dnada 0.1.2

An application for creating customized synthetic biology automation instructions

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.