BiBaBenchBuddy is a desktop and web application designed for molecular biology workflows. It provides practical tools for calculations, visualization, and protocol support, helping streamline routine lab work and reduce manual errors.
- DNA digestion calculator
- Ligation calculator
- Gibson assembly calculator
- PCR setup & optimization tools
- Dilution and concentration calculators
- Gel electrophoresis and western blot simulator
- Buffer library & calculator
- Clean, fast, mobile-friendly interface
🌐 WebApp Open webapp ↗
The latest version is accessible from any browser via this link: https://bi-ba-bench-buddy.app
For a standalone experience with native performance:
- Download:
- Windows Version:
- All versions: Releases overview
Click the Settings icon in the top right:
- Sync: Log in with Email or GitHub to keep your sessions and settings synced across your laptop and web browser.
- AI Settings: Paste your API keys (e.g., Google Gemini, OpenAI, or Groq) to unlock the AI Buffer Assistant and smarter protocol generation.
- Appearance: Choose from various themes, including Modern Dark, Glass MacOS, and curated styles like pretty pink💕.
🧬 Calculators (Lab Math)
- Digestion: Batch process restriction digests with a vast library of NEB and Thermo enzymes.
- Ligation: Calculate optimal vector-to-insert molar ratios for standard ligations.
- Gibson Assembly: Multi-fragment assembly planning with molarity and volume calculations.
- Protein:
- Protein Concentration: Accurately determine protein concentration using A280 readings, MW, and extinction coefficients.
- Sample preparation: automatically creates the sample preparation mix table for the measured protein samples in the Protein Concentration tool.
- PCR Calculator:
- PCR Mix: Calculate mastermixes for multiple samples with different template concentrations.
- Ta Calculator: Advanced annealing temperature prediction using the nearest-neighbor model. Provides Tm, MW, and GC content analysis.
- OE-PCR: Plan Overlap Extension PCRs for site-directed mutagenesis or fragment joining.
- Product Sequence: Automatically generate the final DNA sequence based on your primers and template.
- Dilution: Simple or serial dilution calculations with molarity or percentage support.
🧪 Lab & Visualization
- Gel Simulator: Simulate agarose gels. Manually enter band sizes or paste your DNA sequence and select enzymes to visualize the fragments on gel automatically. Mark bands for extraction directly on the gel.
- Western Blot: Predict protein migration patterns. Select specific PAGE gel types and use specialized protein ladders.
- Plasmid Analyzer:
- Map Visualization: View circular or linear plasmid maps with auto-detection of common features and ORFs.
- Alignment: Align two sequences to identify mismatches
- Image Annotator (BETA): Upload your own gel or blot images. Add annotations, arrows, and lane labels.
🤖 Protocols & AI
- General AI Assistant: Available via the top-bar icon to answer lab-related questions or explain tool functionalities.
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- Protocol Library: A searchable database of standard molecular biology protocols that can be customized and exported.
- AI Buffer Assistant: A conversational AI optimized for lab chemistry. Describe the buffer you need (e.g., "1X TAE with 10mM EDTA"), and it will generate a recipe you can save to your history.
- Gibson assambly tool
- Primer designer tool
- General extra's for all tools
If you wish to run this locally:
git clone https://github.com/your-username/your-repo.git
cd your-repo
npm install
npm run dev #web
npm run app:dev #desktopThe following issues are known:
- Ta Calculator - The Annealing Temperature (Ta) logic is currently being refined and may not be 100% accurate for high-GC or complex primer pairs.
- Image Annotator - This tool is in active beta. While basic labeling and exporting work, some advanced selection and scaling features may still behave unexpectedly.
- Sequence Analyzer - The feature labeling is not very nicely visualized yet.
Zie: CHANGELOG.md Of bekijk Releases
If you like this app, feel free to buy me a coffee :)
