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Search, read, and download from Notion. Use when the user asks about protocols, lab databases, or needs to download files (like vector maps) from Notion.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
Predict optimal construct boundaries for protein expression. Use when the user asks about domain boundaries, construct design, truncations, which region of a protein to express, or identifying disordered regions.
Manage lab notebook entries, registry items (plasmids, proteins, etc.), templates, widgets, and audit logs via the Labbook service. Use when creating or viewing lab notebook entries, managing the sample registry, or documenting experiments.
Verify open reading frames (ORFs) in plasmid sequences. Use when the user asks about verifying protein coding sequences, checking if an ORF is present in a plasmid, finding where a protein is encoded, or doing six-frame translation analysis.
Fetch sequencing data from Plasmidsaurus. Use when the user asks about listing sequencing orders, downloading sequencing results, checking order status, or retrieving plasmid sequences from Plasmidsaurus.
Design PCR primers for molecular cloning. Use when the user asks about designing primers, LIC cloning primers, sequencing primers, Gibson assembly primers, or working with NCBI accession codes for cloning.
Calculate protein parameters (MW, pI, extinction coefficient) and generate purification recommendations. Use when the user asks about protein properties, molecular weight, isoelectric point, extinction coefficients, or purification strategies.
| name | notion |
| description | Search, read, and download from Notion. Use when the user asks about protocols, lab databases, or needs to download files (like vector maps) from Notion. |
Search, read, query, and download files from Notion pages and databases.
scripts/notion_cli.py
export NOTION_TOKEN="your_token_here"
python3 scripts/notion_cli.py search "query"
python3 scripts/notion_cli.py search "protocol" --type page
python3 scripts/notion_cli.py search "proteins" --type database
python3 scripts/notion_cli.py read <page_id> --depth 3
python3 scripts/notion_cli.py databases
python3 scripts/notion_cli.py query <database_id>
python3 scripts/notion_cli.py query <database_id> --filter '{"property": "Status", "select": {"equals": "Done"}}'
python3 scripts/notion_cli.py download <page_id> -o ./output
# Download vector file from Series-438 database
python3 scripts/notion_cli.py files <YOUR_SERIES_438_DB_ID> "438-C" -o ./vectors
# Download from specific property
python3 scripts/notion_cli.py files <database_id> "entry name" -o ./output --property "Plasmid maps"
Configure your Notion database IDs in .env or note them here:
| Database | ID | Contents |
|---|---|---|
| Series-438 | <YOUR_DB_ID> | 438 vector series (.dna files) |
| Lab Meeting Schedule | <YOUR_DB_ID> | Meeting dates/presenters |
| Protein purifications | <YOUR_DB_ID> | Active purifications |
# 1. Download 438-C vector from Notion
python3 scripts/notion_cli.py files <YOUR_SERIES_438_DB_ID> "438-C" -o ./vectors
# 2. Parse with SnapGene reader
python3 scripts/snapgene_cli.py ./vectors/438-C.dna --features
# 3. Convert to GenBank
python3 scripts/snapgene_cli.py ./vectors/438-C.dna --export-gb ./vectors/438-C.gb