Alhambra, formerly tilesetdesigner, is a package for designing DNA tile systems, currently focused on DX tiles. It uses stickydesign to create sticky end sequences, peppercompiler with spuriousSSM to create core sequences, and xgrow to simulate systems. It uses an extensible system for tileset design, and a flexible YAML format for describing the tilesets.
Alhambra is designed to be installed as a Python package. To install the current (semi-)stable version from the Python Package Index, you can simply use
pip install alhambra
Alhambra is designed to work with Python 3, and may fail with Python 2.
To install development versions, you can check out this github repository, and
use pip -e or some other method for installing Python packages. Multiple
versions can be handled through virtualenv.
All Alhambra requirements should be handled through setuptools dependencies, but note that xgrow and peppercompiler both rely on C code being compiled, which may fail.
Documentation is available online on readthedocs.io. In particular, see the tutorial. It is also available in the docs/ folder.
Most user-facing functions are on the TileSet class.
Please send any questions to Constantine Evans, at cevans@evanslabs.org or cge@dna.caltech.edu.
- v1.1.0: fixes broken workaround for ruamel.yaml bug now fixed upstream, adds double-tile sensitivity, includes seed file to make xor example work.