Protocols

Versioned, forkable standard operating procedures with structured equipment and materials tracking.

What is a protocol?

Protocols (also called procedures or SOPs) are detailed instructions for carrying out a specific laboratory or computational procedure. On Libre Biotech, protocols are versioned documents that combine step-by-step instructions with structured metadata: free-text sections, catalog-linked equipment and materials, and citable references.

Protocols serve two purposes:

• Reproducibility — Every process references the exact protocol version that was followed, including the equipment types and materials required
• Community knowledge — Published protocols can be forked, improved, and reviewed by others

Browsing protocols

The protocol library is accessible from Protocols in the main navigation, or from the public-facing Explore page (for public protocols). Protocols are organised by category:

• Sample Preparation
• Measurement & QC
• Data Transformation
• Sequencing
• Management

Creating a protocol

Navigate to Protocols → New Protocol. The form is laid out in sections, all on a single page:

1. Procedure details — Title (required), description, category, URL, visibility, and license (default CC-BY-4.0)
2. Initial version — Version number (default 1.0), effective date, and changelog
3. Protocol sections — Four optional free-text sections: Safety & Hazards, Preparation Notes, Timing, and Completion Notes (see below)
4. Equipment from Catalog — Dynamic rows for generic equipment types with specifications and notes
5. Materials from Catalog — Dynamic rows with cascading type → product selects, quantity, unit, and notes
6. References — Citations with optional DOI, URL, and type (paper, manual, protocol, book, or website)
7. Procedure steps — Numbered instructions; add, remove, and reorder as needed

All dynamic sections (equipment, materials, references, steps) support adding and removing rows with + and trash buttons. Click Create Procedure when finished.

Structured sections

Protocols support four optional free-text sections that appear alongside the procedure steps. These sections complement the structured Equipment & Materials Catalog links — use the catalog for structured, cross-referenceable equipment and material data, and the text sections for narrative detail. All sections support Markdown formatting.

Pre-step sections

These appear above the procedure steps, providing context a researcher needs before starting:

Section	Purpose	Example content
Safety & Hazards	PPE requirements, chemical hazards, disposal instructions	“CT Conversion Reagent is corrosive. Wear gloves and eye protection. Dispose via chemical waste.”
Preparation Notes	Narrative detail about reagent preparation, equipment setup, sample requirements, or any other pre-procedure context that doesn’t fit in the catalog’s structured fields	Buffer reconstitution steps, instrument calibration, input sample specs (“200–500 ng gDNA in ≤20 µL water, OD 260/280 ≥ 1.8”)
Timing	Estimated duration, time-sensitive steps, scheduling notes	“Total time: ~3.5 hours. Desulphonation incubation: 15–20 min (do not exceed 20 min).”

Post-step section

Section	Purpose	Example content
Completion Notes	Expected results, storage conditions, troubleshooting tips, and any other post-procedure information	Use Markdown headings to organise, e.g. ## Expected Results, ## Storage, ## Troubleshooting

Equipment & Materials from Catalog

Protocols link to the shared Equipment & Materials Catalog for structured, cross-referenceable tracking. Two catalog sections appear on the protocol form:

Equipment

Click + Add Equipment to add a row. Select a generic equipment type from the dropdown (e.g., “Microcentrifuge”), then optionally add specifications (e.g., “≥10,000 × g”) and notes. Add as many rows as needed; remove any row with the trash button.

Materials

Click + Add Material to add a row. Each row has:

1. Material type — Select a generic type (e.g., “Bisulfite conversion kit”)
2. Product — A cascading select that automatically filters to show only products registered under the chosen type. Select a specific product (e.g., “EZ DNA Methylation-Gold Kit (Zymo Research) #D5005”) or leave as “generic (any)” if the protocol is vendor-independent
3. Quantity and Unit — How much is needed (e.g., “1” / “kit”)
4. Notes — Variant details, size constraints, or other context (e.g., “1.5 mL” for a microcentrifuge tube, “Aerosol-resistant filter tips” for pipette tips)
5. Alternative products — Click + Alternative beneath a material row to add interchangeable products. For example, a bisulfite conversion protocol that works with either the 50-reaction kit (D5005) or the 200-reaction kit (D5006) would list D5005 as the primary product and D5006 as an alternative with a note like “Larger pack size (200 rxn)”. Each alternative has its own product select (filtered to the same type) and an optional note

How catalog items are displayed

On the protocol view page, equipment and materials appear as collapsible cards:

• Equipment — Each item shows the type name as a link to the catalog type page, with specifications and notes
• Materials (product specified) — The product name is shown as the primary link (to the product detail page), with vendor and catalog number. The generic type appears as a small badge for context
• Materials (generic only) — The type name is shown as the primary link (to the catalog type page), with the category as a badge
• Alternative products — Listed beneath the primary product as an “Alternatives” sub-list, each linking to its own product detail page with any notes shown

This enables cross-protocol queries like “show me all protocols that require a microcentrifuge.” See the full catalog documentation for details on the type/product hierarchy, kit components, SDS links, and process-level tracking.

References

Each protocol version can include structured references to papers, manuals, other protocols, books, or websites. Each reference has:

• Citation — Free-text citation (required)
• DOI — Digital Object Identifier, automatically linked to https://doi.org/...
• URL — Direct link to the resource, or upload a PDF (max 10 MB) which is stored locally on the server. Uploaded files take precedence over the URL field
• Type — One of: paper, manual, protocol, book, or website

References are displayed as a numbered list on the protocol page, with clickable DOI and Link badges. Uploaded PDFs are served directly from the platform, ensuring references remain accessible even if the original vendor URL changes.

Versioning

Protocols are versioned. When you update a protocol, a new version is created while previous versions remain accessible. This ensures that processes linked to older versions still reference the exact instructions that were followed.

1. Navigate to the protocol page
2. Click Edit (New Version)
3. Make your changes — the edit form is pre-filled from the previous version:
   • All four protocol sections (Safety, Preparation Notes, Timing, Completion Notes)
   • Equipment rows with selected types, specifications, and notes
   • Material rows with selected types, products (auto-restored in the cascading select), quantities, units, notes, and any alternative products
   • References and procedure steps
4. Add a changelog note describing what changed (required)
5. Click Create New Version

Each version is immutable once created. Catalog links are stored per-version, so adding a new equipment requirement in version 2.0 does not alter version 1.0.

Forking

Forking creates a copy of a protocol under your name, which you can then modify independently. This is how the community improves protocols collaboratively.

1. Navigate to the protocol you want to fork
2. Click Fork
3. The forked protocol appears in your protocol list with a link back to the original
4. Edit and version it as your own

The fork tree (visible on the protocol page) shows all forks and their lineage.

Community features

• Star — Mark protocols you use frequently for quick access
• Suggest improvements — Propose changes to protocols you don't own
• Review suggestions — Protocol owners can accept or reject improvement suggestions

Linking protocols to processes

When creating or editing a process, select a protocol from the library. The process records which protocol version was used, creating a traceable link between the instructions and the actual work performed. At the process level, you can additionally record the specific equipment products and material products used (with lot numbers and expiry dates), complementing the generic type requirements defined in the protocol.