BenchOS

Generate AKTA or UNICORN chromatograms from uploaded .res or .zip files with PyCORN, export csv or xlsx traces, and attach the results to BenchOS entries or registry items. Use when the user provides a chromatogram export file and wants plots, extracted data, or BenchOS-linked results.

Assemble BenchOS demo multi-insert multi-insert constructs, compute HiFi assembly reaction volumes, and export the final assembled sequence. Use when the user wants a BenchOS CLI or agent-driven version of the BigBac Assembler tool.

Calculate BenchOS buffer recipes from preset or custom stock-solution inputs and export the resulting recipe. Use when the user wants a BenchOS CLI or agent-driven version of the Buffer Calculator tool.

BenchOS CLI command reference for workspace, memory, API, and skill-management operations. Use when generating, reviewing, or troubleshooting benchos-cli command usage.

Decision trees and workflows for molecular cloning in structural biology labs. Use when the user asks about LIC vs Gibson, construct design, tag strategy, codon optimization planning, multi-subunit assembly, or clone verification workflow.

Codon optimize DNA or protein sequences for expression using the BenchOS-managed IDT integration. Use when the user asks to codon optimize for insect, E. coli, mammalian, yeast, or vector-specific expression.

Assemble and purify macromolecular complexes for structural biology. Use when the user asks about SEC complex assembly, stoichiometry, expected elution positions, A260/A280 interpretation, or fraction-selection strategy.

Review gel or blot images in the BenchOS Gel Annotator, add ladder or lane annotations, quantify bands with ROI boxes or line profiles, and persist exports back into notebook entries.

Simulate GraFix-style migration distances for protein complexes across configurable sucrose gradients and rotor presets. Use when the user wants a quick comparative sedimentation-style simulation from complex sizes, rotor choice, spin rate, and run time.

Baculovirus expression system guidance for recombinant protein production. Use when the user asks about Sf9, Sf21, Hi5, bacmid generation, V0/V1 production, infection strategy, or insect-cell expression troubleshooting.

Search Notion, inspect pages and databases, and read page block content through BenchOS-managed API routes. Use when the user asks to find protocols, open Notion pages, inspect database schemas, or query lab databases stored in Notion.

Calculate BenchOS 50 µL PCR reactions, plasmid dilution guidance, and optional master-mix volumes. Use when the user wants a BenchOS CLI or agent-driven version of the PCR Calculator tool.

PHENIX workflow guidance for cryo-EM model building, map analysis, real-space refinement, and validation. Use when the user asks how to use PHENIX for map sharpening, docking, rebuilding, refinement, or validation.

Insert raw or accession-resolved DNA sequences into BenchOS demo plasmid backbones and export the final plasmid FASTA. Use when the user wants a BenchOS CLI or agent-driven version of the Plasmid Creator tool.

List Plasmidsaurus sequencing jobs, inspect item details, and download results or reads into the BenchOS workspace. Use when the user asks to check sequencing status, fetch sequencing outputs, or pull Plasmidsaurus data into BenchOS.

Design LIC, sequencing, and optional Gibson or CPEC-style fragment primers from an NCBI accession or pasted DNA sequence. Use when the user wants naming-ready primer sets generated inside BenchOS.

Calculate protein parameters such as molecular weight, pI, extinction coefficient, and basic purification recommendations. Use when the user asks about protein properties or planning purification from sequence.

Query Quartzy labs, inventory, order requests, and item types through BenchOS-managed API routes. Use when the user asks to inspect supply inventory, check request status, or create or update Quartzy order requests.

Calculate reaction buffer recipes while accounting for protein stock-buffer contributions. Use when the user asks for reaction setup volumes, compensation buffers, or multi-component biochemistry recipes.

Servalcat workflow guidance for reciprocal-space cryo-EM refinement and Fo-Fc map calculation. Use when the user asks about half-map refinement, omit maps, weighted difference maps, or reciprocal-space validation strategy.

Parse SnapGene .dna files from the BenchOS workspace, inspect SeqViz payloads for registry attachments, and compute encoded proteins for plasmid registry items. Use when the user asks to read SnapGene files, inspect plasmid maps, or extract protein/primer information from a .dna file.

Standard BenchOS workflow for workspace updates, memory operations, and LabBook API tasks via benchos-cli. Use for routine BenchOS execution requests (files, memory, APIs, onboarding rules).

Create Twist quotes and orders for clonal genes or gene blocks through the BenchOS-managed Twist integration. Use when the user asks to check available vectors, get a quote, or place a synthesis order.

Render and print labels on the lab Zebra printer through a controlled BenchOS integration. Use when the user asks for sample labels, tube labels, barcode labels, or raw ZPL previews.