An application for creating customized synthetic biology automation instructions
Project description
DNAda
DNAda is a web application that integrates the j5 DNA assembly software with robotic liquid handlers.
Background
J5 is a powerful DNA assembly software that can be used to design and optimize DNA assembly protocols. However, it is not directly compatible with robotic liquid handlers. DNAda is a web/command-line application that integrates j5 with robotic liquid handlers by converting a j5 assembly design into a series of liquid handler compatible instructions. This enables a user without progamming experience to design DNA assembly protocols on a user-friendly canvas, DeviceEditor, and then convert the design using J5 and subsequently DNAda into a series of instructions that can be executed on a liquid handler.
CLI Installation
Note, it is highly recommended to use a virtual environment to install the dependencies.
For example,
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh
source ~/mambaforge/bin/activate
mamba create -y -n dnada
conda activate dnada
mamba install -y python==3.11
pip install dnada
Alternatively, setup from the source code by running
git clone https://github.com/JBEI/dnada.git
cd dnada/backend/app
python setup.py install
Note, there is currently a bug in autoprotocol-python. To temporarily resolve this bug until it gets patched, identify the location of the autoprotocol library identified in your virtual environment and apply the fix-oligosynthesizeolig-serialization.patch file. For example,
cd ~/mambaforge/envs/dnada/lib/python3.11/site-packages/
patch -p1 < ~/dnada/backend/app/fix-oligosynthesizeoligo-serialization.patch
Quick Start
There is a sample J5 design file available in the examples/
directory in the github repo.
After installing the DNAda CLI through pip or github, to run DNAda on that design file,
execute:
cd dnada/examples
dnada_cli example_j5_output.zip
After a few seconds you should see a new .zip
archive generated with the
name automation_instructions.zip
.
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