PyLynx

About

PyLynx is a command-level Python interface to the Lynx liquid-handling robot by Dynamic Devices. PyLynx works using the TCP/IP interface to the Lynx to communicate with a universal method.

Raise an issue, post on labautomation.io, or contact stefanmgolas@gmail.com if you have any questions.

VVP Commands

Commands to the 96-channel VVP use Pandas dataframes (with some extra functionality) to specify volumes. This makes it easy to access and modify command data.

To initialize a VVP command array, run

from pylynx import VVPArray
array = VVPArray()

Here is the initialized array:

print(array)
    0    1    2    3    4    5    6    7    8    9    10   11
A  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
B  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
C  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
D  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
E  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
F  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
G  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
H  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0

This can be modified with standard numpy notation:

array.loc['A':'C',] = 20.0
array.loc[:,8:10] = 30.0

print(array)
     0     1     2     3     4     5     6     7     8     9     10    11
A  20.0  20.0  20.0  20.0  20.0  20.0  20.0  20.0  30.0  30.0  30.0  20.0
B  20.0  20.0  20.0  20.0  20.0  20.0  20.0  20.0  30.0  30.0  30.0  20.0
C  20.0  20.0  20.0  20.0  20.0  20.0  20.0  20.0  30.0  30.0  30.0  20.0
D   0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  30.0  30.0  30.0   0.0
E   0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  30.0  30.0  30.0   0.0
F   0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  30.0  30.0  30.0   0.0
G   0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  30.0  30.0  30.0   0.0
H   0.0   0.0   0.0   0.0   0.0   0.0   0.0   0.0  30.0  30.0  30.0   0.0

And the dataframe can be run as a VVP command as shown:

lynx.aspirate_96_vvp(plate = plate, array = array)

Normalization

Create a VVPArray of volumes that normalize the concentrations in a plate with the normalize function.

data = np.random.randint(1, 11, size=(8, 12))
df = pd.DataFrame(data)
normalization_vols = normalize(df, v1 = 30, c2 = 5)

Example Script

from pylynx import (LynxInterface, get_host_ip, VVPArray, MethodWorktable,
                    list_labware)
import numpy as np
import pandas as pd


data = np.zeros((8, 12))
data[:, :3] = 20
df = pd.DataFrame(data)
array = VVPArray(df)

worktable = MethodWorktable("Demo Workspace")

worktable.clear_worktable()
list_labware("Demo Workspace")
worktable.add_labware_to_location("tips_1", "LXB-96-950F", "Loc_02")
worktable.add_labware_to_location("plate_1", "96 Well Plate", "Loc_04")
worktable.add_labware_to_location("plate_2", "96 Well Plate", "Loc_06")
worktable.save_worktable()


ip = get_host_ip()
lynx = LynxInterface(ip=ip, port=47000, simulating=True)

lynx.setup()


lynx.load_tips(tips="tips_1")
response = lynx.aspirate_96_vvp(plate = "plate_1", array = array)
response = lynx.dispense_96_vvp(plate = "plate_2", array = array)
lynx.eject_tips(tips="tips_1")



lynx.tip_pickup_sv('tips_1', row = 2, column = 5)
lynx.aspirate_sv('plate_1', vol = 30, row = 1, column = 8)
lynx.dispense_sv('plate_1', vol = 30, row = 2, column = 2)
lynx.tip_eject_sv('tips_1', row = 2, column = 5)

Installation instructions:

Install 32-bit Python here. PyLynx has been tested on Python 3.9+.
Install git here.
Run git clone https://github.com/stefangolas/PyLynx.git from the command line
Run cd pylynx
Run pip install -e .
Set an environment variable called MM4_DATA_PATH to point to the directory containing your MM4 workspaces
Run pylynx-configure <Workspace_name>
Run pylynx-new-project
Run py example_script.py

Common Errors:

"pip is not recognized as an internal or external command"
See this stack overflow answer: https://stackoverflow.com/a/23709194

Errors relating to pip installing pandas
Try running pip install pandas==2.0.0

Configuration Tool

The pylynx-configure tool modifies the universal method to be compatible with the chosen workspace in the following ways:

Delete method worktable sides (e.g. Left, Right) that don't exist in the workspace
Delete method commands that are not possible in the workspace
Delete method worktable resource locations that are not in the workspace

The user must change utf-16 to utf-8 in the workspace worktable XML (e.g. Lynx.Left.Worktable) manually before running this tool

stefangolas/PyLynx