autoprotocol 10.3.0

Description:

autoprotocol 10.3.0

Autoprotocol is the standard way to express experiments in life science. This repository contains a python library for generating Autoprotocol.

Installation
To work from the latest stable release:
pip install autoprotocol
check the the releases for more information about the changes that will be downloaded.
Alternatively to get more up-to-date features:
git clone https://github.com/autoprotocol/autoprotocol-python
cd autoprotocol-python
python setup.py install
check the changelog for information about features included on master but not yet released.


Building a Protocol
A basic protocol is written by declaring Protocol.ref objects and acting on them with Protocol.instruction methods.
import json
from autoprotocol.protocol import Protocol

# instantiate a protocol object
p = Protocol()

# generate a ref
# specify where it comes from and how it should be handled when the Protocol is done
plate = p.ref("test pcr plate", id=None, cont_type="96-pcr", discard=True)

# generate seal and spin instructions that act on the ref
# some parameters are explicitly specified and others are left to vendor defaults
p.seal(
ref=plate,
type="foil",
mode="thermal",
temperature="165:celsius",
duration="1.5:seconds"
)
p.spin(
ref=plate,
acceleration="1000:g",
duration="1:minute"
)

# serialize the protocol as Autoprotocol JSON
print(json.dumps(p.as_dict(), indent=2))
which prints
{
"instructions": [
{
"op": "seal",
"object": "test pcr plate",
"type": "foil",
"mode": "thermal",
"mode_params": {
"temperature": "165:celsius",
"duration": "1.5:second"
}
},
{
"op": "spin",
"object": "test pcr plate",
"acceleration": "1000:g",
"duration": "1:minute"
}
],
"refs": {
"test pcr plate": {
"new": "96-pcr",
"discard": true
}
}
}


Extras
Select SublimeText snippets are included with this repository.
To use them copy the autoprotocol-python SublimeText Snippet folder to your local Sublime /Packages/User directory.


Documentation
For more information, see the documentation.


Contributing
For more information, see CONTRIBUTING.