You're viewing an older version of the aµtoPULSE help. For the latest version, visit online help 1.3.
This manual provides basic information and instructions to help you set up and operate aµtoPULSE for the first time.
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Caution | Read the manual before operating this equipment. No user serviceable parts. Only qualified service personnel shall service this equipment. |
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Electric Shock Hazard | Danger High Voltage - Disconnect all sources before servicing. |
We provide you with an accessory kit that includes everything you need to get started, contained in several places inside the packaging. These items include:
Inside the Instrument:
2.5 gal (10L) Waste Container
25 ft Peristaltic Pump Tubing
Tube Adapter Box:
1.5 mL Tube Adapters
15 mL Tube Adapters
50 mL Tube Adapters
Inside the Kit Foam:
1.5 mL Tube Rack
15 mL Tube Rack
50 mL Tube Rack
Chip Rack
Servicing Tool Kit
Chip Starter Kit
Lifting Handle Tool Kit
In the Kit Foam Box:
1.5 mL Conical Tubes
15 mL Conical Tubes
50 mL Conical Tubes
10 g Calibration Weight
100 g Calibration Weight
SIM Card Ejector
Capacitive Sensor
Ethernet Cable
Power Cable
Long Base Chip Gasket
Single Base Chip Gasket
Peristaltic Tube Assembly
25 ft Peristaltic Pump Tubing
Buffer Needle
Plastic Quick-Turn Tube Coupling Plugs, for 3/32" Barbed Tube ID
Installation Certificates (for customers located in China only)
Warranty Letters (for customers located in China only)
aµtoPULSE Front View
Gantry: Moves the tubes and chips, with the Gripper handling placement and the Arm directing the gripper for accurate positioning.
Gripper and Arm
Door: Allows access to internal components and ensures safety during operation by stopping the gantry if open during active runs.
Deck: Holds all the tubes and chips you need to run an experiment, consisting of 12 nests for the compatible tube and chip racks.
LED Indicator: Indicates different instrument statuses during operation. For example, multi-color: aµtoPULSE is idle, white to green: running a protocol, red: an error has occurred, etc. See Instrument Overview for detailed information.
Waste Tray: Collects any spilled liquid during protocol runs.
Important: If you find liquid in the tray due to a system error, check the source of the leak and contact support@formulatrix.com.
Station (as a whole unit): Serves as the main component to run the protocols. The station components include:
Concentration Station
Concentration Station Components
Base Chip: Connects with the chip’s air receiver to supply the chip with air from the instrument.
Buffer Needle: Transfers buffer solution from the reservoir to the conical tube.
Microtube Scale: Measures the weight of small-volume samples (1.5 mL).
Conical Tube Scale: Measures the weight of high-volume samples (50 and 15 mL).
Permeate Tubing Assembly: Facilitates the transfer of permeate liquid.
Chip Clamp: Holds the chip securely in place during the operation to ensure an airtight seal inside the chip.
Cleaning Station
Cleaning Station Components
aµtoPULSE Right Side View
Power Button: Press the button to turn the instrument on or off. Refer to Instrument Overview to identify the LED indicator on the button.
Chiller Connector Hole: Provides a pass-through for the chiller connectors to reach the cold pad on the deck.
Connection Panel 1:
Ethernet Port: Connects the aµtoPULSE wired network to your computer.
USB Port: Allows the software to update via a flash drive and connection with other devices.
Peristaltic Pump Panel: Peristaltic pumps transfer buffer and cleaning solutions throughout the system. The pumps are assigned to each station based on configuration: one pump for each Concentration Station and two pumps, plus one Waste Drain pump for Cleaning Station. See Instrument Overview for more information.
Connection Panel 2:
Pneumatic Ports: Connects to the FORMULATRIX Pump Box for the required pressure and vacuum inputs.
Waste Level Sensor Interface: Connects the instrument with the waste reservoir’s level sensor.
E-Stop Port: Connects to the optional FORMULATRIX emergency stop button for quick instrument shutdown.
Buffer Reservoir: Stores buffer solution needed during profile runs.
Side Vent: Allows the power supply access to fresh air.
Cleaning Solution Reservoir: Stores cleaning solution needed during cleaning cycles.
Waste Container: Collects waste permeate from the instrument.
Power Panel:
Power Entry: Plug in the power cable to supply power to the system.
Power Switch: Switches power to the instrument.
aµtoPULSE Back View
Chips are the filtering device of aµtoPULSE with the following components:
aµtoPULSE Chip Front View
Barcode: Identifies the membrane material and its MWCO.
Filter Membrane: Separates permeate from the sample, with both membranes (upper and lower) used in high-volume filtration and only the lower membrane for low-volume filtration.
Diaphragm: The two diaphragms circulate the sample and buffer through the chip’s membrane.
Transfer Tube: Allows liquid to flow into and out of the chip from the tubes.
aµtoPULSE Chip Back View
Pick-up Notch: Ensures the correct gripper position when picking up the chip.
Air Port: Receives air flow from the instrument, actuating the diaphragm pump and control valves to control the liquid flow.
| Item | 1.5 mL Microtube | 15 mL Conical Tube | 50 mL Conical Tube |
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| Tube Adapter |
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| Tube |
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| Tube Rack |
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| Chip Rack |
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Open the aµtoPULSE software from your browser by typing: http://autopulse-[device serial #].local.
E.g., http://autopulse-4/local for instrument AP-1-0004.
Enter your username and password to log in.
aµtoPULSE Software Login
Once you access the aµtoPULSE software, navigate through the pages to run protocols and operate the instrument. The basic pages are described below.
Open the Explorer page to view, open, add, and manage protocols. All defined protocols are listed on this page.
Explorer Page
The Editor page is where you define labware and create profiles for your protocols. Identify the sections from the description below.
Editor Page
Section 1: Command Bar
Note: The protocol name is editable. Click on it to rename.
: Upload the labware and profile data file for a quick protocol setup, or download CSV file templates.
: Customize more specific protocol settings, such as enabling/disabling chip cleaning.
: Create a new profile or adjust the parameters of an existing one.
: Enables auto-scanning on the Station if the tube adapters are in place.
Section 2: Labware and Profile Tab
Switch between the tabs to open the labware and profile list.
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| Labware Tab | Profile Tab |
Section 3: Station and Deck Panel
This section is a visual representation of the instrument’s station and deck. Expand the panel by clicking on the arrow
or title to switch between the displays.
Station: Click the Edit button
on each card to define the tube at the station. The Station cards below are the configuration of 3 Concentration Stations (grey) and 2 Cleaning Stations (blue).
Station Card Panel
Deck: Drag and drop your desired racks from the Labware tab, and then click on the wells to specify your preferred tubes and chips.
Deck is Empty
Defined Labware on Deck
To create a new protocol, see Creating a Protocol.
View available generic labware in the Labware Manager page. You can also calibrate and adjust the chip and labware definition to your experiment needs by clicking the EDIT button. This page is only accessible to Administrators.
EDIT Button in Labware Manager
Switch between the pages below from the Tools menu to enhance system control and customization.
Admin-only function to register and manage user accounts. For regular users, only the Account and Change Password menus are available to update your password and account info.
User Management Page
Proper instrument setup is critical for ensuring the aµtoPULSE functions optimally. The steps below will guide you through setting up the instrument basics to ensure safety, efficiency, and cleanliness.
Route the corresponding tubing according to the connections diagram and put the ends inside the buffer reservoir, cleaning reservoir, and waste container. The reservoirs must be adequately filled and maintained for continuous operation.
To help you monitor the liquid level in the waste container, aµtoPULSE provides a level sensor that warns you if it needs emptying. The sensor is detachable by simply pulling the velcro off its original location. Then, you can attach it to an empty container in the same orientation outside the container’s wall.
Note: Make sure that the sensor contacts the container wall securely to ensure accurate detection.
The standard recommendation for cleaning is 0.1 M NaOH, but depending upon the application, different cleaning agents can be used. For example, if the only concern is sterility from bio-burden, the cleaning agent can be 10% NaClO or 3% H2O2. For protein removal, 0.1 M NaOH or even detergents can be used. But for detergents, you need to be cautious and should perform a thorough rinsing afterward. Other cleaning agents that can be used include:
Place the tube adapter on the station:
Warning! Do not apply downward pressure when installing the adapter, as it may damage the load cell.
Here are some best practices to ensure optimal use of the deck area:
The scales in aµtoPULSE require periodic calibration to ensure accurate measurements. Perform calibration after initial installation, significant temperature changes, or noted volume inaccuracies. Follow the steps below to calibrate.
In the aµtoPULSE software Navigation Bar, click Tools and select Calibration.
Navigate to the selected Station panel (for example, Station 1). Each station is calibrated individually and has three scales: Left Scale, Low Volume Scale, and Right Scale.
Calibration Page
Check the Last Calibration time displayed in the upper-right corner of the station’s panel. Click EDIT to start calibration.
Last Calibration Time
Do the following for each scale:
Left Scale and Right Scale
Click TARE to zero the scale.
Place the 100 g calibration weight on the center of the scale.
In the Calibration Weight field, enter 100.
Click CALIBRATE to initiate the calibration process. The Calibrated Weight should match the calibration weight entered.
Repeat steps a-d for the other scale.
Low Volume Scale
Important! The low volume scale is fragile—even a light touch can exceed its limit. We highly recommend following each step carefully and avoiding direct contact with the scale to prevent damage.
Activate the Low Volume Scale Movement toggle to lift the scale.
Click TARE to zero the scale.
Turn off the Low Volume Scale Movement toggle to lower the scale.
Place the 10 g calibration weight on the center of the scale.
Activate the Low Volume Scale Movement toggle to lift the scale.
In the Calibration Weight field, enter 10.
Click CALIBRATE to initiate the calibration process. The Calibrated Weight should match the calibration weight entered.
Turn off the Low Volume Scale Movement toggle to lower the scale.
Click the SAVE button 
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Repeat steps 3-5 for the remaining stations.
Note: The Cleaning Station(s) do not have a Low Volume Scale.
Creating a protocol involves defining labware, stations, and creating profiles in the Editor page. Follow the instructions below thoroughly.
In the Explorer page, click Add Protocol, then OPEN.
Note: For quicker access, you can double-click the Add Protocol button.
Click Add Protocol in the Explorer Page
OPTIONAL: In the Editor page, click the Import button to load your predefined profile and labware data in a CSV file. Refer to the Importing Labware and Profile CSV topic for more information. Otherwise, you can manually define your protocol by continuing to step 3.
Click Import in the Editor Page
Defining Labware and Stations:
Note: If the tube adapters are already on the stations, click the Scan Adapters button . Then, proceed to step b.
In the Station panel, click the Edit button on the selected station card, and then specify the tube adapters in Concentration and Cleaning Stations.
Concentration Station Tube Settings
Cleaning Station Detail Information
Note: If you have more than one Cleaning Station, only the Left Tube Adapter and Right Tube Adapter settings will need to be adjusted for the additional stations. All other parameters will be derived from the first Cleaning Station configuration.
Expand the Deck panel to display the Virtual Deck as shown below.
Deck Panel in the Editor Page
Drag the desired labware from the Labware list to the Virtual Deck to match your planned layout. The virtual layout must match the physical layout on the Deck.
Click on each well of the assigned labware and define the settings as follows.
Tube: If a tube is in place, activate the toggle, then fill in the Liquid Type, Starting Volume, Starting Concentration, and Density.
Define Tube Parameters
Chip: Select the MWCO if a chip is in place.
Select Chip MWCO
After defining all selected labware, continue to create a profile.
On the Command Bar, click the Profile button and set up the following:
Creating a Profile
Select the MWCO size according to your preference.
Method: Choose Concentrate or Buffer Exchange. If you choose Buffer Exchange, define the Buffer Source from the provided options.
Note: You can still concentrate your sample with the Buffer Exchange method.
From the Select labware panel, define the tube based on your selected method and deck configuration.
Fill in the Target Value, Start Exchange, Step Size, Est. Final Concentration, and Exchange Volume.
The system will use the default Advanced Setup. If you want to use another setup, select it from the available options or click the Edit button
to create a new customized setup.
Advanced Setup Menu
Click CREATE to complete the protocol creation process.
Repeat steps a-g to create more profiles. Your profile(s) will appear in the Profile tab.
To run the protocol, select the profiles you want to execute, then click RUN.
.png "Click RUN to Execute Profile(s)")
Click RUN to Execute Profile(s)
The aµtoPULSE Filtration Chips are rated for 300 mL of total permeate. Overuse of the chips can result in a loss of sample or damage to the device. For short-term reuse, chips must be stored wet in a sealed vessel. Long-term storage (>1 week) is not recommended unless a bactericide is added.
Note: It is highly recommended to run a chip cleaning cycle before storing to clear out any residue, especially if your sample can crystallize.
Required Tool and Material:
To store the chip:
Place the chip vertically in the storage vessel (transfer tubes facing up).
Fill the vessel with enough water to submerge the chip (excluding transfer tubes).
OPTIONAL: Seal and store the vessel in the refrigerator.
Label the stored chip with the total volume permeated. Note this volume for your chip's lifetime records. Dispose of the chip if the total volume permeated exceeds 300 mL, functionality of the chip beyond this can not be guaranteed.
To ensure durability and optimal performance, consider the chemical compatibility of materials used in the device. Some chemicals are safe for continuous use, while others can cause damage and should be avoided. Certain substances may only be suitable for limited use and require additional testing.
Warning! The aµtoPULSE system and filter chips are not compatible with all chemical solutions. Use of solutions that are not recommended could damage samples, chips, or the aµtoPULSE instrument. Damage resulting from improper solution use may void the device warranty.
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| APOWH-V12R125 |