[plugins] Publish scientific viewer plugins

.agents/plugins/marketplace.json

@@ -2118,6 +2118,30 @@
         "authentication": "ON_INSTALL"
       },
       "category": "Finance"
+    },
+    {
+      "name": "structure-viewer",
+      "source": {
+        "source": "local",
+        "path": "./plugins/structure-viewer"
+      },
+      "policy": {
+        "installation": "AVAILABLE",
+        "authentication": "ON_INSTALL"
+      },
+      "category": "Research"
+    },
+    {
+      "name": "sequence-viewer",
+      "source": {
+        "source": "local",
+        "path": "./plugins/sequence-viewer"
+      },
+      "policy": {
+        "installation": "AVAILABLE",
+        "authentication": "ON_INSTALL"
+      },
+      "category": "Research"
     }
   ]
 }

plugins/sequence-viewer/.codex-plugin/plugin.json

@@ -0,0 +1,50 @@
+{
+  "name": "sequence-viewer",
+  "version": "0.1.8",
+  "description": "Open and inspect biological sequence and alignment files in an interactive viewer.",
+  "author": {
+    "name": "OpenAI",
+    "email": "support@openai.com",
+    "url": "https://openai.com/"
+  },
+  "homepage": "https://openai.com/",
+  "repository": "https://github.com/openai/plugins",
+  "license": "MIT",
+  "keywords": [
+    "sequence",
+    "alignment",
+    "msa",
+    "fasta",
+    "fastq",
+    "genbank",
+    "embl",
+    "a3m",
+    "stockholm",
+    "bioinformatics"
+  ],
+  "skills": "./skills/",
+  "mcpServers": "./.mcp.json",
+  "interface": {
+    "displayName": "Biological Sequence & Alignment Viewer",
+    "shortDescription": "Open biological sequence and alignment files in Codex",
+    "longDescription": "Biological Sequence & Alignment Viewer helps you open and inspect FASTA, GenBank, EMBL, FASTQ, and multiple sequence alignment files directly in Codex. Inspect exact feature segments and FASTQ QC, translate selections, search and navigate motifs, focus annotated features or reference coordinates, filter alignment rows, change molecule-aware display and analysis options through chat, compute an exploratory guide tree, and ask follow-up questions grounded in the current viewer state.",
+    "developerName": "OpenAI",
+    "category": "Research",
+    "capabilities": [
+      "Interactive",
+      "Read"
+    ],
+    "websiteURL": "https://openai.com/",
+    "privacyPolicyURL": "https://openai.com/policies/privacy-policy/",
+    "termsOfServiceURL": "https://openai.com/policies/terms-of-use/",
+    "defaultPrompt": [
+      "Open this FASTQ and summarize read length, GC, and Q30 in the viewer",
+      "Open this alignment, focus the conserved motif, and compute an exploratory guide tree",
+      "Open this GenBank file and inspect the selected feature and six-frame translation"
+    ],
+    "composerIcon": "./assets/icon.png",
+    "logo": "./assets/logo.png",
+    "brandColor": "#3F8F83",
+    "screenshots": []
+  }
+}

plugins/sequence-viewer/.mcp.json

@@ -0,0 +1,9 @@
+{
+  "mcpServers": {
+    "sequence-viewer": {
+      "command": "node",
+      "args": ["./dist/server.mjs"],
+      "cwd": "."
+    }
+  }
+}

plugins/sequence-viewer/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 OpenAI
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

plugins/sequence-viewer/README.md

@@ -0,0 +1,35 @@
+# Biological Sequence & Alignment Viewer
+
+Biological Sequence & Alignment Viewer opens sequence and multiple-sequence-alignment files in an interactive rich view directly inside Codex.
+
+## Open A Sequence Or Alignment
+
+- Click a supported file in the Codex workspace tree to open the native rich preview.
+- Ask Codex to open a supported local sequence or alignment to render the viewer inline in chat.
+- Use **Open in side pane** inside the viewer to move the same live view to the right pane.
+- Use **Return to chat** to move it back without losing mode, focus, selection, or alignment state.
+
+## Supported Files
+
+- FASTA and plain biological sequence: `.fasta`, `.fa`, `.fas`, `.fna`, `.faa`, `.ffn`, `.frn`, `.mfa`
+- Explicit aligned FASTA: `.aln-fasta`, `.afa`, `.afasta`
+- GenBank and RefSeq flat files: `.gb`, `.gbk`, `.genbank`, `.gbff`
+- EMBL and ENA flat files: `.embl`, `.emb`
+- FASTQ: `.fastq`, `.fq`
+- Common alignment formats: CLUSTAL, Stockholm, A2M, A3M, MSF, PHYLIP, NEXUS, and PIR
+
+The read-only viewer supports sequence and alignment modes, exact compound annotations, source and six-frame translation, aggregate FASTQ QC, motif search, selections, consensus and conservation metrics, an exploratory UPGMA guide tree, and model context for follow-up questions about the current view. You can also ask Codex to switch records; focus coordinates, annotated features, alignment cells, or reference positions; search and navigate motif hits; filter, hide, or restore alignment rows; change modes, references, molecule-aware palettes, tracks, and analysis scopes; clear or reset the view; compute the guide tree; or move the mounted viewer to the side pane.
+
+## Data Handling
+
+The plugin runs a local MCP server. Native workspace opens use Codex host-managed resource handles. Chat opens expose an opaque local plugin resource through standard MCP `resources/read`.
+
+File contents are sent to the embedded viewer, not returned to the model as tool output merely to open the file. The plugin does not impose its own file-size cap; Codex host behavior and normal local memory constraints still apply. When the MCP host supplies active workspace roots, chat opens are confined to those roots.
+
+## Marketplace Package
+
+This package is a generated, self-contained runtime bundle for the Codex official plugin marketplace. It includes the manifest, local MCP server runtime, viewer assets, agent guidance, and small synthetic smoke fixtures needed to validate supported formats.
+
+## License
+
+OpenAI-authored files are available under the [MIT License](LICENSE). Bundled third-party dependencies and their available license or notice texts are listed in `THIRD_PARTY_NOTICES.md`, which is included in the generated marketplace bundle.