farnunglab

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.

Predict optimal construct boundaries for protein expression. Use when the user asks about domain boundaries, construct design, truncations, which region of a protein to express, or identifying disordered regions.

Manage lab notebook entries, registry items (plasmids, proteins, etc.), templates, widgets, and audit logs via the Labbook service. Use when creating or viewing lab notebook entries, managing the sample registry, or documenting experiments.

Verify open reading frames (ORFs) in plasmid sequences. Use when the user asks about verifying protein coding sequences, checking if an ORF is present in a plasmid, finding where a protein is encoded, or doing six-frame translation analysis.

Fetch sequencing data from Plasmidsaurus. Use when the user asks about listing sequencing orders, downloading sequencing results, checking order status, or retrieving plasmid sequences from Plasmidsaurus.

Design PCR primers for molecular cloning. Use when the user asks about designing primers, LIC cloning primers, sequencing primers, Gibson assembly primers, or working with NCBI accession codes for cloning.

Calculate protein parameters (MW, pI, extinction coefficient) and generate purification recommendations. Use when the user asks about protein properties, molecular weight, isoelectric point, extinction coefficients, or purification strategies.

Decision trees and workflows for molecular cloning in structural biology labs. Use when the user asks about cloning strategies, LIC vs Gibson, biGBac assembly, tag selection, expression system choice (insect vs E. coli), codon optimization, or designing constructs.

Query and manage Quartzy lab inventory, order requests, and webhooks. Use when the user asks about lab supplies, reagent inventory, placing orders, checking order status, or creating new order requests in Quartzy.