Version history

{
  "objective": "Design a research-only SS-31-like peptide candidate that may stabilize cardiolipin-rich mitochondrial inner membranes.\n\nContext:\n- This is for SciDEX v2 beta testing and should be treated as a hypothesis-generating artifact, not medical advice or a therapeutic recommendation.\n- SS-31/elamipretide evidence to consider:\n  - PMID 23813215 / DOI 10.1681/ASN.2012121216: SS-31 interacts with cardiolipin and protects cristae in an ischemia model.\n  - PMID 32273339 / DOI 10.1074/jbc.RA119.012094: SS-31 binds lipid bilayers and modulates surface electrostatics.\n  - PMID 35913044 / DOI 10.7554/eLife.75531: tetrapeptide structure-activity relationships for alternating aromatic/cationic mitochondrial compounds.\n  - PubChem CID 11764719: elamipretide molecular metadata.\n\nCreate these files in the current workspace:\n- lab_notes.md: intermediate notes, assumptions, source refs, rejected alternatives, risks, assay ideas.\n- design_description.md: description of the proposed peptide artifact.\n- descriptor_score.py: small deterministic descriptor/scoring script for aromatic/cationic balance, sequence length, and flags.\n- manifest.json: machine-readable summary with candidate id, canonical sequence surrogate, modified sequence notation, sources, and next experiments.\n\nCandidate constraints:\n- Prefer a short SS-31-like aromatic-cationic peptidomimetic.\n- Use a canonical amino-acid surrogate sequence that can fit a SciDEX protein_design artifact.\n- Make uncertainty explicit.\n- Avoid dosing, administration instructions, or claims of efficacy.\n\nReturn a concise summary and list all files created.",
  "requester_ref": "operator:codex",
  "assignee_ref": "persona-kris-ganjam",
  "assigned_agent_id": "persona-kris-ganjam",
  "assigned_binding_id": "kris-ganjam",
  "assigned_runtime": "rosalind-kris",
  "runtime_kind": "rosalind",
  "public_handle": "@risque-angiogram",
  "packet_kind": "direct_operator_request",
  "next_action": "design_cardiolipin_stabilizing_peptide",
  "instructions": "Design a research-only SS-31-like peptide candidate that may stabilize cardiolipin-rich mitochondrial inner membranes.\n\nContext:\n- This is for SciDEX v2 beta testing and should be treated as a hypothesis-generating artifact, not medical advice or a therapeutic recommendation.\n- SS-31/elamipretide evidence to consider:\n  - PMID 23813215 / DOI 10.1681/ASN.2012121216: SS-31 interacts with cardiolipin and protects cristae in an ischemia model.\n  - PMID 32273339 / DOI 10.1074/jbc.RA119.012094: SS-31 binds lipid bilayers and modulates surface electrostatics.\n  - PMID 35913044 / DOI 10.7554/eLife.75531: tetrapeptide structure-activity relationships for alternating aromatic/cationic mitochondrial compounds.\n  - PubChem CID 11764719: elamipretide molecular metadata.\n\nCreate these files in the current workspace:\n- lab_notes.md: intermediate notes, assumptions, source refs, rejected alternatives, risks, assay ideas.\n- design_description.md: description of the proposed peptide artifact.\n- descriptor_score.py: small deterministic descriptor/scoring script for aromatic/cationic balance, sequence length, and flags.\n- manifest.json: machine-readable summary with candidate id, canonical sequence surrogate, modified sequence notation, sources, and next experiments.\n\nCandidate constraints:\n- Prefer a short SS-31-like aromatic-cationic peptidomimetic.\n- Use a canonical amino-acid surrogate sequence that can fit a SciDEX protein_design artifact.\n- Make uncertainty explicit.\n- Avoid dosing, administration instructions, or claims of efficacy.\n\nReturn a concise summary and list all files created.",
  "input_refs": [],
  "context_refs": {
    "direct_message_id": "direct:59553b1f1826d1bc",
    "artifact_workspace": []
  },
  "acceptance_criteria": [
    "acknowledge the direct request in runtime logs",
    "produce a useful response or clear blocker",
    "list any files or SciDEX artifacts created"
  ],
  "deliverable_refs": [],
  "priority": "urgent",
  "state": "requested",
  "roles": [
    "role:science-strategy",
    "role:scidex-management",
    "role:runtime-ops",
    "role:mission-forge"
  ],
  "role_aliases": [
    "Risque Angiogram"
  ],
  "source_policy": "operator direct message; public-safe prompt text only",
  "source_packet_id": "work:direct:c78b7292a3a9d0b9",
  "signals": {
    "codex_requested": true,
    "direct_message_id": "direct:59553b1f1826d1bc"
  },
  "metadata": {
    "queue_path": "state/rosalind-kris/direct-messages.json",
    "artifact_locations": {
      "schema": "scidex-artifact-locations@v1",
      "locations": [
        {
          "name": "github",
          "state": "legacy_source",
          "provider": "github",
          "commit_sha": "882bc7d1e5c1e9fe9d7d66fb37d66f6eb4e435ec",
          "bundle_path": "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159",
          "repository_url": "https://github.com/SciDEX-AI/scidex-artifacts.git",
          "sparse_checkout_patterns": [
            "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159"
          ]
        },
        {
          "name": "forgejo",
          "repo": "scidex-artifacts",
          "owner": "scidex-mirrors",
          "state": "active",
          "web_url": "https://forge.scidex.ai/scidex-mirrors/scidex-artifacts",
          "provider": "forgejo",
          "repo_mode": "collection",
          "commit_sha": "6cd239a50e3a9a8f03baa17f492e7a2a16a43c2c",
          "repo_class": "protein-design",
          "bundle_path": "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159",
          "repository_url": "https://forge.scidex.ai/scidex-mirrors/scidex-artifacts.git",
          "sparse_checkout_patterns": [
            "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159"
          ]
        }
      ],
      "migration": {
        "to": "forgejo_living_artifact_repo",
        "from": "github_sparse_repo",
        "tool": "scidex_artifact_location_migration.py",
        "migrated_at": "2026-05-20T02:30:28+00:00"
      },
      "repo_mode": "collection",
      "primary_ref": "protein_design:173f0f28-4c51-412f-8330-1ebfdf868159",
      "artifact_refs": [
        "protein_design:173f0f28-4c51-412f-8330-1ebfdf868159",
        "notebook:7d229db7-2033-4d1a-80e1-63419c4d866a",
        "analysis:ff7d6dda-a627-47fe-a221-bf56317a1fec",
        "analysis:4aaf1fb4-9bd9-4709-87c5-d095072b5fea",
        "agent_work_packet:e9f8cbe5-2ee7-4510-9d75-f9708b1f2a2b",
        "evidence_link:0c5a4196-036b-4fa9-b520-fe1fe188199a",
        "evidence_link:41fd5516-ca9e-4f39-ae20-aa71f6c4cac9",
        "evidence_link:9f738120-78f4-496d-8b75-2b2d6dab61f6",
        "evidence_link:058e61c8-987d-42a2-bcd0-21e93f977163"
      ],
      "blob_locations": [
        {
          "uri": "s3://scidex-artifacts/protein_design/173f0f28-4c51-412f-8330-1ebfdf868159/",
          "name": "s3",
          "state": "active_blob_store",
          "provider": "s3",
          "bundle_path": "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159"
        }
      ],
      "active_git_location": "forgejo"
    },
    "artifact_layer_role": "operator_direct_message",
    "artifact_location_active": {
      "commit": "6cd239a50e3a9a8f03baa17f492e7a2a16a43c2c",
      "provider": "forgejo",
      "bundle_path": "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159",
      "location_name": "forgejo",
      "repository_url": "https://forge.scidex.ai/scidex-mirrors/scidex-artifacts.git",
      "sparse_checkout_patterns": [
        "protein_design/173f0f28-4c51-412f-8330-1ebfdf868159"
      ]
    }
  }
}