opentrons-magnetic-block

Automate magnetic bead-based purification and separation on Opentrons Flex platforms.

34|7|Updated Nov 29, 2025
One-click install
npx skills add https://github.com/jkitchin/skillz --skill opentrons-magnetic-block
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: opentrons-magnetic-block
Source: https://github.com/jkitchin/skillz/tree/main/skills/laboratory/opentrons-magnetic-block
Command: npx skills add https://github.com/jkitchin/skillz --skill opentrons-magnetic-block

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

The Opentrons Magnetic Block provides unpowered magnetic separation to immobilize beads in wells, enabling supernatant removal and bead-based workflows on a Flex deck.

Core Features & Use Cases

  • Unpowered magnetic separation: Move plates onto the block and wait for beads to collect.
  • Bead-based workflows: DNA/RNA purification, SPRI workflows, and immunoprecipitation automation.
  • Flex-only optimization: Designed for gripper-based workflows with fixed magnet positions.

Quick Start

Place a plate on the magnetic block, initiate a 2–5 minute bead separation delay, then remove supernatant via pipetting.

Frequently Asked Questions about opentrons-magnetic-block

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate bead separation for DNA/RNA purification on Opentrons Flex?

Bead separation on Flex uses the Opentrons Magnetic Block to immobilize magnetic beads in wells. Place your sample plate on the unpowered block, wait 2–5 minutes for beads to collect at the magnet, then pipette off the supernatant. This automates DNA/RNA extraction, PCR cleanup, and library preparation workflows without powered equipment.

Can I use the magnetic block for PCR cleanup and SPRI workflows?

Yes. The magnetic block supports bead-based PCR cleanup and SPRI (solid-phase reversible immobilization) workflows on Flex. Beads bind target DNA/RNA or proteins, the magnet collects them, and you remove contaminants via supernatant removal and wash cycles.

What plate types and deck setup do I need for magnetic bead separation on Flex?

Magnetic bead separation requires standard 96-well plates compatible with the Opentrons Magnetic Block and Flex gripper-based plate movement. The block occupies a fixed magnet position on the Flex deck; your protocol handles plate positioning and timing for bead settling.

How long should beads settle on the magnetic block before removing supernatant?

Beads typically settle in 2–5 minutes on the magnetic block. The exact duration depends on bead size, buffer viscosity, and sample volume. Build this delay into your Flex protocol between plate placement and pipetting to ensure complete magnetic collection.

What workflows beyond DNA extraction can I automate with magnetic bead separation?

Magnetic bead separation on Flex supports immunoprecipitation, protein purification, cell sorting, and library preparation. Any workflow requiring bead-based capture and immobilization of target molecules can use the unpowered magnetic block for hands-off, automated separation.

Do I need a powered magnetic separator for Flex bead-based workflows?

No. The Opentrons Magnetic Block is unpowered; beads collect passively under magnetic force. This simplifies deck integration and reduces equipment costs while automating separation timing and supernatant removal via pipetting.