Autoprotocol is a standard way to express experiments in life science. This repository contains a python library for generating Autoprotocol.
$ git clone https://github.com/autoprotocol/autoprotocol-python
$ cd autoprotocol-python
$ python setup.py install
or, alternatively:
$ pip install autoprotocol
check the releases tab on this repository to see the latest release that will be downloaded, to be completely up to date it's safest to clone and install this repository as above
A basic protocol object has empty "refs" and "instructions" stanzas. Various helper methods in the Protocol class are then used to append instructions and refs to the object such as in the simple protocol below:
import json
from autoprotocol.protocol import Protocol
#instantiate new Protocol object
p = Protocol()
#append refs (containers) to Protocol object
bacteria = p.ref("bacteria", cont_type="96-pcr", storage="cold_4")
medium = p.ref("medium", cont_type="micro-1.5", storage="cold_4")
reaction_plate = p.ref("reaction_plate", cont_type="96-flat", storage="warm_37")
#distribute medium from 1.5mL tube to reaction wells
p.distribute(medium.well(0).set_volume("1000:microliter"), reaction_plate.wells_from(0,4), "190:microliter")
#transfer bacteria from source wells to reaction wells
p.transfer(bacteria.wells_from(0,4), reaction_plate.wells_from(0,4),
["10:microliter", "20:microliter", "30:microliter", "40:microliter"])
#incubate bacteria at 37 degrees for 5 hours
p.incubate(reaction_plate, "warm_37", "5:hour")
#read absorbance of the first four wells on the reaction plate at 600 nanometers
p.absorbance(reaction_plate, reaction_plate.wells_from(0,4).indices(), "600:nanometer",
"OD600_reading_01092014")
print json.dumps(p.as_dict(), indent=2)The script above produces the following autoprotocol:
{
"refs": {
"medium": {
"new": "micro-1.5",
"store": {
"where": "cold_4"
}
},
"bacteria": {
"new": "96-pcr",
"store": {
"where": "cold_4"
}
},
"reaction_plate": {
"new": "96-flat",
"store": {
"where": "warm_37"
}
}
},
"instructions": [
{
"groups": [
{
"distribute": {
"to": [
{
"volume": "190.0:microliter",
"well": "reaction_plate/0"
},
{
"volume": "190.0:microliter",
"well": "reaction_plate/1"
},
{
"volume": "190.0:microliter",
"well": "reaction_plate/2"
},
{
"volume": "190.0:microliter",
"well": "reaction_plate/3"
}
],
"from": "medium/0"
}
},
{
"transfer": [
{
"volume": "10.0:microliter",
"to": "reaction_plate/0",
"from": "bacteria/0"
}
]
},
{
"transfer": [
{
"volume": "20.0:microliter",
"to": "reaction_plate/1",
"from": "bacteria/0"
}
]
},
{
"transfer": [
{
"volume": "30.0:microliter",
"to": "reaction_plate/2",
"from": "bacteria/0"
}
]
},
{
"transfer": [
{
"volume": "40.0:microliter",
"to": "reaction_plate/3",
"from": "bacteria/0"
}
]
}
],
"op": "pipette"
},
{
"duration": "5:hour",
"where": "warm_37",
"object": "reaction_plate",
"shaking": false,
"op": "incubate"
},
{
"dataref": "OD600_reading_01092014",
"object": "reaction_plate",
"wells": [
"A1",
"A2",
"A3",
"A4"
],
"num_flashes": 25,
"wavelength": "600:nanometer",
"op": "absorbance"
}
]
}
The easiest way to contribute is to fork this repository and submit a pull request. You can also write an email to us if you want to discuss ideas or bugs.
- Max Hodak: max@transcriptic.com
- Jeremy Apthorp: jeremy@transcriptic.com
- Tali Herzka: tali@transcriptic.com
autoprotocol-python is BSD licensed (see LICENSE). Before we can accept your pull request, we require that you sign a CLA (Contributor License Agreement) allowing us to distribute your work under the BSD license. Email one of the authors listed above for more details.