Aquarium-SD2 Strain Builder Tools (aqbt)

This repo contains many Aquarium-related tools for constructing new engineered strains.

Features

• Automated design and Aquarium workflow submission of plasmid assemblies
• Automated design and Aquarium workflow submission of yeast constructions
• Conversion of Aquarium strain definitions to engineered GFF with FASTA.
• JSON-schema validated serialization of Aquarium models
• Aquarium <-> Benchling integration
• Aquarium <-> SynBioHub integration (coming soon)
• Common file type conversions GFF <> FASTA <> Genbank <> JSON <> Benchling <> Aq <> SBOL (planned)
• Aquarium database faker for unit testing

Usage

Installation

pip install .

Install BLAST locally using the following:

pyblast install

Credentials

AqBuildTools (aqbt) requires a credentials.toml file to connect with Aquarium, Benchling and SynBioHub (coming soon). The following creates the default scope for a aqbt session:

[aquarium.production]
login = 'mylogin'
password = 'mypass'
url = 'http://aquarium.org'

[benchling.production]
apikey = 'sk_398dfg983nsdfsdflksj'
initials = 'UWBF'
schema = 'Aquarium DNA'
prefix = 'aq'
folder_id = 'lib_ILUNzz6N'
id = 'src_KE6uFvex'

[session.default]
aquarium = 'production'

from aqbt import AquariumBuildTools

aqbt = AquariumBuildTools.from_toml('credentials.toml')

Examples

Querying the Aquarium server

Connecting to Benchling and Synbiohub

Plasmid construction

Strain construction

Generating GFFs

Related repos

trident, DASi, Benchling API, Terrarium, pyblast, primer3-py-plus