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Public reference for users and research teams exploring Protoly.

Protoly Documentation

Protoly is a structured workflow platform for experimental science. It helps teams define reproducible procedures, turn them into machine-readable workflows, publish them, and connect selected workflows to automation through NanoScience Lab.

The platform is especially aligned with advanced materials, nanomaterials, chemistry, electrochemistry, and lab automation, but the underlying workflow model is broader than a single scientific domain.

Typical Workflow

  1. Create a new record and choose the relevant content kind.
  2. Add core scientific context such as title, description, abstract, and metadata.
  3. Build the workflow in Step Builder with steps, parameters, materials, and references.
  4. Use AI assistance to draft, refine, or expand the scientific content where useful.
  5. Keep the record private for collaboration or move it toward publication, export, or automation.
Canonical product flow: create structured record -> define workflow -> enrich metadata -> share or publish -> export or automate.

AI Assistant

Protoly includes an integrated AI assistant that helps users create, refine, and organize scientific content directly inside the platform. The AI is meant to accelerate protocol design, improve structure, and reduce the time needed to move from an idea or paper to a reproducible workflow.

What The AI Can Help With

  • Draft new protocol-first records from a plain-language prompt.
  • Write or improve titles, descriptions, abstracts, and structured scientific text.
  • Correct, expand, simplify, or reorganize drafted content.
  • Suggest groups and steps for Step Builder workflows.
  • Support drafting for multiple content kinds such as protocol, review, and related record types.

Workflow-Oriented AI Use

  • AI can help shape a complete draft that is ready to be reviewed inside Protoly.
  • Structured workflow drafts can then be edited in Step Builder for reproducibility.
  • Supported module steps can be added where a workflow matches the available step catalog.
  • The goal is faster movement from idea -> structured workflow -> review-ready documentation.

AI + Reproducibility

  • AI helps design and refine the scientific record, but users still review and approve what gets applied.
  • When AI-generated content is moved into Step Builder, it becomes part of a more structured and reproducible workflow.
  • Protoly is designed so AI-assisted drafts can evolve into supported, automation-aware workflows rather than remaining loose text.
  • This makes it easier to produce workflows that are clearer, more repeatable, and easier to prepare for hardware-supported execution.

Unified Record Model

Protoly uses one primary scientific record model and then adapts presentation and metadata based on selected content kind. This avoids fragmenting the workflow across multiple disconnected entities.

Core Record

  • Title, description, abstract, visibility, and author data.
  • Dynamic type-specific metadata.
  • Step Builder workflow with parameters and materials.
  • References, co-authors, media, and supporting information.

Content Kinds

  • Protocol
  • Mini Review
  • Review
  • Negative Results
  • Other configured content kinds

What Changes By Content Kind

  • Badging and presentation on cards and public pages.
  • Dynamic metadata fields shown during create and settings flows.
  • Publication positioning and how users describe outcomes or results.

What Stays Shared

  • One public ID format.
  • One workflow model in Step Builder.
  • One publication pipeline.
  • One automation/export foundation.

Step Builder

Step Builder is the structured workflow layer of Protoly. It converts a scientific procedure into an ordered, machine-readable representation that can later support reproducibility, export, review, and selected automation flows.

Workflow Structure

  • Parallel groups organize phases of work.
  • Each step captures one action.
  • Steps can be manual, structured, or module-linked.
  • Groups and steps support ordering, timing, and visual review.

What A Step Can Contain

  • Instruction text and notes.
  • Duration and operating conditions.
  • Materials, reagents, electrodes, and substrates.
  • Quality control, citations, and execution metadata.

Why It Matters

  • Improves reproducibility compared with free-text methods alone.
  • Creates a cleaner path to export and workflow versioning.
  • Makes workflows easier to review for supported automation pathways.
  • Supports publication-ready materials and methods generation.

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.

Automation & Execution

Protoly does not stop at documentation. Selected workflows can move toward execution through structured workflows, workflow versioning, and NanoScience Lab automation request flows.

Automation Requests

  • Users submit a record for automation consideration.
  • The request captures intent, constraints, and execution goals.
  • Medic Tech evaluates feasibility and prepares the workflow for hardware execution where relevant.
  • Results, materials, and documentation can flow back into the broader research lifecycle.

Execution Readiness

  • Structured steps are easier to validate and translate than free text.
  • Supported module steps create clearer automation intent during review.
  • Workflow versions support traceability across revisions and pulls.
  • Not every workflow is fully automated; mixed manual + module execution is valid.
Browse public records Browse templates About NanoScience Lab

Supported Workflow Modules

These module categories represent the kinds of structured actions Protoly can describe for automation-aware workflows. The exact supported set evolves as connected systems expand.

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.
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.
Liquid Transfer
liquid_handling
Workbench liquid transfer workflow between defined source and destination locations.
Wait
timing
Programmed wait/hold steps to maintain reaction or resting windows.
Pause Process
timing
Pause all running process outputs for a fixed duration
LED Illumination
illumination
LED illumination with timed or continuous operation and pulse support.
UV Illumination
illumination
UV illumination with timed or continuous operation and pulse support.
IR Illumination
illumination
IR illumination with timed or continuous operation and pulse support.
Sterilization UV
sterilization
UV sterilization cycle for decontamination phases in automated workflows.
Exhaust
airflow
Timed or continuous airflow control for ventilation and process safety.
Camera
imaging
Integrated camera capture for imaging during execution.
Environment Sensors
environment
General environmental sensing module
Manual Step
manual_operation
Manual protocol step for actions that are user-guided and not mapped to direct hardware control.
Cyclic Voltammetry
ministat
Cyclic Voltammetry electrochemical method
Linear Sweep Voltammetry
ministat
Linear Sweep Voltammetry electrochemical method
Constant Voltage Voltammetry
ministat
Constant Voltage Voltammetry electrochemical method
Chronoamperometry
ministat
Chronoamperometry electrochemical method
Multistep Voltammetry
ministat
Multistep Voltammetry electrochemical method
Sinusoidal Voltammetry
ministat
Sinusoidal Voltammetry electrochemical method
Square Wave Voltammetry
ministat
Square Wave Voltammetry electrochemical method
Electrochemical Module
electrochemistry
Voltage or current driven electrochemical operation for controlled synthesis and evaluation workflows.
Microplate Endpoint
microplate
Endpoint colorimetric read for finished assay plates.
Microplate Kinetic
microplate
Time-series colorimetric read for kinetic assays.
Microplate Absorbance
microplate
Absorbance read for supported microplate assay workflows.

Pineapple Protocol Layer

Pineapple Protocol Layer is the structured workflow exchange used by Protoly for moving workflow state across authoring, versioning, desktop delivery, and connected execution environments.

  • Preserves workflow intent beyond plain text documentation.
  • Supports export, import, version tracking, and machine-delivery flows.
  • Reduces ambiguity between author, reviewer, operator, and execution system.
  • Improves long-term portability of structured workflows.
Use Pineapple JSON when a workflow must move between Protoly and connected execution software without losing structured meaning.

Publishing

Publishing in Protoly is built on top of the same unified scientific record. Records can move from private drafting to review, PDF generation, and public publication without leaving the core model.

What The Publishing Layer Supports

  • Protocol papers and methods-focused publications.
  • Full papers and results-driven content.
  • Event-linked issue calls for conferences, workshops, and special editions.
  • Review workflow, revision, and approval states.

Why Structured Records Help

  • Metadata is already normalized before submission.
  • Workflow content can support materials and methods generation.
  • References, co-authors, and supporting files stay attached to the same record.
  • Public IDs remain stable across lifecycle stages.

Event-Linked Issues

Protoly journals can run conference-linked, workshop-linked, and special issue publication calls without splitting the publication workflow into a separate product line.

  • Conference organizers can invite Protoly for event-linked journal issue publication.
  • Accepted papers can be routed into a specific issue with a public archive page.
  • Special editions, invited collections, and recurring issue programs can use the same journal workflow.
  • This lets organizers and editors extend an event into a formal journal issue workflow without maintaining a parallel publication stack.
Journal Journals overview

Events

Protoly supports event hosting for conferences, workshops, summits, symposiums, training programs, and other scientific or technical gatherings. Each event has its own public page, organizer workflow, and configurable content structure.

What Events Support

  • Public event pages with template-driven sections and branding.
  • Organizer roles and organizer-only management flows.
  • Abstract submission and abstract review when enabled.
  • Program or schedule publishing for accepted sessions and talks.
  • Optional public sections for speakers, committees, sponsors, themes, gallery, contact, and fee information.

Current Event Flow

  • Create the event and configure its public content.
  • Add organizers and control visibility or status.
  • Open abstract intake if the event accepts submissions.
  • Review responses, prepare schedules, and publish the live event page.
  • Optionally connect the event to downstream publication flows such as event-linked journal issues.

Why Use Events In Protoly

  • Keep event communication, abstract handling, and schedule publishing in the same ecosystem as protocols and publications.
  • Present scientific programs with a structured and branded public page instead of scattered documents and forms.
  • Extend event outputs into later publication workflows when needed, without rebuilding the information elsewhere.
Upcoming events

Profiles & Messaging

Protoly includes researcher identity and collaboration features around the scientific workflow layer.

  • Public-facing researcher profiles.
  • Connection requests for collaboration.
  • Direct messaging after connection approval.
  • Public profile visibility remains limited to selected fields.

Developers

Core contributors currently maintaining the Protoly workflow, automation exchange, and application stack.

  • Dr. Ishu Singhal
  • Dr. Ayushi Mishra
  • Dr. Inder Kumar Gupta