Aquarium strain builder tools
Project description
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
Project details
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