Documentation
Single-page reference for Protoly Protocol Builder.

Protoly Documentation

Protoly is Medic Tech's protocol builder for advanced materials research. It standardizes how protocols, case studies, 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 case studies, 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 protocol type.
  3. Add steps, reagents, safety notes, and checkpoints.
  4. Keep it private for collaboration or publish publicly when ready.
  5. Convert to a paper or submit an automation request to NanoScience Lab.

Core Entities

Protocols

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

Case Studies

Applied outcomes, characterization data, and performance results linked to protocols.

Publications

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

Events

Conferences and proceedings with abstract submission, review, and scheduling.

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 protocol 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, tags, and applications
  • DOI and publication metadata (if published)

Type-Specific Fields (Dynamic)

The protocol type drives the extra fields you see. Not all protocols 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, protocol type, tags.
  • 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).
  • Protocol type (required) with dynamic fields.
  • Tags 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 Conversion Tools

  • Request academic paper conversion from Settings.
  • 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 conversion request 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.

Case Studies

Case studies describe outcomes and performance metrics for protocols used in real scenarios.

Typical Fields

  • Application or use case
  • Characterization and analysis data
  • Performance metrics and outcomes
  • Challenges, limitations, and future directions
  • Safety considerations and references

Publishing

  • Public visibility for community reuse
  • Paper conversion workflow for journals
  • Peer review status and revision history

Core Fields

  • Linked protocol (required).
  • Title, description, and application type.
  • Experimental conditions and key findings.
  • Outcome (successful, partial, unsuccessful).
  • Performance metrics and statistical data.

Recommended Structure

  • Summary of the use case and motivation.
  • Experimental conditions and settings.
  • Key findings with characterization outputs.
  • Limitations, risks, and future directions.
  • References and supporting data where applicable.

Citations & Evidence

  • Use inline citations in key findings and experimental conditions.
  • Import references in bulk when migrating from an external library.
  • Link evidence to the related protocol for traceability.

Publication Metadata

  • DOI, publication title, journal name, and date (optional).
  • References and supporting files for publication workflows.
Case studies show real outcomes. Link them to a public protocol for maximum impact.

Create & Maintain

  • Link to a protocol to show reproducibility.
  • Update challenges, safety considerations, and references.
  • Materials & methods are generated from the Step Builder.
  • Keep private while drafting, publish when ready.

Paper Conversion

  • Convert to a paper with structured metadata.
  • Submit for review and respond to feedback.
  • Publish as a case study paper or proceedings item.
View public case studies

Publications

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

Paper Conversion

  • Submit a protocol or case study 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

  • Associate papers with events and issues.
  • Editorial board and guidelines are shared across journals.
  • Proceedings can be public even before papers are published.

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.

Events & Proceedings

Protoly includes a conference management layer for scientific events.

  • Organizers create events with metadata, schedules, and committees.
  • Abstract submission workflows with review and payment verification.
  • Proceedings collections for publishing accepted papers.

Public Event Pages

  • Event overview, dates, venue, and key sections.
  • Registration fees, travel info, and contact details.
  • Abstract submission link and public schedule (oral only).
Upcoming events Proceedings overview

Organizer Controls

  • Invite organizers, manage committees, and update public sections.
  • Confirm payments and generate presentation IDs.
  • Build oral schedules and publish proceedings.

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.
  • Case studies capture outcomes and metrics tied to protocols.
  • 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.