Part and linker collections

Introduction

As described and illustrated in the usage section (1a. Accessing BASIC part collections), basicsynbio contains a collection of Parts and Linkers accessible from within the API. In contrast to previous approaches, accessing these collections doesn’t require 3rd-party database access or even an internet connection. Below is a list of selected collections to browse and instructions for contributing part collections to the API.

Browse selected collections

Collections can be searched and viewed using SeqViz at the basicsynbio webapp. Alternatively collections can be viewed through the links below, displaying the PartLinkerCollection key, id, name and description.

• BASIC_BIOLEGIO_LINKERS[“v0.1”]

• BASIC_CDS_PARTS[“v0.1”]

• BASIC_PROMOTER_PARTS[“v0.1”]

• BASIC_SEVA_PARTS[“v0.1”]

Contributing part collections to basicsynbio

The following steps are required to add new part collections or versions of part collections to the API. Please feel free to contact hainesm6 directly for help with this:

1. Generate a genbank file containing all parts in the collection as separate elements.

2. Via a pull-request (refer to Contributing), complete the following:

   • Add the genbank file to the basicsynbio.parts_linkers sub-package.

   • Using importlib.resources and basicsynbio.parts_linkers.main.make_collection(), make or update the collection in basicsynbio.parts_linkers.basic_parts.

   • Where required, update the parts_linkers sub-package __init__.py file to import the collection.