BenchOS

A lab operating system for molecular and structural biology

Many labs distribute research knowledge across spreadsheets, wikis, lab notebooks, and word of mouth. BenchOS brings all information together into one agentic operating system. BenchOS is a Farnung Lab project.

See highlightsPreprint coming soonGitHub

Registry + ELN + SchedulingAI AgentConstruct EditorCryo-EM TrackingKnowledge Database

Highlights

An overview of BenchOS

BenchOS is designed as one connected platform: registry values feed notebook widgets, scientific properties are calculated automatically, and Benchmate can use the full integrated context directly inside the lab workflow.

BenchOS agent01

Benchmate

Benchmate is the BenchOS chat agent. Benchmate is designed to help you work faster. Because notebook entries, registry records, scheduling, and derived scientific values like absorption coefficients or molecular weights of your proteins live in the same system, Benchmate can use that context directly to calculate experimental setups, organize information, handle files, and act on BenchOS data.

ELN02

Notebook

Capture daily experiments, protocols, observations, and results in an electronic lab notebook built for real scientific work. Your registry items appear inside notebook entries as live widgets, so calculated properties like molecular weight and absorption coefficients stay linked, current, and usable in context.

Database03

Registry

Track the materials behind every experiment, from plasmids, cell lines and protein preparations to instruments and cryo-EM grids. The Registry gives teams a clear, searchable source of truth for the assets they use and produce, with properties like molecular weight and absorption coefficients calculated automatically and available across BenchOS.

Construct Editor04

Construct Editor

The Construct Editor lets scientists edit and visualize plasmids alongside other non-canonical DNA structures, including DNA forks, mismatch bubbles, and more. It gives sequence design a live visual workspace, so construct maps, structural features, and experimental edits can be inspected and adjusted interactively.

Knowledge Data Bank05

The Universe

The Universe turns registry data into a richer scientific view of your proteins. It is Uniprot on steroids with your lab's knowledge about a protein.

Tools & Skills06

Interactive tools

BenchOS can generate interactive tools that help with molecular biology work instead of leaving useful calculations or visual checks trapped in static text. These tools can support tasks like planning, analysis, sequence-aware decisions, and experiment setup inside a live interface. The same tools can also be harnessed as agentic skills from the CLI, so repeatable scientific workflows can run in BenchOS or from the command line.

Lab Organization07

Equipment Booking

Coordinate shared instruments with a scheduling system built for busy labs. Equipment Scheduling makes it easier to see availability, reserve time, and manage bookings across the team.

Planning08

Lab Calendar

Keep experiments, timelines, and upcoming work visible in one shared calendar. The Lab Calendar gives teams a live operational view of what is happening in the lab and what is coming next.

Biology-Native Records

BenchOS works with the actual objects your lab cares about

Plasmids, preps, expression runs, cryo-EM grids, references, and experiment notes can be connected as structured entities instead of being scattered across databases, spreadsheets, wikis, notebooks, and word-of-mouth.

benchos

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BenchOS for
structured lab workflows

BenchOS links constructs, samples, experiments, and files so the agent can work with the same context as the underlying records.

See highlights See record types