All pull requests

Pull requests

• Systems-biology simulation support (phase 0): BioModels tools, simulators in the executor, execute_code timeout

  #306·justaddcoffee opened Oct 7, 2026Collaborator·

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• Reword new-job placeholder to be broader (#99)

  #304·LRSEvan opened Oct 6, 2026·

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• Public job visibility 4/5: job visibility API

  #302·cmungall opened Oct 5, 2026Collaborator·

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• Public job visibility 3/5: use the visibility flag in the backend

  #301·cmungall opened Oct 5, 2026Collaborator·

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• Public job visibility 2/5: row-level security for public jobs

  #300·cmungall opened Oct 5, 2026Collaborator·

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• Public job visibility 1/5: add jobs.is_public column

  #299·cmungall opened Oct 5, 2026Collaborator·

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• Public job visibility 5/5: share-dialog switch

  #297·cmungall opened Sep 28, 2026Collaborator·

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  4

• Contributions from the 387labs fork: thread-safe engine init, test determinism, platform fixes

  #294·eman-cickusic opened Sep 15, 2026·

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• Expose the OpenScientist agent through A2A with UI controls

  #293·cmungall opened Sep 12, 2026Collaborator·

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• Let an operator pin the omp sampling temperature

  #289·LucaCappelletti94 opened Sep 3, 2026Collaborator·

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• feat: prototype machine-verifiable HCMO evidence exports

  #284·dhuzard opened Aug 28, 2026·

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  10

• feat: persist live Codex turn events

  #283·dhuzard opened Aug 27, 2026·

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  8

• fix: make agent tooling portable on Windows

  #282·dhuzard opened Aug 27, 2026·

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  5

• ci: add reproducible cross-platform quality tiers

  #281·dhuzard opened Aug 27, 2026·

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  8

• docs: air-gapped install guide

  documentation
  #278·justaddcoffee opened Aug 21, 2026Collaborator·

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  5

• docs: align README and design docs with current architecture

  #249·dhuzard opened Jul 24, 2026·

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  13

• fix(airgap): reset HOME before dropping privileges in the firewall entrypoint

  #246·justaddcoffee opened Jul 23, 2026Collaborator·

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• Fix CI secret-scan job by replacing licensed Gitleaks Action with scoped CLI scan

  #227·justaddcoffee with CopilotAI opened Jul 15, 2026·

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• MARDUK 4/4: rare-disease knowledge — Mondo subset, playbooks, uPheno/NAMO

  #208·caufieldjh opened Jul 8, 2026Collaborator·

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• MARDUK 3/4: DisMech disease-mechanisms tools

  #207·caufieldjh opened Jul 8, 2026Collaborator·

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• MARDUK 2/4: persistent user-scoped memory

  #206·caufieldjh opened Jul 8, 2026Collaborator·

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• MARDUK 1/4: rare-disease mode + Monarch Initiative tools

  #205·caufieldjh opened Jul 8, 2026Collaborator·

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• fix(executor): surface OOM kills as a clear error, not a bare exit code

  #202·justaddcoffee opened Jul 7, 2026Collaborator·5 tasks done·

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• fix: smooth out fresh-install friction (ports, migrations, mounts, docs)

  #194·justaddcoffee opened Jun 6, 2026Collaborator·

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• Validate citations against PubMed, fix bad attributions, auto-generate References

  #191·justaddcoffee opened Jun 2, 2026Collaborator·

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