29:25 -04:00
  • f371e540bb Merge pull request #592 from mims-harvard/docs/skills-sweep-new-tools-since-v1.4.1 Shanghua Gao 2026-09-16 13:26:09 +08:00
  • 0142e85518 Sweep skills for gaps left by ~48 new tool families since v1.4.1 #592 docs/skills-sweep-new-tools-since-v1.4.1 Shanghua Gao 2026-09-16 01:14:42 -04:00
  • 04f513e69f Merge pull request #590 from mims-harvard/docs/protein-structure-skill-boltz Shanghua Gao 2026-09-15 19:11:57 +08:00
  • d8b9ab638b Stop the Claude Desktop bundle rejecting Python 3.14 Shanghua Gao 2026-09-15 07:09:26 -04:00
  • 1ef2c892d7 Merge pull request #589 from mims-harvard/docs/literature-skill-new-search-tools Shanghua Gao 2026-09-15 19:08:10 +08:00
  • 656ffa22b8 Fix stale complex-prediction limitation in protein-structure-prediction skill #590 docs/protein-structure-skill-boltz Shanghua Gao 2026-09-15 06:55:02 -04:00
  • 2a4700e55f Add Consensus, Noodle, and Exa to the literature-deep-research skill #589 docs/literature-skill-new-search-tools Shanghua Gao 2026-09-15 06:51:18 -04:00
  • e2eeda7fc8 Merge pull request #588 from mims-harvard/fix/alphagenome-ruff-format-drift Shanghua Gao 2026-09-15 18:46:51 +08:00
  • 794959cef3 style: fix ruff-format drift in alphagenome_tool.py #588 fix/alphagenome-ruff-format-drift Shanghua Gao 2026-09-15 03:37:37 -04:00
  • 8ea803e1ae Merge pull request #587 from mims-harvard/feature/alphagenome-regulatory-variant-pipeline Shanghua Gao 2026-09-15 15:28:39 +08:00
  • a6afe6e469 Cross-reference regulatory-variant-analysis from the rare-disease consequence filter #587 feature/alphagenome-regulatory-variant-pipeline Shanghua Gao 2026-09-15 01:01:21 -04:00
  • 3993097ed3 Cross-reference alternative sequence models when AlphaGenome isn't the fit Shanghua Gao 2026-09-15 00:20:47 -04:00
  • 341e8b6dd9 Fix wrong tool name and add robustness/generality gaps in the regulatory-variant-analysis pipeline update Shanghua Gao 2026-09-15 00:06:01 -04:00
  • 862de585d2 Weave AlphaGenome/Atlas into the regulatory-variant-analysis pipeline Shanghua Gao 2026-09-14 23:52:17 -04:00
  • 9841a91cdc Cross-reference regulatory-variant-analysis from the rare-disease consequence filter feature/alphagenome-atlas-support Shanghua Gao 2026-09-15 01:01:21 -04:00
  • 8913995c0a Point users hitting the stale Claude Desktop extension at the fix (#586) Shanghua Gao 2026-09-15 12:58:11 +08:00
  • 1cfb4a4982 Cross-reference alternative sequence models when AlphaGenome isn't the fit Shanghua Gao 2026-09-15 00:20:47 -04:00
  • d1cca22ff8 Fix wrong tool name and add robustness/generality gaps in the regulatory-variant-analysis pipeline update Shanghua Gao 2026-09-15 00:06:01 -04:00
  • 8d75a58700 Weave AlphaGenome/Atlas into the regulatory-variant-analysis pipeline Shanghua Gao 2026-09-14 23:52:17 -04:00
  • 76ec310ca9 Keep MCP tools running when upstream drift cannot break the call (#584) Shanghua Gao 2026-09-14 22:42:41 +08:00
  • 406add8bf0 Record reviewed MCP contracts in a lockfile and check drift in CI (#583) Shanghua Gao 2026-09-14 17:03:12 +08:00
  • ed17df70e1 Repin drifted Folklore and Genomic Intelligence MCP contracts (#582) Shanghua Gao 2026-09-14 16:46:56 +08:00
  • 8abf87d3d4 Feature: register Exa's web-search MCP server (#563) (#567) Shanghua Gao 2026-09-14 11:41:01 +08:00
  • 267e7c62a7 Fix: verify MCP tool contracts per-tool instead of aborting the whole category (#580) Shanghua Gao 2026-09-14 11:40:49 +08:00
  • 2a6b1507e3 Fix: stop short English function words from disabling guideline relevance filtering (#581) Shanghua Gao 2026-09-14 11:40:42 +08:00
  • 4679b3039d Feature: add Consensus_search_papers tool (#562) (#568) Shanghua Gao 2026-09-14 10:38:10 +08:00
  • b0c928b601 fix: preserve all sections of guideline abstracts (#576) zhv50 2026-09-13 21:24:24 -05:00
  • af05bdb3c3 Add AlphaGenome Atlas support; fix 7 bugs found via live-key testing (#579) Shanghua Gao 2026-09-14 10:23:15 +08:00
  • 5fec426fd3 fix: honor zero result limits in OpenAlex guideline search (#578) zhv50 2026-09-13 16:08:00 -05:00
  • 1af8aff05e fix: retain biomedical query terms in guideline searches (#577) zhv50 2026-09-13 03:01:12 -05:00
  • 1bf9cf48f5 fix: validate DailyMed Set IDs before XML requests (#575) zhv50 2026-09-13 02:59:13 -05:00
  • 0e9774020b fix: finish UniProt mapping jobs containing only failed IDs (#573) zhv50 2026-09-13 02:59:07 -05:00
  • 04760aac69 Update regulatory-genomics and variant-interpretation skills for AlphaGenome Atlas #579 Shanghua Gao 2026-09-13 03:58:34 -04:00
  • 7775083783 fix: preserve Ensembl reverse-strand region coordinates (#572) zhv50 2026-09-13 02:54:19 -05:00
  • 5d445f474c fix: validate ClinicalTrials.gov NCT identifiers before lookup (#571) zhv50 2026-09-13 02:54:09 -05:00
  • e5f1b4b38a Add AlphaGenome Atlas support and fix bugs found via live-key testing Shanghua Gao 2026-09-13 03:48:11 -04:00
  • a354a6c977 fix: preserve encoded DuckDuckGo redirect targets (#570) zhv50 2026-09-12 23:44:44 -05:00
  • 7a0ceb2f3a Feature: add SerpBase backend to web_search (#564) (#569) Shanghua Gao 2026-09-09 20:48:15 +08:00
  • ed62f45f90 Merge remote-tracking branch 'origin/main' into fix-412 #412 codex/pr182-main-merge Shanghua Gao 2026-09-07 04:04:05 -04:00
  • 752188d0f4 Merge pull request #566 from mims-harvard/feature/uspto-per-page-ocr Shanghua Gao 2026-09-07 16:01:45 +08:00
  • 94edeb42fc Merge pull request #512 from mims-harvard/codex/boltz-api-tools Shanghua Gao 2026-09-07 15:58:23 +08:00
  • bb87788731 Merge remote-tracking branch 'origin/main' into fix-412 Shanghua Gao 2026-09-07 03:24:27 -04:00
  • be5f1bbfca Make USPTO downloader OCR fallback per-page, not whole-document #566 feature/uspto-per-page-ocr Shanghua Gao 2026-09-06 23:54:37 -04:00
  • ddb67f1825 Merge pull request #565 from mims-harvard/docs/setup-skill-agent-cross-references Shanghua Gao 2026-09-07 08:46:39 +08:00
  • 780ed6b6c2 Cross-reference the Codex and Antigravity plugin skills from setup #565 docs/setup-skill-agent-cross-references Shanghua Gao 2026-09-06 10:34:03 -04:00
  • 22661b6053 Merge pull request #561 from mims-harvard/fix/issue-559-retire-clue-tools Shanghua Gao 2026-09-05 07:35:35 +08:00
  • b2b2e47e7f Merge pull request #560 from mims-harvard/fix/issue-557-graph-ui-host-origin-guard Shanghua Gao 2026-09-05 07:35:27 +08:00
  • 683085e664 Merge pull request #555 from krudo-taco/fix/issue527-markitdown-python-cap Shanghua Gao 2026-09-05 07:35:09 +08:00
  • 6e14a7ee68 Fix #559: retire CLUE.io tools (site shut down, no new API keys) #561 fix/issue-559-retire-clue-tools Shanghua Gao 2026-09-04 19:20:36 -04:00
  • f24e7ff68a Fix #557: validate Host/Origin in ToolGraphWebUI (same gap as #531) #560 fix/issue-557-graph-ui-host-origin-guard Shanghua Gao 2026-09-04 17:31:24 -04:00
  • 7b0e8f30bc Fix: make easyocr and python-docx optional imports in USPTO downloader (#521) (#558) Shanghua Gao 2026-09-05 06:54:49 +08:00
  • 1283c9009d Register the ocr extra with the runtime-readiness health check #558 fix/issue-521-uspto-lazy-imports Shanghua Gao 2026-09-04 17:50:46 -04:00
  • 2d032bd21d Fix #521: make easyocr and python-docx optional imports in USPTO downloader Shanghua Gao 2026-09-03 18:30:42 -04:00
  • 01c910cb8c Fix #531: validate Host/Origin headers to close a DNS-rebinding gap (#556) Shanghua Gao 2026-09-05 05:36:07 +08:00
  • 3c6f2606e4 Fix #531: validate Host/Origin headers to close a DNS-rebinding gap #556 fix/issue-531-host-origin-guard Shanghua Gao 2026-09-03 18:25:38 -04:00
  • d6fe965f3b fix(deps): declare websockets and urllib3, and audit module-scope imports #555 zhihaovme50 2026-09-02 01:40:40 -05:00
  • f937203c9e fix(deps): stop pointing users at markitdown[all] in hints and docs zhihaovme50 2026-09-01 20:26:44 -05:00
  • 92e820b7c7 fix(deps): name MarkItDown converter extras instead of all zhihaovme50 2026-09-01 20:23:52 -05:00
  • 66d4b90996 Merge remote-tracking branch 'origin/main' into fix-435 #435 agent-expose-agentic-prompts Shanghua Gao 2026-09-01 21:08:03 -04:00
  • e47ed77734 Merge remote-tracking branch 'origin/main' into fix-512 #512 codex/boltz-api-tools Shanghua Gao 2026-09-01 20:44:09 -04:00
  • 1c00756467 fix(mcpb): declare openpyxl for bundled Excel tools (#551) zhv50 2026-09-01 19:20:02 -05:00
  • d5454b4248 feat: add get_marsilea_info package tool (#529) Yimin Zheng 2026-09-02 02:19:51 +02:00