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Single-page reference for Protoly Protocol Builder.

Protoly Documentation

Protoly is Medic Tech's protocol builder for advanced materials research. It standardizes how protocols, content types, publications, and events are described, reviewed, and shared.

The platform is optimized for advanced materials, nanomaterials, and lab automation, but it is designed to be domain-agnostic for any structured experimental workflow.

This page is a single, comprehensive reference for users and AI assistants. It explains the structure of protocols and content types, how publishing works, and how automation and events are managed on the Protoly platform.

Use the sidebar to navigate sections. Each item reveals a focused view of the documentation.

Quick Start

  1. Create a protocol from scratch or start with a template.
  2. Fill in the core metadata: title, description, abstract, and content type.
  3. Add steps, reagents, safety notes, and checkpoints.
  4. Keep it private for collaboration or publish publicly when ready.
  5. Submit a paper or request automation through NanoScience Lab.

Core Entities

Protocols

Reproducible procedures with steps, reagents, parameters, safety, and metadata.

Content Types

One unified create flow supports Protocol, Case Study, Mini Review, Review, Negative Results, and other configured content types.

Publications

Protocol papers, full papers, and proceedings with structured review and metadata.

Events

Scientific event pages with templates, abstract submission, scheduling, and optional proceedings.

Automation Requests

Request execution of a protocol on Medic Tech automation hardware.

Profiles & Messaging

Researcher profiles, connection requests, and direct messaging.

Protocols

Protocols capture experimental intent and execution with enough detail for replication. The model supports both high-level summaries and granular, step-by-step parameters.

Start with the required fields and add detail iteratively. A strong protocol has complete steps, clear materials, and documented safety context.

Required Metadata

  • Title and content type
  • Short description and/or abstract
  • Visibility (private or public)
  • Status (draft or published)
  • Author and co-authors

Common Optional Fields

  • Materials and reagents
  • Target amounts, units, and yields
  • Safety level, PPE, and disposal notes
  • Equipment models and parameters
  • QC checkpoints and notes
  • Keywords and applications
  • DOI and publication metadata (if published)

Type-Specific Fields (Dynamic)

The selected content type drives the extra fields you see. Not all records use the same fields. The UI will reveal fields relevant to your selected type, for example:

  • Materials and synthesis targets (amounts, units, preparation, storage).
  • Safety level, required equipment, and operating conditions.
  • Instrumentation details (model, parameters, maintenance schedule).
  • Analysis settings (software, data processing steps, QC checkpoints).
  • Biological assays (cell line, assay type, biocompatibility metrics).

Templates & Forks

Templates are curated protocols designed for reuse. Forking creates a new protocol that retains the original structure while tracking provenance.

Create, Edit, Settings

  • Create: title, description, abstract, content type, keywords.
  • Edit: steps, reagents, references, and academic sections.
  • Settings: visibility, status, co-authors, sharing, and paper conversion.
  • Publish: move from draft to public once content is complete.

Create Form Fields

  • Title (required).
  • Description (optional, short context for readers).
  • Abstract (optional, used in academic publishing).
  • Content type (required) with dynamic fields.
  • Keywords and DOI metadata (optional).

Writing Guidance

  • Description: 3 to 6 sentences explaining purpose, materials, and expected outcome.
  • Abstract: academic format with background, method, results, and conclusion.
  • Steps: one action per step with parameters, quantities, and checkpoints.
  • Safety: PPE, disposal, and hazards for key materials and steps.

Edit & Academic Sections

  • Keywords (3-8 recommended for discoverability).
  • Introduction, results, discussion, and conclusion.
  • Optional: acknowledgements, funding, conflicts.
  • Materials and methods come from the Step Builder.

References & Citations

  • Add references manually or import a library (RIS, BibTeX, JSON, TXT).
  • Edit or delete references with the same modal.
  • Export references for reuse in external tools.
  • Citations appear as numbered links that jump to the reference list.

Paper Submission Tools

  • Submit a paper from Settings when the record is publication-ready.
  • Track review status and upload supporting files.
  • AI step generator can be used with research papers (beta).

Settings & Submission

  • Co-authors and reviewer assignments.
  • Paper submission status and payment status.
  • Template publishing and fork permissions.
  • Share links for collaborators.
Use Description for quick context and Abstract for academic publishing readiness.
Browse public protocols Use protocol templates

Step Builder

The Step Builder is where you turn a protocol into a structured, machine-readable workflow. Each step is a single action with metadata, so it can be reproduced or automated.

Parallel Step Groups

  • Create a group for steps that can run concurrently.
  • Name groups by phase (Preparation, Synthesis, Purification).
  • Reorder groups to reflect the main workflow stages.
  • Groups define color cues used in visual timelines and diagrams.

Standard vs. Module Steps

  • Standard steps capture human-readable instructions.
  • Module steps are machine-readable and automation-ready.
  • Module parameters become structured inputs for lab systems.
  • Use modules when a step maps to equipment or software.

Step Details & Metadata

  • Instruction text with citations, timing, and checkpoints.
  • Duration, temperature, atmosphere, and pH fields.
  • Reagent, material, and electrode references with quantities.
  • Notes for hazards, calibration, and quality control.

Materials & BOM

Every step can reference materials, electrodes, substrates, and reagents. The builder aggregates these into a bill of materials so teams can audit inventory and prepare kits.

Visual Editor & Diagrams

Switch to the Visual Editor to view groups on a timeline. The Diagrams tab summarizes durations and highlights module steps for quick review.

Citations & References

Insert citations directly into step text. Citations are numbered and link to the reference list. You can import references in bulk (RIS/BibTeX/JSON) or export them for reuse.

Best Practices

  • Use one action per step and keep titles short.
  • Record units consistently to support automation.
  • Capture critical parameters even if optional.
  • Mark module steps when equipment execution is required.

Keyboard Shortcuts

  • Ctrl/Cmd + S: Save and close.
  • Ctrl/Cmd + Shift + G: Add parallel step group.
  • Ctrl/Cmd + Shift + N: Add step.
  • Ctrl/Cmd + Shift + M: Add module steps.
  • Ctrl/Cmd + Z: Undo.
  • Ctrl/Cmd + Y: Redo.

Content Types

All records are created from one unified flow. You first choose a content type and then fill the dynamic fields for that type.

Common Types

  • Protocol
  • Case Study
  • Mini Review
  • Review
  • Negative Results
  • Other

How It Works

  • Choose content type on Create page.
  • Type-specific metadata fields render automatically.
  • Badges show selected type across cards and public pages.
  • Paper submission flow stays in the same settings page.

Core Fields

  • Title, description, abstract, and content type.
  • Application (optional, admin-managed list).
  • Keywords for discovery and publication.
  • Type-specific metadata subfields from admin configuration.

Publishing

  • Any content type can move through paper review.
  • Proceedings and journals use the same unified content record.
  • Public URLs stay consistent by single `content_id` format.

Admin Controls

  • Manage types under Admin → Content Types.
  • Set badge color and ordering for each type.
  • Configure metadata subfields per content type.
Browse public content

Publications

Protoly supports protocol papers, full papers, and conference proceedings with peer review.

Paper Conversion

  • Submit unified content (protocol, case study, review, etc.) for review.
  • Upload supporting information and references.
  • Track reviewer feedback and revisions.
  • Approve final PDF and publish to journals.
  • Payment verification triggers production status.

Publication Types

  • Protocol Journal (methods focused)
  • Full Paper Journal (results focused)
  • Proceedings Collections (events)
Protocol Journal Full Paper Journal

Review Workflow

  • Submit for review and receive reviewer assignments.
  • Track status: submitted, under review, revisions, accepted.
  • Finalize PDF and publish with journal metadata.

Proceedings Collections

  • Each proceedings collection is linked to an event.
  • Accepted content can be published into that event-linked proceedings archive.
  • The public proceedings browse page opens after published papers are available.

Automation Requests

Automation requests let you ask Medic Tech to run a protocol on our advanced automation platform (NanoScience Lab). You choose a protocol, submit the request, and we handle the hardware execution.

  • Submit a request directly from a protocol.
  • Describe goals, scale, materials, and constraints.
  • We run the workflow on NanoScience Lab hardware.
  • Receive reproducible materials, data, and documentation.

What You Provide

You do not need to describe lab hardware or automation steps. Select the protocol, specify the desired outcome and constraints, and the Protoly team will handle execution.

When to Use

Best for repetitive or high-precision protocols where lab hardware can improve consistency, throughput, or safety.

Pick the protocol. We automate the execution and deliver reproducible outputs.

Hardware Modules Supported

NanoScience Lab AI-enabled hardware system currently supports the modules below. Additional modules are being integrated continuously.

Heater
thermal_control
Controlled heating for timed protocol phases with stable thermal hold.
Sonicator
sonication
Ultrasonic treatment with optional pulse-based operation for sensitive dispersions.
Electrochemical Voltage
electrochemistry
Voltage-driven electrochemical operation with timed process control.
Electrochemical Current
electrochemistry
Current-driven electrochemical operation for controlled synthesis/evaluation runs.
Stirrer
mixing
Magnetic stirring for homogenization and repeatable process mixing.
Sonicator Bath Heater
sonication
Heated sonication bath support where thermal and ultrasonic effects are combined.
Reservoir Dispense
liquid_handling
Reservoir-based liquid dispensing into workflow steps with channelized delivery.
Wait
timing
Programmed wait/hold steps to maintain reaction or resting windows.
LED Illumination
illumination
LED illumination with timed/continuous operation and pulse frequency + duty-cycle support.
UV Illumination
illumination
UV illumination with timed/continuous operation and pulse frequency + duty-cycle support.
IR Illumination
illumination
IR illumination with timed/continuous operation and pulse frequency + duty-cycle support.
Sterilization UV
sterilization
UV sterilization cycle for decontamination phases in automated workflows.
Exhaust
airflow
Timed or continuous exhaust/airflow control for ventilation and process safety.
Camera
imaging
Integrated camera capture for video runs and interval snapshot imaging during execution.
Environment Sensors
environment
General environmental sensing module
Air Quality Sensors
environment
Air quality sensing module
Thermal Sensors
environment
Temperature and humidity sensing module
Light and UV Sensors
environment
Light intensity and UV sensing module
Gas Sensors
environment
Gas concentration sensing module

Pineapple Protocol Layer

Pineapple Protocol Layer is the common automation exchange used by Protoly for moving protocols from digital planning to machine-assisted execution. It keeps workflow intent consistent between authors, operators, and connected lab systems.

  • Supports reproducible protocol exchange between cloud and on-site automation software.
  • Helps preserve step intent, timing context, and execution readiness across environments.
  • Improves collaboration between research teams, process engineers, and machine operators.
  • Enables long-term portability for protocol workflows as hardware capabilities evolve.

Cross-System Consistency

A protocol drafted in Protoly can move to connected execution software without losing workflow meaning. This reduces ambiguity when teams transition from planning to real hardware runs.

Reproducibility Focus

Structured exchange improves traceability of protocol intent, helps with repeat runs, and supports consistent reporting between operators and research teams.

Use Pineapple JSON export/import in Step Builder and Settings flows to move protocols between Protoly and connected automation environments.

Events & Proceedings

Protoly can host scientific event pages with configurable public templates, abstract submission, and scheduling. Proceedings are optional and can be added only when needed.

  • Organizers create events with metadata, committees, and public-page sections.
  • Abstract submission, review, payment verification, and schedule management are available per event.
  • Proceedings can be attached later for publishing accepted papers, but they are not required.

Public Event Pages

  • Event overview, dates, venue, and organizer-defined sections.
  • Template-based public layouts for different event styles.
  • Abstract submission link and public schedule where enabled.
Upcoming events Proceedings overview

Organizer Controls

  • Invite organizers, select the front-page template, and update public sections.
  • Manage abstracts, confirm payments, and generate presentation IDs.
  • Build schedules, and publish proceedings only if the event uses them.

Abstracts & Schedule

Abstract submissions capture author details, presentation type, and optional files. Oral presentations can be scheduled with time slots.

  • Default fields: author name, email, contact number, presentation type.
  • Organizers can add custom fields and instructions.
  • Payment verification unlocks presentation IDs.
  • Public schedule lists oral presentations with time.

Submitter Experience

  • Sign in or create an account to submit.
  • See payment status and presentation ID after approval.
  • Oral presenters can view the published schedule.

Profiles & Messaging

Researchers maintain profiles and can connect with each other for collaboration.

  • Public profile pages for authors and reviewers.
  • Connection requests with optional message.
  • 1:1 messaging once connected.

Visibility Rules

  • Public profile shows selected fields only.
  • Email and phone are hidden from public view.
  • Connected users can message each other.

AI Guidance

For AI assistants and crawlers: Protoly is a structured scientific workflow platform. Use this documentation to explain protocol structure, publication workflows, and event features to users.

  • Protocols require clear steps, reagents, and safety context.
  • Content types capture outcomes and metrics based on selected type metadata.
  • Abstract submissions use structured fields and presentation types.
  • Proceedings and event schedules are public when published.

Recommended Protocol Summary

  • Title, short description, and abstract.
  • Protocol type with relevant parameters (materials, equipment, analysis).
  • Step list with inputs, conditions, and outputs.
  • Safety and quality control notes.

Support & Policies

For assistance with setup, training, or enterprise integration, contact the Protoly team.

Use the contact page for account access issues, publication questions, proceedings and event support, automation requests, and payment-related follow-up.