Documentation, Coding, Bioinformatics, Scripts, examples, e-learning

How to use pydna, a python library to plan and simulate DNA assembly, cloning and genome engineering

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Pydna is a python package that provides a human-readable formal descriptions of 🧬 cloning and genetic assembly strategies in Python 🐍 for simulation and verification. Pydna can be used as executable documentation for cloning.

Pydna provides simulation of:

  • Primer design
  • PCR
  • Restriction digestion
  • Ligation
  • Gel electrophoresis of DNA with generation of gel images
  • Homologous recombination
  • Gibson assembly
  • Golden gate assembly

The training material contains documentation to install the library and jupyter notebooks describing how to get started with the library and examples.

DOI: https://doi.org/10.1186/s12859-015-0544-x

Licence: MIT License

Keywords: Synthetic Biology, Genetic Engineering, Molecular biology, Cloning, DNA engineering, genome engineering, Annotation

Target audience: Biologists and bioinformaticians

Resource type: Documentation, Coding, Bioinformatics, Scripts, examples, e-learning

Status: Active

Prerequisites:

  • basic python scripting knowledge

Learning objectives:

  • Learn how to install pydna
  • Learn the basics of pydna: reading sequences, simulate basic operations, writing files
  • Learn about more specific features through examples

Date created: 2025-04-11

Authors: Björn Johansson, Manuel Lera-Ramirez, Peilun Xie, Lucas Levassor

Contributors: Filipa Pereira, BjornFJohansson, manulera, hgbrian, bruno2git, hiyama341, dgruano, louisabraham, jan-glx, hristog, amijalis, jxu10

Scientific topics: Synthetic biology, Bioinformatics, Molecular biology, Genetic engineering, Metabolic engineering, Genetics

External resources:
pydna
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