メニュー
Calculate reaction buffer recipes accounting for protein stock contributions. Use when the user asks about designing reaction buffers, calculating buffer volumes, compensation buffers, or setting up biochemistry experiments with proteins.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
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.
| name | reactor |
| description | Calculate reaction buffer recipes accounting for protein stock contributions. Use when the user asks about designing reaction buffers, calculating buffer volumes, compensation buffers, or setting up biochemistry experiments with proteins. |
| allowed-tools | Bash(reactor_cli:*) |
A CLI tool for calculating reaction buffer recipes that account for buffer components contributed by protein stocks.
scripts/reactor_cli.py
# List available presets
python3 scripts/reactor_cli.py --list-presets
# List predefined stock concentrations
python3 scripts/reactor_cli.py --list-stocks
# Calculate using presets
python3 scripts/reactor_cli.py \
--protein-preset kinase_panel \
--buffer-preset kinase_assay \
--volume 100
# Calculate with direct specifications (concentration)
python3 scripts/reactor_cli.py \
--protein "CDK2:50nM:stock=10uM:buffer=HEPES/20mM,NaCl/150mM" \
--buffer "HEPES:1M->25mM" \
--buffer "NaCl:5M->100mM" \
--volume 100
# Calculate using pmol amounts (auto-converted to concentration)
python3 scripts/reactor_cli.py \
--protein "PolII:70pmol:stock=5.17uM:buffer=HEPES/20mM,NaCl/150mM" \
--buffer "HEPES:1M->20mM" \
--volume 100
# Calculate using molar ratios with reference
python3 scripts/reactor_cli.py \
--reference 70pmol \
--protein "PolII:1x:stock=5.17uM:buffer=HEPES/20mM" \
--protein "DSIF:1.5x:stock=50.8uM:buffer=HEPES/20mM" \
--buffer "HEPES:1M->20mM" \
--volume 100
# Use compensation buffer mode (creates concentrated buffer)
python3 scripts/reactor_cli.py \
--protein "MyProtein:100nM:stock=5uM:buffer=HEPES/20mM,NaCl/300mM" \
--buffer "HEPES:1M->25mM" \
--buffer "NaCl:5M->150mM" \
--volume 50 \
--mode compensation \
--fold 10
# Output as JSON
python3 scripts/reactor_cli.py \
--protein-preset kinase_panel \
--buffer-preset storage \
--volume 100 \
--json
Direct Mode (default): Calculates exact volumes of each buffer component to add, accounting for contributions from protein stocks.
Compensation Mode: Creates a concentrated buffer (e.g., 10X) that compensates for buffer components in protein stocks. Useful for preparing batch buffers.
"Name:Amount:stock=StockConc[:buffer=Component/Conc,Component/Conc,...]"
Amount can be specified as:
50nM, 1uM, 100mM70pmol, 100fmol, 1nmol (auto-converted to concentration based on volume)1.5x, 2x (requires --reference flag)Examples:
"CDK2:50nM:stock=10uM" - Simple protein without buffer info"CDK2:50nM:stock=10uM:buffer=HEPES/20mM,NaCl/150mM" - Protein with storage buffer components"PolII:70pmol:stock=5.17uM:buffer=HEPES/20mM" - Using absolute pmol amount"DSIF:1.5x:stock=50.8uM:buffer=HEPES/20mM" - Using molar ratio (with --reference 70pmol)"Name:StockConc->FinalConc"
Examples:
"HEPES:1M->25mM" - HEPES from 1M stock to 25mM final"NaCl:5M->150mM" - NaCl from 5M stock to 150mM final"Glycerol:100%->10%" - Glycerol from 100% to 10% finalProtein Presets (built-in):
kinase_panel - CDK2 and MEK1 for kinase assayspurification_stocks - His-tagged protein and TEV proteasereconstitution - Nucleosome reconstitutionpolii_elongation_complex - Pol II elongation complex (PolII, DSIF, IWS1, ELOF1, SPT6, PAF1c, P-TEFb, CSB, DNA-RNA, ntDNA)Buffer Presets (built-in):
lysis - Cell lysis buffer (50mM HEPES, 300mM NaCl, 1mM TCEP, 5% glycerol)gel_filtration - SEC buffer (25mM Tris, 150mM NaCl, 1mM EDTA, 10% glycerol)storage - Protein storage buffer (20mM HEPES, 150mM NaCl, 0.5mM TCEP, 10% glycerol)kinase_assay - Kinase reaction buffer (25mM HEPES, 100mM NaCl, 10mM MgCl2, 1mM DTT, 1mM ATP)cryo_em - Cryo-EM buffer (20mM HEPES, 150mM NaCl, 1mM TCEP)elongation_buffer - Elongation assay buffer (20mM HEPES, 75mM NaCl, 10% glycerol, 1mM TCEP, 1mM ATP, 3mM MgCl2)Presets can be loaded from external YAML or JSON files using --presets-file. Default locations searched:
~/.config/reactor/presets.yamlCommon laboratory stock concentrations are predefined:
--list-stocks to see all)--reference)