Myra User Manual

Version 2.0 Rev B

Revision History
Revision Number Revised On Revision Description

2.0 Rev A 17/09/2021 Sample Prep and Setup mode added.

2.0 Rev B 07/10/2021 Calibration instructions updated.

2
Contents
Disclaimer...............................................................................................................................................................8

Technical Support .................................................................................................................................................9

Intended use of the Myra Instrument ..............................................................................................................10

Safety Information...............................................................................................................................................11

Warning Symbols ............................................................................................................................................11

Proper Use Warnings ......................................................................................................................................12

Type Plate Symbols .........................................................................................................................................13

Biological Safety ..............................................................................................................................................14

Decontamination of Instrument ................................................................................................................14

Disposal of Waste ........................................................................................................................................14

Return Merchandise Authorisation ..........................................................................................................14

Introduction .........................................................................................................................................................15

Instrument ............................................................................................................................................................16

Specifications ...................................................................................................................................................16

General Features ..............................................................................................................................................17

Accessories .......................................................................................................................................................19

Consumables ....................................................................................................................................................19

Installation............................................................................................................................................................20

Unpacking the Myra Instrument ..................................................................................................................20

Hardware Installation.....................................................................................................................................20

Software Installation .......................................................................................................................................21

Running Myra Software on Macintosh operating systems .....................................................................21

Updating Software ..........................................................................................................................................22

Upgrading Firmware ......................................................................................................................................22

Getting Started .....................................................................................................................................................23

Travel Locks .....................................................................................................................................................23

Connecting the Head ......................................................................................................................................24

Loading the Deck ................................................................................................................................................25

Using the HEPA Filter ....................................................................................................................................26

Using the UV Light .........................................................................................................................................27

Calibrating Blocks, Plates and Tubes ...........................................................................................................28

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 Block or Plate Position ................................................................................................................................29

Height Calibration.......................................................................................................................................30

LED Indicator Colours....................................................................................................................................31

Software Overview .............................................................................................................................................32

New Document ................................................................................................................................................32

Tool Bar .............................................................................................................................................................33

Open Assay or Myra Run Files .................................................................................................................33

Help Icon ......................................................................................................................................................34

Instrument Icon ...........................................................................................................................................34

Instrument Communication Icon..............................................................................................................35

File Tabs ............................................................................................................................................................36

Navigator Bar ...................................................................................................................................................36

File Active Windows.......................................................................................................................................37

Creating a New Assay ........................................................................................................................................38

Assay Setup ......................................................................................................................................................38

Information ..................................................................................................................................................38

Reaction Setup .............................................................................................................................................42

Diluent Reagent ...........................................................................................................................................43

Controls ........................................................................................................................................................44

Assay Profile – Mic Only................................................................................................................................44

Assay Analysis – Mic Only ............................................................................................................................45

Saving a New Assay .......................................................................................................................................45

Creating a New Run - qPCR ..............................................................................................................................46

Adding Assays .................................................................................................................................................46

Updating Changes to an Assay .................................................................................................................47

Run Setup .........................................................................................................................................................48

Samples Editor .............................................................................................................................................48

Choosing qPCR Reaction Plates ................................................................................................................48

Filling Cells...................................................................................................................................................50

Well Filter .....................................................................................................................................................50

Colours ..........................................................................................................................................................51

Name .............................................................................................................................................................51

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 Barcode Reader ............................................................................................................................................53

Water Load Samples ...................................................................................................................................53

Type ...............................................................................................................................................................53

Dilution Series..............................................................................................................................................55

Dilution Reagent..........................................................................................................................................57

Creating and Allocating Groups ...............................................................................................................57

Linking an Assay to a Sample ...................................................................................................................58

Optional Columns .......................................................................................................................................58

Import Samples............................................................................................................................................59

CSV Export or Copy to Clip Board ...........................................................................................................60

Sample Editor Warnings ............................................................................................................................60

Deck Layout – qPCR .......................................................................................................................................61

Configuration ...............................................................................................................................................61

Plate Library .................................................................................................................................................63

Plate Editor ...................................................................................................................................................65

Tube Type .....................................................................................................................................................65

Components .................................................................................................................................................66

Sample Templates .......................................................................................................................................68

Reaction Plate Configuration.....................................................................................................................68

Run Separation ................................................................................................................................................70

Advanced Settings ..........................................................................................................................................71

Starting a Mic Run...........................................................................................................................................73

Create Simple Transfer - General ......................................................................................................................74

Sources ..............................................................................................................................................................74

Importing Sample Sources .........................................................................................................................75

Destinations......................................................................................................................................................76

Normalisation ..............................................................................................................................................77

Pooling ..........................................................................................................................................................77

Custom setup mode ....................................................................................................................................77

Importing Destination Requirements.......................................................................................................77

Deck Layout – Simple Transfer .....................................................................................................................79

Advanced Settings – Simple Transfer ..........................................................................................................81

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Create Sample Prep & Setup – General............................................................................................................83

Sample Prep .....................................................................................................................................................83

Assays – Sample Prep .....................................................................................................................................84

Run Setup – Sample Prep ...............................................................................................................................85

Samples Editor .............................................................................................................................................85

Source Plate Visual Tool.............................................................................................................................86

Barcode Reader ............................................................................................................................................87

Import or Export Sample Data ..................................................................................................................87

Sample Editor Warnings ............................................................................................................................87

Deck Layout – Sample Prep ...........................................................................................................................88

Configuration ...............................................................................................................................................88

Components .................................................................................................................................................88

Sample Templates .......................................................................................................................................88

Advanced Settings – Sample Prep ................................................................................................................89

Connecting to the Myra ......................................................................................................................................90

Starting the Run ...................................................................................................................................................92

Creating Myra Templates ..................................................................................................................................93

Create a Template............................................................................................................................................93

Using a Template.............................................................................................................................................93

During a Run: Execution ....................................................................................................................................94

Pausing or Aborting a Run ........................................................................................................................94

Run Status.........................................................................................................................................................94

Messages ...........................................................................................................................................................96

Re-Run Option .................................................................................................................................................96

Reports ..................................................................................................................................................................97

Report Configuration ......................................................................................................................................97

Report Preview ................................................................................................................................................97

Run Properties .............................................................................................................................................98

Reactions .......................................................................................................................................................98

Assays ...........................................................................................................................................................98

Deck Layout .................................................................................................................................................98

Report Options ................................................................................................................................................99

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Laboratory Information Management System (LIMS) Settings .................................................................100

Acknowledgement of Registered Trademarks .............................................................................................102

References ...........................................................................................................................................................103

7
Disclaimer
All rights reserved. No parts of this work may be reproduced in any form or by any means – graphic,
electronic, or mechanical, including photocopying, recording, taping, or information storage and
retrieval systems – without the written permission of the publisher.

Products that are referred to in this document may be either trademarks and/or registered trademarks
of the respective owners. The publisher and the author make no claim to these trademarks.

While every precaution has been taken in the preparation of this document, the publisher and the
author assume no responsibility for errors or omissions, or for damages resulting from the use of
information contained in this document or from the use of programs and source code that may
accompany it. In no event, shall the publisher and the author be liable for any loss of profit or any
other commercial damage caused or alleged to have been caused directly or indirectly by this
document.

The Myra instrument has been designed and is intended for Research Use Only.

Copyright © 2019 Bio Molecular Systems. All Rights Reserved.

8
Technical Support
Bio Molecular Systems provides customer support for all technical and service issues related to the
Myra instrument. For technical support, please contact our support staff via:

Address: Suite 504, 24 – 30 Springfield Ave, Potts Point NSW 2011, AUSTRALIA

Phone: +61 (02) 9332 1694 (Hours of operation are 9:00 – 17:00 AEST)

Email: [email protected]

Web: www.biomolecularsystems.com

A support package should be provided with all questions related to software issues. See
NOTE Help Icon on how to generate a support package. Please avoid sending screen captures as they have
limited information about the issue.

9
Intended use of the Myra Instrument
The Myra instrument is intended to be used to setup reactions for molecular biology related
applications, in areas of research that include medical, agricultural, forensic science and basic life
science.

The Myra instrument is intended for use by laboratory technicians and physicians trained in
molecular biology.

Myra is intended for Research Use Only.

10
Safety Information
Before using the instrument, it is important to read this user manual in order to familiarise yourself
with the Myra instrument. Follow all instructions to ensure proper operation of the Myra instrument.
Do not use any accessories or external equipment other than that specified. Safety warnings must be
adhered to at all times to avoid risk in personal injury and/or damage to the instrument. If the
equipment is used in a manner not specified by the manufacturer, the protection provided by the
equipment may be impaired. The advice given in this manual is intended to supplement, not
supersede, the normal safety requirements established in the user’s country.

Warning Symbols
The following safety warnings appear throughout this manual.

WARNING
Electrical hazard.

WARNING
Follow the instructions to avoid risk in personal injury.

CAUTION
Follow the instructions to avoid damage to the instrument.

PINCH
POINT
Keeps fingers and hands clear of sliding parts to avoid personal injury.

BIOLOGICAL There is potential for exposure to infections agents when working with equipment used in molecular biology.
HAZARD To avoid exposure to such hazards, ensure that proper personal protective equipment is worn, and that
laboratory best practise is adhered to.

ATTENTION
Follow the instructions to ensure optimal instrument performance.

11
Proper Use Warnings

WARNING Malfunctioning Lid Open Sensor

Do not use the Myra instrument if the lid sensor is no functioning or if the lid lock is damaged. There is a
high risk of personal injury to the user through parts that are moving rapidly.

WARNING Lethal voltages inside the instrument.

When the instrument is connected to line power, terminals may be live. Opening covers or removing parts is
likely to expose live parts.

WARNING Power supply grounding.

Power supply must be connected to an outlet with appropriate grounding means.

WARNING Main supply cord.

Do not replace detachable main supply cord with an inadequately rated cord.

UV HAZARD
UV radiation hazard.
Use only with lid down. Protect eyes and skin from exposure to UV light. Do not use if lid windows are
damaged or lid safety switch is malfunctioning.

CAUTION
Positioning the Instrument.
Do not position the instrument so that it is difficult to operate the disconnecting device.

CAUTION
Do not obstruct the back vents.
Keep the back vents free from obstruction to prevent interference with the HEPA filter.

CAUTION
Do not move the Myra instrument during operation.
Movement may impair the proper function of the instrument resulting in poor performance.

CAUTION Remove travel locks before powering on the Myra.

Remove the travel locks before powering the instrument on. Failure to remove the travel locks may result in
damage to the unit if the axis drivers try to move.

CAUTION Authorised Service Only

There are no user serviceable parts inside the instrument. Service should only be performed by an
authorised party.

CAUTION
Transport Myra using travel locks and approved packaging.
Always transport the Myra with the travel locks applied and in the original shipping container. Failure to
apply travel locks and use the correct shipping container when moving the Myra will void your warranty.

12
Type Plate Symbols

Regulatory Compliance Mark

This device is compliant with applicable ACMA technical standards for EMC.

FCC Declaration of Conformity

This device complies with Part 15 of the FCC Rules. Operation is subject to the following two
conditions: (1) this device may not cause harmful interference, and (2) this device must accept any
interference received, including interference that may cause undesired operation.

UL Listing
UL has tested representative samples of the product and determined that it meets UL’s requirements
for Laboratory Equipment.

CE Marking
The device is in compliance with the essential requirements and other relevant previsions of Low
Voltage Directive 2006/95/EC.

WEEE
Waste Electrical and Electronic Equipment Directive 2012/19/EU. Do not dispose of the instrument with
general waste.

13
Biological Safety
Handle biological material with care and in accordance with the required safety regulations. Always
wear safety glasses, gloves, and a lab coat. The user must take the necessary precautions to ensure
that the surrounding workplace is safe and that the instrument operators are suitably trained and not
exposed to hazardous levels of infections agents1.

BIOLOGICAL Decontamination
HAZARD Cleaning and decontamination of the instrument is necessary as a safeguard when the instrument and any
accessories are to be transferred to the manufacturer or certified maintenance body for repair, service or
returns.

Decontamination of Instrument

Surfaces of the Myra instrument, including the deck and pipette head, can be decontaminated using a
solution of sodium hypochlorite (NaOCl). A solution containing 1 gL-1 available chlorine will be
suitable for sanitation in a general lab environment; stronger solutions (5 gL-1) are recommended
when dealing with high risk situations2. A UV light is also available for decontamination (see Using
the UV Light).

Disposal of Waste

The disposal of wastes must be in accordance with all national, state and local health and safety
regulations and laws.

Return Merchandise Authorisation

To ensure employee safety, Bio Molecular Systems requires that a Return Merchandise Authorisation
declaration be completed and shipped with all returned items. Failure to comply will result in
equipment being returned at the sender’s expense.

Contact BMS via the email address [email protected] to receive an RMA form.
Complete the RMA form and attach a signed copy to the outside of the shipping container before
shipping the instrument. Ship back to:

5-7 Tonka Street

Yatala, QLD 4207
AUSTRALIA

Please direct questions and enquiries regarding the RMA form to [email protected].

1 Biosafety in Microbiological and Biomedical Laboratories, HHS

(www.cdc.gov/od/ohs/biosfty/biosfty.htm).
2World Health Organization. Laboratory Biosafety Manual – 3rd ed. Geneva: World Health
Organization; 2004.

14
Introduction
Myra is a compact, lightweight, high precision and easy to use liquid handling system. Myra is the
first liquid handling system with an integrated camera and state of the art algorithms to enable Myra
to see what it needs to do. This allows Myra to automate and simplify calibration and look for errors
in deck layout such as missing plates or tubes (in development – expected in 2022).

Using our high-performance axis control combined with intelligent path planning, makes Myra one
of the fastest in class single channel pipetting systems on the market. Other notable features of the
Myra include:

• Best in class accuracy of less than 10% and precision of less than 5% CV for 1 L pipetting
volumes.

• High precision pipette tip positioning for small aperture tubes such as 384 well plates.

• Pressure based liquid level sensing that can monitor the aspirate and dispense process for
errors.

• An interchangeable pipette head gives you more flexibility with your workflow.

• Multi-dispense pipetting with greater accuracy to reduce time and save on pipette tips.

• An enclosed pipette tip waste container minimises the footprint area and ensures minimal
contamination of the laboratory environment.

• The software contains simplified solutions for standard laboratory processes including qPCR,
NGS library quantification, and more, available at the click of a button.

Myra and Mic Integration

A seamless workflow between the Myra liquid handling system and Mic cycler for qPCR makes for
an easy day in the lab. Run Myra and Mic instruments from the one user interface. No exporting or
importing of sample names required. Setup – run – analyse all in one location. Setup experiments for
multiple Mic cyclers using one Myra liquid handling system and analyse in one file using the Project
software feature.

15
Instrument
Specifications

Dimensions W: 360 mm, L: 460 mm, H: 310 mm (610 mm lid

open)
Physical
Weight 10 kg

AC Input 100-240 VAC, 50/60 Hz 4.0 A

Electrical

Position control Closed loop, 100 m resolution

Level detection type Pressure sensing

Technical Calibration High precision camera

Strategy Single or multi-dispense

Volume Range 1 – 50 L

Tips per rack 384

Precision3 1 L 5% CV
Pipette Head 2 L 2.5% CV
5 – 50 L 1% CV

Accuracy4 1 L 10%
2 L 5%
5 – 50 L 1%

Tip disposal Internal waste tub with capacity for up to 1000 tips
Contamination Control UV light High intensity 70 mW, 280 nm UV LED

HEPA 99.98% at 0.3 m

Temperature 18 – 30oC
Operating Environment
Relative Humidity 20 – 80%

3 𝜎
Measured as percentage coefficient of variation ( 𝑛−1 ) of ten consecutive dispensations of water.
𝑥̅
4
Measured as percentage variation of mean volume from expected volume of ten consecutive dispensations of water.

16
General Features

1 Lid Provides access to the deck and keeps contaminants out during a run.

Used to hold the axis drives in place during transport to prevent damage. Locks must be
2 Travel locks removed prior to turning on the system.

Minimises contamination from the external environment. Filter can easily be replaced by
3 HEPA filter the user when required.

4 Axis drivers Control the movement of the pipetting head in x, y and z direction.

Six SBS positions including waste tub. Contains Easy-Fit-SBS™ positioning clips that
5 Deck ensure optimum and sturdy positioning with minimal effort.

Captures used pipette tips that are discarded by the pipette head. Smart-Tip-Capture™
6 Waste tub ensures the tips are evenly distributed across the tub. A lid with small aperture holes is
designed to reduce the potential for contamination after the tips are discarded.

Stainless steel interchangeable pipetting head with on-board control unit. The head
contains all the calibration information making it easy to swap out. The standard head is
7 Pipette head compatible with our 50 µL robot tips in a 384 well format and can be used for volumes
as low as 1 µL.

LED light at 280 nm wavelength used to decontaminate the internal deck. The UV light
8 UV light is mounted onto the axis drivers so that it can move around the whole deck area to
maximise exposure to the UV.

Used by the robot to visualise the deck to simplify calibration and ensure proper deck
9 Camera layout.

When illuminated blue, indicates that the instrument is powered ‘On’; green, the
10 LED indicator instrument is ‘Running’; red, there is an issue; and amber, attention required.

11 USB cable inlet USB connection to a PC.

12 Power inlet Connects to the power adaptor.

13 Power switch Powers the instrument on/off.

14 Air vents Airflow for HEPA filter.

17
18
Accessories

External power supply for the instrument. Provided with

Power adaptor REF MYRA-PA instrument.

Myra loading block REF MYRA-LBMIC SBS dimension loading block for Mic tubes. Loads 2 x 48 well
for Mic racks Mic tube racks.

Designed to hold various generic tube formats. Includes up to

4 x 10 mL bottles or up to 4 x 5 mL tubes, up to 24 x 1.5/2.0
Myra multipurpose mL tubes (tapered or flat bottom) or up to 24 x 0.5/0.6 mL
loading block REF MYRA-LBMB tubes, and up to 12 x 0.2 mL tubes. This generic block should
be sufficient to hold enough tubes for most qPCR applications
including setting up a 384 well plate.

Myra 96 well loading

Designed to hold up to 96 x 0.2 mL tubes including 96 well un-
block REF MYRA-LB96 skirted, semi-skirted plates, or 12 x strip of eight tubes.

Designed to hold various generic tube formats in a 36 well

format. Includes 36 x 1.5/2.0 mL or 36 x 0.5/0.6 mL (inserts)
Myra 36 well loading
REF MYRA-LB36 tubes (tapered or flat bottom). The block comes with a tube
block ejection plate to assist in carefully removing tubes from the
block.

Myra 24 well loading

REF MYRA-LB24 Designed to hold up to 24 x 5 mL tubes.
block

Consumables

Myra 384 well tips REF MYRA-TIPS384-50

Sterile filtered tips are provided in 384 well format, pre-racked.
For volumes between 1 and 50 L.

Mic tubes and caps Strip of four reaction vessels with a volume range of 5 – 30
µL. Preloaded with silicone oil. Pre-packaged into a rack of 48
REF MIC-TUBES tubes, stacked together in a row of 5, and boxed as 4 x 5
stacks.

19
Installation
Unpacking the Myra Instrument
The following items are packaged within the Myra shipping container:

• Myra instrument
• Pipetting head
• Waste tub with lid
• Power adaptor
• Power cable
• 2 m USB cable
• Tips (1 rack of 384 tips)
• Myra loading block for Mic racks
• Myra multipurpose loading block
• USB flash dive containing copy of Myra software and manual
• Myra Quick Start Guide

Hardware Installation
Place the Myra instrument on a level surface.

Connect the instrument to a PC using the provided 2 m USB cable.

CAUTION
Instrument is not to be used with a USB cable greater than 3 m.

Plug the power cord into the adaptor and insert the adaptor into the back of the instrument.

Plug the power cord into a wall socket and switch the power on at the socket.

Power the instrument ‘On’ using the power switch at the back of the instrument.
An illuminated blue light at the front of the instrument will show the instrument is powered on.

20
Software Installation
Install the Myra Software, located on the provided USB Flash drive, onto a PC.
Ensure that the PC meets the following minimum requirements:

• Windows® 10, 64-bit (English version) Operating System

• .NET Framework 4.5 of higher
• Intel i5 processor, 2.4 GHz
• 8 GB of RAM
• 1 GB free hard drive capacity
• Pointer device
• USB Drive
• Adobe® Reader® must be installed to be able to view reports in PDF format.

In the USB Flash drive menu, double click Myra.msi software installer.

Follow the instructions that appear in the Setup Wizard.

If the computer is connected to a network, network policy settings may prevent you from completing
this procedure. For more information, contact your system administrator.

When the software has been successfully installed, the Myra software icon will appear on the PC
desktop.

Running Myra Software on Macintosh operating systems

The Myra software is currently not compatible with Macintosh systems. We recommend using a
virtual machine program, ideally Parallels , VMware Fusion or Oracle VM VirtualBox to run the
Myra Software applications on a Mac without rebooting. This method will allow you to run macOS
and Windows applications concurrently.

To dual-boot between macOS and windows, use Apple’s boot camp (https://support.apple.com/en-
au/HT201468). This method will only allow your computer to switch between booting up macOS or
Windows partitions.

21
Updating Software
Software and firmware updates are available for download at
www.biomolecularsystems.com/myra-downloads/.
Please check the website periodically to see if new software and firmware updates are available.
Registered users will be notified via email upon release of a new software version.

Browse to the Myra software heading of the Downloads page.

To enter the restricted site, you will need to enter your username and password, which will be
provided to you upon registering your instrument online. You can also find example run files to help
you understand the software better.

Download the software update setup file.

Release notes are also provided with each new build.

To initiate the installation, double-click on the setup file and follow the prompts.
The previous version will be uninstalled.

Upgrading Firmware
Some new releases of software will require a firmware update. The software will notify the user of the
requirement to upgrade firmware upon selection of an instrument following the software update.

Select the Upgrade Firmware option in the drop-down list after selecting the Instrument icon.
The instrument will begin to flash the front LED indicator to notify the user the firmware is being
updated.

22
Getting Started
Open the Myra software from the desk top icon.
The software will recognise the instrument via USB by displaying the Instrument icon in the tool bar
(top right).

Multiple instruments can be recognised by the software and will be displayed.

Myra connected to a
PC via USB.

Travel Locks
The travel locks prevent the axis drivers from moving during shipping. It is important to remove the
locks before proceeding further. The software will prompt you to follow the process of removing the
travel locks.

Remove the main driver arm travel locks.

Unscrew the two back locks holding the main driver arm. Screw them into the provided threads at
the back of the instrument.

23
Carefully unscrew the z-axis travel lock.
Store the z-axis travel lock in the provided area labelled on the deck to avoid losing it.

CAUTION
Remove the travel locks before starting a run. Failure to remove the travel locks may result in damage to the
unit if the axis drivers try to move.

Re-locking: Use the travel locks whenever moving the instrument over a distance greater than 5
meters to avoid damaging the axis drivers.

To place the axis drivers into place to allow the travel screws to be applied; select Properties from the
options in the Instrument icon then select Lock Myra for Transport. Follow the on-screen instructions to
lock the arms into place.

CAUTION
Always transport the Myra with the travel locks applied and in the original shipping container. Failure to
apply travel locks and use the correct shipping container when moving the Myra will void your warranty.

Connecting the Head

Connect the pipetting head to the z-axis driver.
1. Align the pipette head with the z-axis connector platform pins.
2. Once flush, pull the handle up to lock the head into place.
3. Head is now inserted and ready for use.

24
All connected instruments are now ready to be used.
On the first use you will need to calibrate consumables and blocks required for the first run (see
Calibrating Blocks, Plates and Tubes).

Loading the Deck

The deck is divided into five SBS positions labelled A through to E. The sixth position is used for the
Waste Tub.

Use the Easy-Fit-SBS™ loading clips to orient and insert tip racks and SBS loading blocks or plates
onto the deck.

Place the tip rack or SBS loading block/plate up against the back strip of the SBS position. Then
simply slide it down into the slot. The Easy-Fit-SBS clips will help you orient the plate into position
while ensuring the plate/block is held firmly into place to improve positional accuracy for the
pipetting head. To remove the plate/block, simply grab the front of the plate/block and pull it up and
out of the deck position.

Insert the Waste Tub.

Simply insert the tub into the empty socket position of the deck and place the lid on top. Tips will be
discarded evenly across the small holes in the lid of the waste tub using our Smart-Capture-Tip™
program. The lid is designed to reduce the potential for contamination after the tips are discarded.
Always empty the waste tub at the end of a run.

CAUTION
Do not allow the waste tub to fill up to more than 75% of the tub volume. Over filling the waste tub will
prevent the tips from being discarded and can cause damage to the head.

The waste tub can be decontaminated with a solution containing 1 gL-1 available chlorine.

BIOLOGICAL
HAZARD
Handle biological material with care and in accordance with the required safety regulations.

25
Using the HEPA Filter
The HEPA filter is used to ensure the air inside the robot is free from most contaminants that could
affect a reaction. It’s rated to keep out 99.98% of all particulates greater than 0.3 m in size. The HEPA
filter will turn on automatically at the start of each run.

CAUTION Avoid blocking the air vents to the HEPA filter

Do not obstruct the air vents at the back of the instrument. This will prevent airflow required for the HEPA
filter resulting in poor contaminant control.

Replace the HEPA filter when required.

Simply unscrew and place aside the panel screws, pull the panel out and up, turn over and remove
the old filter and replace it with a new one. Then reconnect the panel and screw back in place.

26
Using the UV Light
The UV light is a high-powered LED (70 mW) with a peak wavelength of 280 nm. It is used to
decontaminate the internal surfaces of the Myra deck by inducing covalent linkages between the
carbon double bonds of adjacent thymidylate residues, producing thymine dimers that can kill or
disable microorganisms and render DNA un-amplifiable by inhibiting the polymerase during
extension. During UV treatment the main axis arm will move around the deck to ensure all surfaces
within the deck are exposed.

For your safety, the Myra has been built with a clear polycarbonate lid to prevent UV exposure.
Ensure that the lid is closed prior to starting the UV decontamination and do not open it during the
UV procedure.

UV HAZARD
UV radiation hazard
Use only with lid closed. Do not use if lid safety switch has malfunctioned. Protect eyes and skin from
exposure to UV light. Do not use if lid windows are damaged.

To apply UV light decontamination, select the Myra Instrument icon and then UV treatment.
Enter the desired time to apply the UV light (default is 10 min).

The software will ask you to open the lid to test the lid sensor is working to ensure safety during use.

After closing the lid, you will be able to start the UV decontamination procedure. The head will move
across the deck in segments for the nominated time period.

The UV light will turn off at any point the lid is opened during this period.

27
Calibrating Blocks, Plates and Tubes
When using a block, plate or tube for the first time you will need to calibrate the position and/or
height. This is achieved prior to the start of a run. A notification is displayed on the run summary
banner. The run cannot begin until calibration is completed.

Click on Calibrate now… to begin the calibration.

A warning indicting that the lid safety interlock is disabled will appear. Although the speed of the
axis drivers is reduced significantly for safety, you must still exercise caution while calibrating with
the lid open.

WARNING
Lid safety interlock disabled during calibration.
Please exercise caution while calibrating. The robot may move unexpectedly and without warning.

The Myra will initiate calibration by preparing the pipetting head, turning on a white light and
moving to the first position (default will be the tip rack in position A).

You can enter calibration any time using the cog icon on top of each plate in the deck layout.

28
Block or Plate Position
The software will display an image of the block or plate that requires calibration. Typically, this will
be the first well of the block/plate or the first tube type being used. It will also highlight the well
position required in the deck layout display.

Position the centre of the white cross hairs to the centre of the well that is being calibrated.
You have the option to zoom in on the position to help orient the cross hairs to the centre.
Once you click on the targeted position the red cross hairs will move to the set position indicating the
new calibration point.

When calibrating Myra 384 Well Tips, it is important to remove the first tip in the rack to the find the centre
NOTE of the empty hole. This will ensure uniformity across all tip racks and avoid the need to calibrate each new
rack.

Click the green tick to accept the new position.

You can select the red cross to revert to the previous co-ordinates.

29
Height Calibration

You will need to height calibrate all of the different plate types used in the run. The software will
determine which wells need calibrating and will display their positions on the deck layout.

Place the plate into the indicated position.

Its preferable to use empty wells, however, full wells can be used but expect some loss of liquid due
to tip retention. Ensure that you do not use wells that are at maximum capacity to avoid overflowing
the contents as the tip enters the consumable (most common reagents will not be).

Click on Calibrate Selected to begin height calibration of all the required wells of a plate or Mic
tubes.
The head will pick up a tip and probe the depth for each well or Mic tube. A new tip will be used for
each required well.

30
For the Mic tubes the pipette head will use level detection to locate the oil level rather than the base of
the tube. This is to ensure the pipette never enters the oil during pipetting.

At completion, the instrument will display the height calibrated values and will ask you to confirm
those numbers.

Tips and individual tubes do not require height calibration. The system will detect the heights of
individual tubes during the run.

Select Next Plate to move through the calibration process.

Alternatively select a plate in the deck layout.

Select the Finish button, when done or to abort calibration.

You will not be able to start a run until calibration is completed successfully.

LED Indicator Colours

The LED indictor will change colour and flash during particular instrument operations.

Blue constant: The instrument is switched on and Idle.

Blue flashing: The instrument has been selected to Start a run. This instrument can no longer be
selected by another user until the designated run has completed.

Green: The instrument is Running.

Green flashing: The instrument has completed the run successfully.

Red flashing: The run has been Aborted or the instrument has had an issue during the run.

Yellow flashing: Attention required (e.g. ran out of tips or liquid during the run).

The next section will describe in more detail how to use the Myra software.

31
Software Overview
The software is divided into a number of sections:

1. New document
2. Tool bar
3. File tabs
4. Navigator bar
5. File active windows

New Document
The New Document page is where you begin and contains a menu of items for creating an Assay or
Run. These are divided into various application types. They include:

qPCR: allows you to setup real-time PCR assays

Simple Transfer: allows you to setup simple transfers of liquid from one source to another,
normalisation of samples to a set concentration, or pooling samples into a single destination

Sample Preparation and Setup: allows you to setup sample preparation protocols and real-time PCR
reactions simultaneously.

There are three other short cut options on the Start Page:

Recent: access to recently saved assays or runs.

Templates: access to templates when running the same setup frequently (see Creating Myra
Templates).

Quick Links: access to helpful information regarding the use of the instrument and software
including tutorials, guides and example runs.

32
Tool Bar
The top section of the user interface is referred to as the Tool bar and consists of the following:

New: opens up the Start page where you can select from the various menu options.

Open: open a saved Assay or Run from a file directory.

Save: save an open Assay or Run.

Save As: save an open Assay or Run under another file name or as a Template.

Help: access to Myra Manual, Create Support Package and About Myra PC.

Instrument: Myra instruments in communication with the PC are displayed in the tool bar.

Instrument Communication: detect available instruments connected to the PC.

Open Assay or Myra Run Files

There are three file types:

Assay File: contains all the information regarding a set of targets for a run including the assay
components such as chemistry type, primer sequences, reagents, and required volumes; run profile
for Mic; and Analysis options for Mic (orange beaker).

33
Run File: contains the assays used, sample annotation, deck layout, run execution information, and
reports for a Myra run (Myra icon with green running man).

Run Template: contains a complete pre-run including sample annotation. A template can be used for
repetitive runs using the same layout each time. (Myra icon with blue rubber stamp). The amount of
detail saved can be as simple as plate positions to as complex as sample and reagent positions along
with any dilutions and intermediate master mixes.

Help Icon

The Help icon is used to access the following options:

Myra Manual: an electronic version of the user manual is stored within the software.

Create Support Package: create a support package after experiencing any fault with the software or
hardware. The support package contains a compressed log file of the run. Select a folder to save the
support package to. Email the zipped support package file to [email protected].

About Myra PC: information about the version of Myra PC software.

Instrument Icon

Instruments in communication with the PC will be displayed in the tool bar as an Instrument icon.
The serial number or name of the instrument is displayed next to the communication symbol.
The status of the instrument is also displayed beneath the name:

Idle: instrument can be used to start a run.

Setup: the run is being configured but has not yet started.

Running: instrument is running and cannot be used until the run is completed.

Lid Open: the lid has been opened during a run and the instrument has paused to avoid injury.

Click on the instrument icon to display the following options:

Connect: allows you to select the instrument to start your run. This will bring up the tip and Mic tube
availability and the Start Run option.

34
Hide Instruments: select Hide Instrument if you do not wish to display a particular instrument in the
software. Use this option if you want to avoid cluttering your PC with other instruments you are not
using but are in communication with.

Unhide: to unhide an instrument, select the down triangle to display a list of hidden
instruments; then select the instrument you wish to unhide.

Properties change the name of the instrument; and there is also information regarding the serial
number, firmware version, head type, head serial number and head firmware version.

Lock Myra for Transport: use this function to move the travel axis arms into position to allow
you to apply the travel locks required to move the instrument over distances greater than 5 m
(see Travel Locks).

UV Decontamination: used to decontaminate surfaces of the Myra deck (see Using the UV Light ).

Instrument Communication Icon

The instrument communication icon is used to search for instruments.

On software start up the icon will flash automatically indicating the software is searching for
instruments.

35
File Tabs

Every open file will be displayed with its name on a tab. Multiple files can be open at the one time.
The file being displayed in the main window will be highlighted in blue. Files that need to be saved
will have an asterisk just before the file name. If a file is linked to a run in-progress, selecting the
instrument running it will open the associated tab.

Use the down arrow to view files that might be out of view if multiple tabs are open at the one time.

Navigator Bar
To the left-hand side of the main user interface is the Navigator bar. The
Navigator bar allows you to view the different sections for an Assay or Run
Setup.

Some sections contain subsections that can be viewed by expanding the

navigator tree.

Sections that are open in the main window will be highlighted in blue.
Important sections specific to the file are emphasized in bold.
Remove user created sections by using the delete icon.

36
File Active Windows
In the central area of the user interface are segmented windows that are active for a specific section of
the navigator bar.

37
Creating a New Assay
The Assay contains information regarding the target amplicons and reagent composition with
volumes required. For the Mic there are additional items including the qPCR conditions and the
analysis type required for the assay (e.g. Relative Quantification) along with various analysis
parameters. Once an assay is setup it is stored in a library from where it can be located and added to
any future run. A new run can begin by simply selecting the assay(s) required, which contains all the
necessary information to achieve a Myra and additional Mic run and any associated analysis (Mic
only).

Select Create a new file from the tool bar menu.

Select Assay from the qPCR category in the New Document page.

Assay Setup
If you are not going to use a Mic, we would recommend that you untick the Show Mic compatibility
box to remove any automated error checks that are required for a Mic run.

Information

Select the Chemistry Type.

Choices include Intercalating dye, Hydrolysis Probes, Dual hybridisation Probes, Molecular Beacon probes,
and LUX® Primers.

The type of chemistry selected will also set the default Assay Profile (Mic only).

38
Enter a Target name in the table provided and select the reporter dye.

If using multiple targets for the one assay (multiplexing), enter the new target name in the row below.
If the Show Mic compatibility box is un-ticked, then you may select as many targets as you wish. If your
particular dye is not present, simply select the Other option.

Multiple targets for the one assay are not permissible when using intercalating dyes. However, you
can setup multiple singleplex intercalating dye assays by using the Save As feature. Simply change the
small number of values for the individual assay and keep the rest of the fields the same. Then use the
Save As and give the assay its own name.

When setting up for Mic runs, if your dye is not shown in the drop-down menu simply select the dye
closest to yours (see Mic User Manual for more information about dyes). You cannot use the same
channel dye for two different targets in the same assay for any Mic run.

Enter the Name and Sequence information for each of the oligonucleotide primers (optional).
By default the Name entered as the Target will be displayed as the name of each primer or probe
followed by the oligonucleotide type (e.g. forward primer). You can overwrite the default name by
entering a new name in the cell for oligonucleotide name.

The name entered here will also automatically appear in the reagent component list for each
oligonucleotide.

You have the option to enter the sequences in a 5-prime to 3-prime direction along with any 5’ or 3’
labels in addition to the reporter dye (e.g. quencher molecules).

Untick the oligonucleotide if you do not wish to use it in the reagent component list.
This might be the case if you have combined the oligonucleotides into one tube or you are using
lyophilised material or a pre-made master mix (e.g. kit).

39
Add multiple probes for the same target if required for Allelic Discrimination, by ticking the
Contains Alleles check box.
More than one probe will be available to use per target. A total of four probes can be used for the Mic.

Enter the Target Details (optional).

Provide as much detail as required to describe the target.

Enter the length of the amplicon (optional).

Both items will be captured in the reports.

40
Specific details for each chemistry type and Mic compatibility are found in the table below.

Chemistry Type Detail Notes

This will set the channel required for

Intercalating Dye Select the reporter dye used
acquisition on Mic.

You need to ensure that each probe is

labelled with a different channel dye. A
warning will be displayed if two targets
Enter the name and sequence contain the same channel dye.
information for each probe. Optionally you can provide information
regarding the quencher dyes used, but
the information is not required by the
Hydrolysis Probes or software to execute the run successfully.
Molecular Beacons

A maximum of four probes can be

Add multiple probes for the
selected.
same target if required for
Select the reporter dyes and quenchers
Allelic Discrimination, by
used. This will set the channels required
ticking the Contains Alleles
for acquisition. Probes with the same
check box.
acquisition channel will not be allowed.

Select the reporter/donor dye for the 3’

position in the first probe, which will set
the channel required for acquisition,
Dual Hybridisation Enter the name and sequence and the 5’ quencher/acceptor in the
Probes information for each probe. second probe. The second probe will
also be labelled with a phosphate group
at the 3’ end, which prevents the probe
from initiating polymerase extension.

Select the reporter dye used in

This will set the channel required for
LUX Primers either the forward or reverse
acquisition.
primer sequence.

41
Reaction Setup
Complete the Reaction Setup table.

Enter the name of any component required for the reaction.

Ensure you enter the required volume for each component. A warning will be displayed if the total
volume of the components exceeds the total reaction volume.

Oligonucleotides are automatically populated into the table unless unticked in the oligonucleotide
table. A default name using the Target name will be displayed. Any edited name change will be
recreated in the table.

Tick if the solution is Viscous.

Myra will slow the pipetting speed down when handling viscous reagents to improve pipetting
accuracy. Use this option for reagents such as enzyme mixes that contain a high amount of glycerol.

Tick if the solution is Bubbly.

Myra will reduce the frequency of level sensing to reduce the number of bubbles created and push the
tip a little deeper into the liquid to avoid bubbles that have formed on the surface. Use this option for
reagents that contain high concentrations of surfactants such as lysis buffers.

Tick if you require Myra to mix the solution prior to taking and aliquot.
Use this option to ensure the reagent is mixed to ensure a homogeneous solution prior to taking an
aliquot. This will avoid potential concentration gradients forming and effecting final concentrations in
the reaction mix.

Select the type of tube used to store the component (e.g. 2.0 mL self-standing screw cap tube).
This will assist the software during component allocation on the deck layout (see Deck Layout). The
profile for each tube is also used during a run to ensure pipetting accuracy.

We have included most of the generic tube formats used. Please contact BMS if your tube type is
missing.

42
Enter the volume required for each component.
The default template volume is 1 µL. If you wish to add the template to the master mix, then make
the Source Template value equal to zero and add your template to the components list. A warning will
be displayed telling you that no template will be included in the reaction.

The default total volume is 25 µL. Please change to the volume required. For Mic runs, this volume
will be populated in the Profile Editor. Make sure you untick the Show Mic compatibility warnings if
you wish to use reaction volumes greater than 30 µL.

If using a premade master mix (e.g. kit) then ensure that the volume used is such that the water
volume is zero. The Myra will aliquot the pre-made master mix directly into the reaction tubes
without the need to create an intermediate mix.

Diluent Reagent

You have the option to select another reagent to act as a diluent other than the water. This reagent
will be used for constructing the standard curves (see Dilution Series).

43
Controls

Complete the Controls table.

Enter the name for each control required for the run.

Select what type of controls they are.

The controls listed in this table will always be incorporated into each run setup as the first reactions
for quality control purposes and ensure run integrity. Choices include Positive Control, Negative
Control, NTC, Extraction Control or NRT.

Tick Viscous or Mix Before Use if required.

Same as above, where ticking Viscous will slow down the pipetting or ticking Mix Before Use will mix
the reagent prior to taking an aliquot.

Select the type of tube used to store the component.

This will assist the software during component allocation on the deck layout. The profile for each tube
is also used during a run to ensure pipetting accuracy.

Assay Profile – Mic Only

A generic assay Profile is provided at the beginning. Modify the profile to suite the assay.
The generic assay profile displayed will depend on the type of chemistry and reporter dye selected in
the Information section.

Refer to the Mic User Manual for more information on how to set the assay profile.

44
Assay Analysis – Mic Only
This feature enables you to store all analysis parameters within the assay, thereby avoiding
continually having to edit parameters for each new analysis.

Select the Analysis required for the assay by using the Add button (Optional).
The choices of analysis are: Cycling Analysis, Melt Analysis, Relative Quantification, and HRM. There are
no parameter settings available for Absolute Quantification or Standard Curve in the Assay Setup.

See the Mic User Manual for more details on each analysis type.

Saving a New Assay

Once all the parameters have been entered for the assay, the assay should be saved.
Assays can be saved into the following directory of your PC: Libraries/Documents/Bio Molecular
Systems/micPCR/Assays.

You can create and store assays in subfolders of the main assay library.

Alternatively, you can save the assays into another personal or shared directory including network
drives or external storage drives such as a USB Flash drive.

It is important to have all the assays stored together so that finding them and linking them to a
sample in a run will be easy.

45
Creating a New Run - qPCR
Use this setup application for all PCR and qPCR run setups.

Select Create a new file icon in the tool bar.

Select the option PCR Run: Myra Setup from the New Document page.

Adding Assays
Select the Assays required for the run by selecting
the Add button.
You can select from any library of assays displayed
next to the navigator bar.

By default, the micPCR Library will be displayed.

Select an assay from any directory using the Browse

icon.

Use the file explorer to locate the assay you require from any location including network drives or
external hard drives such as a USB Flash drive.

46
You can create a new assay library Shortcut.
Select the + button next to Personal Shortcuts then browse and select the location of the new directory
you wish to use as a personal assay library.

You can Edit or Delete assay libraries from the list.

Alternatively, you can create a new assay from the run file.
Enter the assay details as described in section Creating a New Assay PCR, and then save the new
assay file by entering a name in the field provided in the Navigator bar and selecting the save icon.

The Information, Profile and Analysis Settings can be viewed and edited once the assay is selected.
Remove assays by using the delete button next to the assay name.

The Run Profile is based on the first assay that is selected. Any following assay selected, which fails to
meet the Run Profile temperatures and hold times, temperature control, or reaction volume will be
determined to be non-compatible for the Mic run (see Mic User Manual for more details).

Updating Changes to an Assay

Further changes can be made to the assay including the Information fields and Analysis Settings.

These changes can be saved to a new or existing Assay file, by clicking on the Save icon located next to
the name of the assay.

47
Run Setup
Samples Editor

The Samples editor is displayed in a table format and allows you to annotate your samples. Failure to
properly annotate samples can affect the run setup and Mic analysis.

Choosing qPCR Reaction Plates

The reaction destination plate must be selected in the Sample Editor. There are a number of options to
choose from.

Select the qPCR Cycler you are going to use.

We have provided a list of the most common cyclers in the market. Chose the Other option if your
cycler is not listed.

48
Now select the reaction plate.
Displayed reaction plates will be based on the options available for the chosen qPCR cycler. We have
selected a number of recommended plates for each of the platforms available. If your plate is not
within the list, simply select the Other option for the cycler and then chose one of the generic options
that best matches your plate type.

The Mic option will allow you to select multiple tube racks for multi-runs.

For non-Mic plates you can select the fill order.

The fill order can be achieved either vertically or horizontally, with every second row or column, and
in checkerboard pattern.

49
Filling Cells

Cells can be filled individually or in groups.

Using the Enter key on your keyboard will move to the next cell down.

Using the Tab key will move to the next column.

Use the delete key to clear a cell.

Copy and then paste columns and rows within the software or other software programs (e.g.
Microsoft® Excel®).

Well Filter

When using any destination plate other than the Mic tubes, a Well Filter display is provided. This
feature enhances the editing process by allowing you to select specific parts of the plate to edit. For
example, you could choose to only edit wells within the centre of a 96 well plate to avoid edge effects
on your block-based cycler. By highlighting the centre wells in the Well Filter, only these wells will be
displayed in the sample editor table. You can choose individual wells, use the Ctrl+ click for a group
of randomly selected wells, or use the row or column feature to quickly select each row or column.

Select the Clear current selection button, top right, to revert to displaying all the wells in the sample
editor table.

Once the wells are edited, they will be coloured in the Well Filter. Using the Display Mode tool, you
have the option to display different categories from Sample, Assay or Group. The colour edited for each
will be displayed in the Well Filter. These colours can also be displayed in the Deck Layout.

50
Colours

Select the Colour you want for each sample (Optional).

Chose any colour from the colour pallet or generate your own colours using the colour chart.

To create a gradient, select the first colour and highlight all the way down to the last colour required,
and then click the Auto fill icon.

Name

Enter the Name of each sample.

Each sample Name will be used as a template by the Myra. Samples with the same characters and
assay will be treated as replicates and will be reported in the Mic software with a mean (𝑥̅ ) and
standard deviation (𝑥𝜎n−1 ) for most analyses.

You can highlight multiple cells within a column and enter the same characters to annotate replicates.
Alternatively, enter the name in one cell, highlight that cell and other cells that will be part of the
replicates (use Ctrl + Click to highlight non-adjacent cells), and then select the Fill down icon to give all
the selected cells the same name.

Use the Auto fill icon to annotate sequential characters (e.g. sample 1, sample 2, sample 3…). To allow
for replicates follow the following process:

51
Enter the first set of characters for the
first name (e.g. Sample 1).

Leave the same number of rows blank

as the number of replicates required
below the first name. Enter the second
name of the sequence (e.g. Sample 2).

Now highlight all the cells required to

complete the filling of the names and
replicates.

Click on the Auto fill icon.

The names will be sequential based on

the first two inputs and the replicates
for each will be automatically filled in
too.

52
To delete a selected list of entered replicates you will need to inactivate the editor by selecting the
escape key. Once inactive you can delete the cells.

Barcode Reader

A barcode reader/scanner can be used to simplify the sample editing process. Any reader that can be
connected to the computer running the Myra software can be used for this.

To use the barcode reader, have the cell of the Samples table that you would like to import the data for
active and then simply scan away. The active cell will automatically move down the table as you scan.

Some barcode readers may need the reader output re-configured for it to move automatically to the
next cell. You may have to scan a barcode in the barcode reader’s manual to change the output
function, where the option may be called carriage return (see your barcode readers manual for more
information).

Water Load Samples

To ensure temperature uniformity all tubes within the rotor should contain the same amount of
liquid. We recommend using water load tubes to meet this criterion. To ensure all strip of four tubes
contain liquid we automatically fill any empty tubes within the strip with water. There is also an
option to fill all unused wells with water. Here the Myra will pipette the reaction volume of water
into all empty tubes of a 48 Mic tube rack.

Type

Select the sample Type.

There are eight options to choose from. The type chosen will determine the way in which the sample
is utilised during analysis.
To change multiple cells at once, highlight the cells, use the F2 key on your keyboard, and then select
from the following options:

Unknown: Any sample that is under investigation. This sample is used as a basic template.

53
Standard: A sample of known quantity, used to generate a standard curve from which an unknown
sample quantity can be calculated, or used to determine amplification efficiency. The standard can be
defined as a template or part of a dilution series (see Dilution Series ).

NTC: A sample that contains no template. NTC’s are used to monitor for amplicon contamination in
the reaction and for the amplification of non-specific amplicons (primer dimers) when using
intercalating dye chemistries. If no sample name is entered the Myra will automatically name it water
and use the water reagent as the template.

Positive: The sample is known to contain the target of interest. A positive control is used to confirm
that the assay is working and helps prevent false negatives.

Negative: The sample is known not to contain the target of interest. A negative control is used to
monitor for contamination of the assay and is helpful in preventing false positives. Unlike the NTC,
the negative control can contain an internal amplification control template to ensure the PCR is
working.

NRT: The sample has not undergone reverse transcription. The NRT control is used to monitor for
genomic DNA amplification during RT-qPCR. Only cDNA, derived from mRNA, should be
amplified during RT-qPCR when used to determine gene expression values. If an assay is positive for
genomic DNA, consider changing the primer design to target intron exon boundaries. If none exist
then improve the extraction of RNA and the removal of genomic DNA from the sample, such as using
a DNase.

54
Dilution Series
Sample concentrations will be used to determine the dilution series for the standard curve. The Myra
will create a dilution series if you enter the same sample Name with different Sample Concentrations.
The first standard will be considered the Template sample with the subsequent standards being
prepared using an intermediate mix dilution series. However, if you wish to use pre-diluted
standards then enter a different Name for each dilution along with the sample concentration. Myra
will treat all these samples as Templates and will not pipette out a dilution series.

Figure: Samples in
the blue border with
the same Name but
different Standard
Concentrations will
be created using the
Myra. The first
standard will be used
as the sample
Template and will be
serially diluted to
create the
subsequent
standards.

Samples in the red

border with different
Names and Standard
Concentrations will
be considered as
pre-diluted sample
Templates.

To ensure the Mic software recognises the different concentrations for analysis for a serially diluted
curve, each Name will be populated with its concentration next to it (e.g. Standard 1000).

Select the units to report.

There is a list of units to choose from. Alternatively, enter your own units, in the provided text box.

Enter a Concentration for each standard.

When using standards, it is a requirement to provide a value for each one. The value can be a
quantifiable absolute or an arbitrary number. Numbers can also be entered in scientific notation (1E03
= 1 x 103 = 1000)

Enter the values one at a time or use the Auto fill option to quickly add a serial dilution and replicates
by doing the following:

55
Enter the first concentration value
(20,000).

Leave the same number of rows blank

as the number of replicates required,
below the first concentration. Enter
the second concentration in the
dilution series (10,000).

Now highlight all the cells required to

complete the dilution series and
replicates.

Click on the Auto fill icon.

The concentrations will be filled based

on the first two inputs and the
replicates for each will be
automatically filled in too.

56
Dilution Reagent

If another reagent has been selected to dilute the samples, it will be displayed in the Deck Layout
under the Mixes table for the dilutions (see Deck Layout – qPCR). The Dilution Reagent is edited in
the Assay setup.

Creating and Allocating Groups

Use sample groups to allow you to calculate statistics for a collection of samples that are not replicates
(e.g. Treatment or Control). You will be required to create and allocate groups when using Relative
Quantification analysis.

Type the group name in the Groups table.

Remove groups by using the Delete button on your keyboard ensuring that you select the first column
in the group row.

The colour for each group can be edited and used to display on both the deck layout and well filter
using the Display Mode feature.

Allocate one or more groups to a sample.

Select the required samples by highlighting the cells in the Groups or Name column. Use Ctrl + Click to
highlight non-adjacent samples. Select the plus button next to the group name to allocate the group.
Or click on the selected cells in the Groups column and use the drop-down list to select the required
group(s) by ticking the box next to the group name, or Select All, and then click the OK button.

Alternatively type the name of the group in the Groups column. If the group exists, a list of options
beginning with the first set of characters will appear. If the group does not exist, it will be captured in
the group list after you have completed entering the name.

To remove a group, form the Groups column, use the delete key of your keyboard, the minus button
next to the group name, or click on the cell to bring up the drop-down list. Then simply un-check the
group from the list provided to remove it or Select All to remove every group.

57
Linking an Assay to a Sample

An assay must be linked to a sample to allow the software to recognise and properly setup the sample
on Myra. Created assay intermediate master mix will be added to the linked sample template. When
using the micPCR software, failure to allocate an assay to a sample will result in the sample not being
analysed.

Link an Assay to a sample.

Select the required samples by highlighting the cells in the Assays column. Use Ctrl + Click to
highlight non-adjacent samples. If using only one assay in the run, the software will automatically
add the assay to any well that has a name entered or is selected as an NTC.

Select the required assay from the Available Assays window then drag and drop the assay into the
highlighted cells. Alternatively, click on the selected cells in the Assays column and use the drop-
down list to select the required assays(s) by ticking the box next to the assay name, or Select All, and
then click the OK button.

To remove an assay, form the Assays column, use the delete key of your keyboard or click on the cell
to bring up the drop-down list. Then simply un-check the assay from the list provided to remove it or
Select All to remove every assay.

The colour of the assay can be edited as well and used with the Display Mode option to highlight the
category type on the deck layout of the sample editor and well filter.

Optional Columns

Additional columns can be added to the Samples editor using the Select visible sample data columns icon.
The following columns can be added or removed from the table:

Input DNA concentration: note the starting amount of DNA per reaction.

Input RNA concentration: note the starting amount of RNA per reaction (RT-qPCR)

RIN: provide an RNA integrity number for each input RNA.

58
Import Samples

Import sample information from a number of file types to simplify sample annotation.

Select the Import Samples icon to import sample information from another source.
You can import from any comma delimitated, tab delimited or space delimited files.
Browse and select the file to import.

Select the fields to import and into which column of the Sample Editor.
Once the run file is selected a table will display all the fields in the file. You have the option to select
the type of delimitation (e.g. comma) and how many rows should be ignored before capturing the
data.
Next, chose the fields to import by linking the column from the files to one of the columns in the
Samples editor using the drop-down menu.

59
You have the option to save the import style as a template.
This will allow you to complete the import faster without having to re-do the matching when
conducting repetitive runs.

CSV Export or Copy to Clip Board

The Samples editor will have two options for copying the data for easy export to third party software:

CSV: save as a CSV file.

Copy to Clip board: copy the data to the clipboard, then paste into another third-party software such
as Microsoft® Word®.

Sample Editor Warnings

Various warnings will be displayed if annotations have not been completed correctly. Some examples
include:

• No reactions have been configured.

• If standards have been selected as Type but no values have been entered into the Standards
Concentration field.
• Assays have not been linked to an edited Sample row.

60
Deck Layout – qPCR
The next stage requires you to layout the deck with the various components required for the run.
These include any plates, consumables, reagents, intermediate mixes and templates. For Mic run
setup the reactions are auto populated onto the loading block for Mic rack. In the deck layout you will
need to Configure the deck with the required plates/blocks and tubes and allocate Components
(reagents and intermediate mixes) and Templates. Each section is represented by tab with an
exclamation icon to indicate that there are items still to be completed.

Configuration

Setup the layout of the block/plates required to achieve the run.

A default deck will be provided on the first run following installation.

Delete a block/plate using the option in the hamburger icon menu for the individual plate. Reaction
plates can’t be deleted.

You can move existing blocks/plates from one position to another by simply dragging them across.

Use the Plate Library to add a different type of plate or block. To change a reaction plate please go
back to the Samples Editor.

You can Zoom in on each block/plate on the deck to display more information such as component
present or tube type.

61
The deck layout will also show the time to complete a run as well as a legend describing the colour of
each component type; which are:

• Water
• Source template
• Standard dilution
• Reagent
• Intermediate mix
• Reaction

A warning is provided for any misconfigurations.

Store a new deck layout as a default or restore one using the options at the top of the Plate Library.

Information about the number of available tips and Mic tubes cannot be accessed until the run is
connected to the Myra (see Create Sample Prep & Setup – General

Use this setup application for preparing samples using crude extraction methodologies followed by
PCR/qPCR run setup. Commercially available kits such as Qiagen QIAprep&amp UM Viral RNA kit
will be available for automation on Myra.

Select Create a new file icon in the tool bar.

62
Select Sample Prep & Setup icon from the Sample Prep section on the New Document page.

Sample Prep
Select the Sample Prep method of choice using ‘+’.

Choices currently available are QIAprep&amp (VTM).

The current software is locked down with the QIAprep&amp (VTM) method available only. It does
not currently allow for user re-configuration.

Assays – Sample Prep

Using ‘+’ select the Assays for the qPCR run or create a new one using ‘+ New Assay’ from the
dropdown menu.

63
See Creating a New Assay for more information on how to setup an Assay.

Run Setup – Sample Prep

Samples Editor

64
The Samples editor for Sample Prep & Setup differs from the PCR Run setup in that the information
input is for the sample source and not for the output reactions. Any controls specified in the assay
setup will be placed into the first wells/tubes of the output reactions source followed by the samples.
The order the samples in the source layout will be reproduced in the output reactions layout.

Choose the source type as either Plate or Tube using the toggle button.

Plate: Choose the Sample Plate Type from the list. Create a new plate if required (see Plate Editor).

Tube: Choose a Sample Tube Type from the list.

When your samples are located in a tube, the tube type selected will be automatically assigned to the
block that is required to hold them (e.g. 36 well loading Block is required for 2 mL screw cap tubes).
The block will be automatically allocated to the deck layout.

Select the output Reaction Plate.

Displayed reaction plates will be based on the options available for the chosen qPCR cycler. If your
plate is not within the list, simply select the Other option for the cycler and then chose one of the
generic options that best matches your plate type.

The fill order can be selected for non-Mic plates. Choices available are vertically or horizontally, with
every second row or column, and in checkerboard pattern.

For Mic runs, there is an option to Fill all unused wells with water to ensure temperature uniformity
(See Water Load Samples for more information).

The source plate along with the reaction plate determines how many reactions are available. The
sample editor will change accordingly.

Determine whether your samples have a Fixed sample volume or needs to Sense sample volume.

65
When Fixed sample volume is selected, a box will appear to enter the volume in µL. The volume
entered will allow Myra to estimate the height of the liquid using the tube/plate profile.

If Sense sample volume is selected, Myra will perform a level sense on the samples to determine the
volume of liquid present in the tube/well. An extra tip and time is required for this level sense.

Select the type of swab that can be found in the sample source, if present.

The choices available are None, Standard and Rhinoswab.

When None or Rhinoswab is selected, Myra will take the aliquot from the centre of the tube to avoid a
collision as Rhinoswab’s tend to sit low and out to the side of the tube.

When Standard is selected, Myra will take the aliquot from the side of the tube to avoid collision with
the swab as they tend to stick up in the centre of the tube.

The pipette head will also ocilate and move more slowly when a swab is present in the tube to better
detect collisions and avoid crashing into or ripping out the swab. The ocilating movement will also
help to push any part of the swab away from the tip. If a collision is detected, the tip will back up and
move to a different location in the tube where there are no collisions before aspirating.

Fill in the Samples table.

The Samples editor is displayed in a table format and allows you to annotate your samples. Failure to
properly annotate samples can affect the run setup and Mic analysis.

See Samples Editor for more information on how to edit the Samples table.

Source Plate Visual Tool

A Visual Source Plate tool is provided on the top right-hand corner of the sample editor. This feature
enhances the editing process by allowing you to select specific parts of the plate or tube block to edit.
For example, by clicking on the desired well in the visual tool, that well will be active in the sample
editor table for editing.

Once the wells are edited, they will be coloured in the Well Filter.

Barcode Reader

66
A barcode reader/scanner can be used to simplify the sample editing process. Any reader that can be
connected to the computer running the Myra software can be used for this.

To use the barcode reader, have the cell of the Samples table that you would like to enter he data for
active and then simply scan away. The active cell will automatically move down the table as you scan.

Some barcode readers may need the reader output re-configured for it to move automatically to the
next cell. You may have to scan a barcode in the barcode reader’s manual to change the output
function, where the option may be called carriage return (see the barcode readers manual for more
information).

Import or Export Sample Data

You can import sample information from a number of file types (e.g. comma delimited, tab delimited
or space delimited files) to simplify sample annotation. See Import Samples for more details on how to
import sample information.

The Samples editor will have two options to either save the entire table as a CSV file or copy the data
to the clipboard for easy export to third party software.

Sample Editor Warnings

Various warnings will be displayed if annotations have not been completed correctly. Some examples
include:

• No samples have been configured.

• No assays have been selected in run.
• Insufficient reactions available for configured source samples.
• There is no assay configured for sample
• Assays have not been linked to an edited sample row.
• Assay incompatible with prep protocol
• Assay reaction volumes are not consistent.
• Assays incompatible with each other
• Fixed volume is less than tube dead volume.

67
Deck Layout – Sample Prep
The next stage requires you to layout the deck with the various components required for the run.
These include any plates, consumables, reagents, intermediate mixes and templates. In the deck
layout you will need to Configure the deck with the required plates/blocks and tubes and allocate
Components (reagents and intermediate mixes) and Templates. Each section is represented by tab with
an exclamation icon to indicate that there are items still to be completed.

Configuration

Setup the layout of the block/plates required to achieve the run.

A default deck will be provided based on the information input in the Assay and Samples editor,
where the sample source, reaction source, multi-purpose block and tips will be automatically added
to the deck.

Your run will need to have the Myra 96 well loading block for all semi-skirted, non-skirted 96 well
plates, individual and strip of eight 0.2 mL tubes. For all 0.5 mL, 1.5 mL and 2 mL tubes, Myra 36 well
loading block will need to be placed on deck. Myra 24 well loading block will need to be placed on deck
for 5 mL tubes. Which position they are on can be determined in the software.

See Configuration on how to zoom in, move or delete existing blocks/plates.

Source and reaction plates can’t be deleted. To change the source or reaction plate/tube type please go
back to the Samples editor.

Components

Allocate the Reagent and Intermediate Mix positions onto the deck layout.

The Reagents and Mixes tables will display all the components required for the run including the
minimum volume required. The exclamation mark icon next to each component on the list indicates
that it has not yet been allocated onto the deck.

You can move a component to any well of the Myra Multi-Purpose Block. See Components for more
information on how to place the Reagents and Mixes to the deck.

Sample Templates

Allocate the Control Template positions onto the deck layout.

The Controls defined in the Assay can be found in the Templates and need to be assigned to the deck
like the components above.

Source Templates have been assigned to source plate/block according to the order specified in the
Samples editor. To change the order of the source templates, please go back to the Samples editor.

Once all the deck layout has been completed you can start the run.

68
Advanced Settings – Sample Prep
In the Information page you will find an option to change the conditions that are set by default.

The same settings as PCR Run have been applied. See Advanced Settings for more information on what
settings are configurable.

69
Connecting to the Myra).

The tip usage displayed is the minimum requirement for the run to complete and that more may be
used depending on the actual run conditions.

As such an icon will be displayed on each tip and Mic plate informing the user of the fact. Only after
connecting to the Myra can you configure the tips and Mic tubes.

Plate Library

The Plate Library consists of a number of different plate and block type groups. Open the group to
show the various types available.

Blocks and tips that are compatible with the Myra will be listed at the top of the Plate Library.

Each Mic run will require a loading block for Mic rack as well as one rack of tips. They can be
positioned anywhere on the available deck space. The loading block for Mic rack will automatically
be added to the deck layout.

You will need to insert the Myra 96 Well Loading Block for all semi-skirted and non-skirted 96 well
plates. Including individual and strip of eight 0.2 mL tubes for numbers greater than that provided on
the Myra Multipurpose Loading Block.

Use the Search feature to find plates quickly.

70
Tick the Recently used box to only show you most commonly used plates.

71
Use the Information icon to view details about each plate.

There are a set of generic plate types for each group.

Use the + icon to create a new plate.

72
Plate Editor

Create a new plate by using the + icon next to the plate group.
Select from the various plate subgroups (e.g. cluster rack).

You can use the existing values and simply provide a new name for your plate; or you can define a
new profile by entering the values in the fields provided.

The options are based on the well opening shape (round or square), well base (e.g. conical or
diamond) and other features including skirting.

Any new profile will need to be calibrated prior to use (see Calibrating Blocks, Plates and Tubes).
The new plate will be stored in the Plate Library. Modify or delete plates in the library through the edit
icon.

Tube Type

You can select the tube type required for blocks that have the option for various tube types (e.g. Myra
Multipurpose block). Tube types must be able to meet the volume required for each component, mix
or template specified.

Right click on the individual well of a plate and select the change tube option.
There are a number of different options available including 0.2 mL, 0.5/0.6 mL, 1.5/2.0 mL, 5 mL or 10
mL bottle. The type of tubes in each well can be displayed by zooming in on the plate.

73
This option is only available if a component or template are allocated to the tube position.
Multiple wells can be selected to change tube types.

For all PCR setup runs, source template tubes that have been assigned the same tube type will be
considered identical. The software will assume that all source template tubes are of the same brand
and shape and therefore have the same tube base position. This will result in only one probe for
liquid level for the same tube types. This is a default option and can be unticked in the Advance
Settings (see Advance Settings).

Components

Allocate the Reagent positions onto the deck layout.

The Reagents table will display all the reagents required for the run including the minimum volume
required. The exclamation mark icon next to each reagent on the list indicates that the component has
not yet been allocated onto the deck.

You can move a reagent to any well on any plate displayed on the deck except for the Mic tubes.

Drag and drop the reagent from the list into a well, use the one at a time drop icon to click each reagent
into a well using the list order; or use the bucket fill icon to add them all at once using the highlighted
wells as a guide to the orientation.

Positions that are compatible with a component tube type will be highlighted in light blue. Those that
are not will be highlighted in light red.

If a tube type has not been selected for a component that has been allocated, a red circle will appear
around the well position. Simply right click on a selected set of tubes to change the tube type.

If using multiple assays, the software will recognise the same reagent name and only provide one
instance of it in the list.

Right click a selected set of tubes to remove them from the deck layout. Or use the Clear all well
contents option in the hamburger menu of the SBS position.

Allocate the intermediate Mixes positions onto the deck layout.

Each intermediate mix required for the run will be displayed along with its total volume. You can
expand the details of the intermediate mix components and volumes by using the + icon. Intermediate
mixes include master mixes for each assay and dilution series.

74
Select the tube type for each intermediate mix prior to or after allocating it to the deck layout.

Move the intermediate mixes across to the wells using the same features described above for the
reagents.

Once the components have been allocated, you can drag them across to other wells or plates.

A warning will be displayed if the total volume of the component exceeds that of the well volume.

You can clear individually highlighted components from the plate using the Clear Well Content option
or all of the components on a plate using the Clear All Well contents option.

Hovering over each component well will bring up a tool tip with information on the contents of each
well.

If another dilution reagent other than water (e.g. buffer) has been selected in the Assay setup then it
will be displayed in the Mixes table for the dilution setup.

75
Sample Templates

Allocate the position of all of the sample Templates required for the run.
Templates can be positioned anywhere on the deck except for the Mic tubes.
The same allocation features are used as described for the Components.

Tube type can be selected prior to or after allocation of the sample templates to the deck layout. If
allocating to a plate format (e.g. 96 deep well plate) you do not need to enter a tube type.

Reaction Plate Configuration

Reaction plates are marked by a red cross hair. The orientation of the samples for various non-Mic
plates can be configured by clicking on the red cross hair.

76
The option to display either the Sample, Assay or Group colours is also available using the red cross
hair icon. This is done by selecting the Display Mode option and then the type required.

Once all the deck layout has been completed you can start the run.

77
Run Separation
For some laboratories is it important to separate the creation of master mix from the distribution of
samples. This might be a process to avoid contamination of the master mix with template during the
setup phase. This could be done using one Myra or achieved on two instruments. To facilitate this
type of setup we provide an option to select Create and distribute the mix only; or to Distribute the
samples only. The default option is to Create and distribute mix and sample.

The run should be setup as normal including the annotation of the samples, however, by selecting the
create and distribute mix only option will mean that only the Component and Mix items will be
displayed and require allocation in the deck layout. There will be no Template to add.

Start the run to begin creating and distributing the mix. Once the run is completed you can then either
re-run the same file again on the PC/Myra combination or transfer the file to another PC/Myra
combination. Now select the option to Distribute samples only. Only the template will now be
present in the deck layout.

A warning will be displayed indicating that either no template or mix will be used depending on the
option selected.

78
Advanced Settings
In the Information page you will find an option to change the following conditions that are set by
default.

There are four options for handling the source template:

Level sense and prompt user when insufficient liquid is detected: for accurate level sensing
where the run will stop with a warning (and how you want to proceed) if there is insufficient
liquid detected.

Level sense but aspirate requested volume from the tube base if insufficient liquid is detected:
for automated aspiration from the base of the tube when the system detects insufficient
liquid. Use this option if you are certain that the source template wells contain enough liquid
to complete the run but often get insufficient liquid warnings due to the shape of the tubes
you are using or the composition of the liquid.

Skip the source template if insufficient liquid is detected – the destination will not contain
any of the source template: for accurate level sensing but if it encounters insufficient liquid, it
will skip that source template and no template will be added to the reactions requiring that
template. Use this option if you are using source template storage where it is common for
some source templates to run out due to differing yield in the extraction process or uneven
source template usage.

Always take the requested volume from tube base without level sensing: for the volume to be
taken from the base of the tube without sensing the liquid level. Use this option if your source
template tubes contain a shallow pool of liquid that often triggers the insufficient liquid
warning or if level sensing sometimes causes bubbles that interfere with the liquid aspiration.
You will not get any warnings if there really is not enough liquid.

Individual source template tubes are identical allows the system to assume that all individual source
template tubes (tubes in storage blocks or cluster racks are omitted) are of the same brand and shape
and therefore have the same tube base position. When this option is enabled, the tubes of the same
type will be probed only once for each tube holder. When turned off, Myra will probe each individual
tube to ensure maximum accuracy and therefore potentially consuming more tips.

Re-use tips allows you to switch this condition off if you believe you would like a new tip for each
new pipetting action. This will result in increased tip usage.

Quick mix targets (excluding Mic tubes) allows PCR reactions to be mixed after their construction in
PCR plates or tubes.

Add an additional volume for each aliquot taken if you need to compensate for different solutions
that may be more difficult to aspirate. Thereby, reducing the possibility of lost liquid.

Make an additional percentage of mix volume if you think you need to compensate more for your
master mix creation.

79
ATTENTION
The default settings have been carefully chosen to work optimally for a wide range of conditions. Only
change these settings if you are certain of their effects.

80
Starting a Mic Run
You can start a Mic run from the Myra software without needing to export any sample information or
start a new Mic run from scratch.

Select the Run icon next to the Mic Runs in the navigator bar.
The micPCR Software will initialise automatically.

Save the run file and select the Mic instrument from the tool bar.

Start the run.

81
Create Simple Transfer - General
Use this setup application for simple transfers of liquid from one source to another, normalisation of
samples to a set concentration, or pooling samples into a single destination.

Select Create a new file icon in the tool bar.

Select the option Simple Transfer from the New Document page.

Sources
Add the input samples from which you want to transfer
from by clicking on + button of the Sources.
Select either a plate, tube or input from a CSV.

Give each source a name by typing in the space provided

in the navigator bar.

Multiple sources can be added as long as the total input

does not exceed the maximum possible well
configuration for the Myra (i.e. 3 x 384 wells).

Plate: choose the Input Plate Type from the list. Create a new plate if required (see Plate Editor).

Tube: Choose a Default Tube Type from the list displayed.

82
Enter the source names.
For plates you can use the Well Filter to highlight specific wells only. Use the Fill down or Auto fill
options to simplify annotation (see Filling Cells).

Provide a concentration if required for normalisation.

Create groups to allow for Pooling of samples (see Creating and Allocating Groups).

Importing Sample Sources

Import various fields into the source editor using the Import from CSV File option or the Import data
from a CSV file when using the Plate or Tube source options.

Select the CSV file to import.

Use the Import Configuration to match the CSV file columns to the Source editor columns.
Pick if the import type is Plates or Tubes.

You have the option to save the options as a template for future imports. Or select an existing import
configuration.

Select the appropriate data separator, and if any rows need be ignored.

The following column options are available:

Plate Name: defines the whole plate ID, this will provide the name for the plate source.

Well: defines the well ID, this will number the individual source wells based on the import ID (e.g.
A1).

Source Name: the name of the sample.

Concentration: the concentration of the sample, which can be used for normalisation.

Groups: an ID that represents a group of samples, which can be used for pooling.

83
Destinations
Create the outputs to where you want to transfer your
sources to by clicking on the + button of Destinations.
Select either a plate, tube or import from a CSV.
Multiple destinations can be setup.

Select the plate or tubes types to transfer to.

Select the sources to use from the drop-down list available.

Enter the final transfer volume.

Enter the number of replicates.

You can choose to group the replicates together consecutively by ticking the Group Replicates option.

84
Normalisation

Normalise samples to a set concentration by ticking the Normalise option.

Choose to transfer either the lowest source concentration or enter a specific volume.

The software will pipette the required volume required based on the source concentrations. Some
normalisations will require a dilution step if the transfer volume is less than the minimum pipetting
volume of 1 mL. In such instances, an additional intermediate plate/tube will be required.

Pooling

Pool sample into tubes/plates using the Pool tick option.

Choose the number of sources to be pooled.

This number can’t exceed the total number of samples selected for the group.

Enter the source volume.

If normalising sample prior to pooling then select if the concentration is per source or total.
You may need to use additional tubes to obtain the selected output volume if the dilution to achieve
the output concentration requires volumes not permittable by the Myra.

Custom setup mode

Alternatively, a custom setup mode can be executed by selecting the toggle button on the top left
corner from ‘simple’ to ‘custom’. Custom mode allows you to define what sources are pooled
together, along with their custom defined output concentration and volume.

Importing Destination Requirements

Import various fields into the destination editor using the Import from CSV File option or the Import
data from a CSV file when using the Plate or Tube destination options.

85
If only normalising individual samples, use the same method as described for Importing Sample
Sources.

There are three ways to import sample pooling from a CSV file to a destination output:

Specify the samples names: sample names are separated by “;”. This does not allow you to specify
the concentration or volume of each – you can specify the total volume and the concentration of each
source (the number that appears in the concentration column for the whole well). Specifying the well
is optional in this case.

Specify each source: on a line that contains a well identifier. Each source can then have a custom
concentration or volume. Sources that are pooled together have the same well number.

Specify both sample names and source: You can have both in the same file if the data agrees. An
example is to have a line with all pooled sources (you can leave the name blank on these lines) and a
column for the total volume and then a line for each source with their custom target concentration (in
a different column from the volume specified).

86
Deck Layout – Simple Transfer
Allocate the sources by dragging plates directly onto a deck position.
Or for tubes, by first selecting a loading block type from the Plates tab, then dragging and dropping
the tube into an available position for the tube type.

87
Allocate the destinations using the same method described for sources.

88
Advanced Settings – Simple Transfer
In the Information page you will find an option to change the following conditions that are set by
default.

There are four options for handling the source template:

Level sense and prompt user when insufficient liquid is detected: for accurate level sensing
where the run will stop with a warning (and how you want to proceed) if there is insufficient
liquid detected.

Level sense but aspirate requested volume from the tube base if insufficient liquid is detected:
for automated aspiration from the base of the tube when the system detects insufficient
liquid. Use this option if you are certain that the source template wells contain enough liquid
to complete the run but often get insufficient liquid warnings due to the shape of the tubes
you are using or the composition of the liquid.

Skip the source template if insufficient liquid is detected – the destination will not contain
any of the source template: for accurate level sensing but if it encounters insufficient liquid, it
will skip that source template and no template will be added to the reactions requiring that
template. Use this option if you are using source template storage where it is common for
some source templates to run out due to differing yield in the extraction process or uneven
source template usage.

Always take the requested volume from tube base without level sensing: for the volume to be
taken from the base of the tube without sensing the liquid level. Use this option if your source
template tubes contain a shallow pool of liquid that often triggers the insufficient liquid
warning or if level sensing sometimes causes bubbles that interfere with the liquid aspiration.
You will not get any warnings if there really is not enough liquid.

Individual source template tubes are identical allows the system to assume that all individual source
template tubes (tubes in storage blocks or cluster racks are omitted) are of the same brand and shape
and therefore have the same tube base position. When this option is enabled, the tubes of the same
type will be probed only once for each tube holder. When turned off, Myra will probe each individual
tube to ensure maximum accuracy and therefore potentially consuming more tips.

Re-use tips allows you to switch this condition off if you believe you would like a new tip for each
new pipetting action. This will result in increased tip usage.

Quick mix targets (excluding Mic tubes) allows destination dilutions/pools to be mixed after their
construction in their plates or tube.

Add an additional volume for each aliquot taken if you need to compensate for different solutions
that may be more difficult to aspirate. Thereby, reducing the possibility of lost liquid.

89
ATTENTION
The default settings have been carefully chosen to work optimally for a wide range of conditions. Only
change these settings if you are certain of their effects.

90
Create Sample Prep & Setup – General
Use this setup application for preparing samples using crude extraction methodologies followed by
PCR/qPCR run setup. Commercially available kits such as Qiagen QIAprep&amp UM Viral RNA kit
will be available for automation on Myra.

Select Create a new file icon in the tool bar.

Select Sample Prep & Setup icon from the Sample Prep section on the New Document page.

Sample Prep
Select the Sample Prep method of choice using ‘+’.

Choices currently available are QIAprep&amp (VTM).

The current software is locked down with the QIAprep&amp (VTM) method available only. It does
not currently allow for user re-configuration.

91
Assays – Sample Prep
Using ‘+’ select the Assays for the qPCR run or create a new one using ‘+ New Assay’ from the
dropdown menu.

See Creating a New Assay for more information on how to setup an Assay.

92
Run Setup – Sample Prep
Samples Editor

The Samples editor for Sample Prep & Setup differs from the PCR Run setup in that the information
input is for the sample source and not for the output reactions. Any controls specified in the assay
setup will be placed into the first wells/tubes of the output reactions source followed by the samples.
The order the samples in the source layout will be reproduced in the output reactions layout.

Choose the source type as either Plate or Tube using the toggle button.

Plate: Choose the Sample Plate Type from the list. Create a new plate if required (see Plate Editor).

Tube: Choose a Sample Tube Type from the list.

When your samples are located in a tube, the tube type selected will be automatically assigned to the
block that is required to hold them (e.g. 36 well loading Block is required for 2 mL screw cap tubes).
The block will be automatically allocated to the deck layout.

Select the output Reaction Plate.

Displayed reaction plates will be based on the options available for the chosen qPCR cycler. If your
plate is not within the list, simply select the Other option for the cycler and then chose one of the
generic options that best matches your plate type.

The fill order can be selected for non-Mic plates. Choices available are vertically or horizontally, with
every second row or column, and in checkerboard pattern.

For Mic runs, there is an option to Fill all unused wells with water to ensure temperature uniformity
(See Water Load Samples for more information).

The source plate along with the reaction plate determines how many reactions are available. The
sample editor will change accordingly.

93
Determine whether your samples have a Fixed sample volume or needs to Sense sample volume.

When Fixed sample volume is selected, a box will appear to enter the volume in µL. The volume
entered will allow Myra to estimate the height of the liquid using the tube/plate profile.

If Sense sample volume is selected, Myra will perform a level sense on the samples to determine the
volume of liquid present in the tube/well. An extra tip and time is required for this level sense.

Select the type of swab that can be found in the sample source, if present.

The choices available are None, Standard and Rhinoswab.

When None or Rhinoswab is selected, Myra will take the aliquot from the centre of the tube to avoid a
collision as Rhinoswab’s tend to sit low and out to the side of the tube.

When Standard is selected, Myra will take the aliquot from the side of the tube to avoid collision with
the swab as they tend to stick up in the centre of the tube.

The pipette head will also ocilate and move more slowly when a swab is present in the tube to better
detect collisions and avoid crashing into or ripping out the swab. The ocilating movement will also
help to push any part of the swab away from the tip. If a collision is detected, the tip will back up and
move to a different location in the tube where there are no collisions before aspirating.

Fill in the Samples table.

The Samples editor is displayed in a table format and allows you to annotate your samples. Failure to
properly annotate samples can affect the run setup and Mic analysis.

See Samples Editor for more information on how to edit the Samples table.

Source Plate Visual Tool

A Visual Source Plate tool is provided on the top right-hand corner of the sample editor. This feature
enhances the editing process by allowing you to select specific parts of the plate or tube block to edit.
For example, by clicking on the desired well in the visual tool, that well will be active in the sample
editor table for editing.

Once the wells are edited, they will be coloured in the Well Filter.

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Barcode Reader

A barcode reader/scanner can be used to simplify the sample editing process. Any reader that can be
connected to the computer running the Myra software can be used for this.

To use the barcode reader, have the cell of the Samples table that you would like to enter he data for
active and then simply scan away. The active cell will automatically move down the table as you scan.

Some barcode readers may need the reader output re-configured for it to move automatically to the
next cell. You may have to scan a barcode in the barcode reader’s manual to change the output
function, where the option may be called carriage return (see the barcode readers manual for more
information).

Import or Export Sample Data

You can import sample information from a number of file types (e.g. comma delimited, tab delimited
or space delimited files) to simplify sample annotation. See Import Samples for more details on how to
import sample information.

The Samples editor will have two options to either save the entire table as a CSV file or copy the data
to the clipboard for easy export to third party software.

Sample Editor Warnings

Various warnings will be displayed if annotations have not been completed correctly. Some examples
include:

• No samples have been configured.

• No assays have been selected in run.
• Insufficient reactions available for configured source samples.
• There is no assay configured for sample
• Assays have not been linked to an edited sample row.
• Assay incompatible with prep protocol
• Assay reaction volumes are not consistent.
• Assays incompatible with each other
• Fixed volume is less than tube dead volume.

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Deck Layout – Sample Prep
The next stage requires you to layout the deck with the various components required for the run.
These include any plates, consumables, reagents, intermediate mixes and templates. In the deck
layout you will need to Configure the deck with the required plates/blocks and tubes and allocate
Components (reagents and intermediate mixes) and Templates. Each section is represented by tab with
an exclamation icon to indicate that there are items still to be completed.

Configuration

Setup the layout of the block/plates required to achieve the run.

A default deck will be provided based on the information input in the Assay and Samples editor,
where the sample source, reaction source, multi-purpose block and tips will be automatically added
to the deck.

Your run will need to have the Myra 96 well loading block for all semi-skirted, non-skirted 96 well
plates, individual and strip of eight 0.2 mL tubes. For all 0.5 mL, 1.5 mL and 2 mL tubes, Myra 36 well
loading block will need to be placed on deck. Myra 24 well loading block will need to be placed on deck
for 5 mL tubes. Which position they are on can be determined in the software.

See Configuration on how to zoom in, move or delete existing blocks/plates.

Source and reaction plates can’t be deleted. To change the source or reaction plate/tube type please go
back to the Samples editor.

Components

Allocate the Reagent and Intermediate Mix positions onto the deck layout.

The Reagents and Mixes tables will display all the components required for the run including the
minimum volume required. The exclamation mark icon next to each component on the list indicates
that it has not yet been allocated onto the deck.

You can move a component to any well of the Myra Multi-Purpose Block. See Components for more
information on how to place the Reagents and Mixes to the deck.

Sample Templates

Allocate the Control Template positions onto the deck layout.

The Controls defined in the Assay can be found in the Templates and need to be assigned to the deck
like the components above.

Source Templates have been assigned to source plate/block according to the order specified in the
Samples editor. To change the order of the source templates, please go back to the Samples editor.

Once all the deck layout has been completed you can start the run.

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Advanced Settings – Sample Prep
In the Information page you will find an option to change the conditions that are set by default.

The same settings as PCR Run have been applied. See Advanced Settings for more information on what
settings are configurable.

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Connecting to the Myra
Once the deck layout has been configured and the components allocated, you can now start the run.

Select the Connect option in the drop-down menu of the Instrument icon.
Only instruments that have the status Idle can be used.

Upon connection a run summary status bar will appear.

Tip and Mic tube availability will be displayed on the deck.

The instrument captures the tip and Mic tube usage from run to run. This only occurs if the user does
not change the position of the Tip racks and Mic tubes from run to run. If so, a warning will be
displayed on connecting to the Myra.

The software is designed to utilise tips and Mic tubes efficiently. As such, any unused Mic tubes from
a previous run will be used first in the next run. If there are insufficient tubes from one Mic tube rack,
a second rack will be added to the run. A total of two Mic tube racks, allowing for 96 samples, can be
used per run.

There is an option to revert to the start of the Mic tube rack.

You can manually set the number of tips or Mic tube strips that are available or disabled on a plate.

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A warning will indicate if any tube or plate has not been calibrated (see Calibrating Blocks, Plates and
Tubes).

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Starting the Run
Begin the run by selecting the Play icon in the run status summary bar.
A confirmation dialogue box will appear. The box shows the positions of the reactions in the Mic tube
rack being used.

You must tick off the items in the pre-run check list before you can execute the run.
Ensure that:

• All tips are present;

• Reagents are present;
• Intermediate mix tubes are present;
• Waste tube has been emptied;
• There are no obstacles in the way.

Ensure that the lid is closed prior to starting the run. A lid sensor will detect if the lid is open and will
prevent the instrument from starting, while a warning will notify you of the fact.

At this point the instrument LED indicator will be flashing blue indicating to other users the
instrument has been ‘booked’ to start a run. No other user can start a run on the instrument until it
has completed this run.

To execute the run, click the Start button in the Start Run dialogue box.
The instrument will automatically activate the lid sensor, ensure there is no pipette tip attached, and
then the start program. The LED indicator will turn green to notify the instrument is running.

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Creating Myra Templates
Templates allow the user to set-up runs that will be used repetitively. For example, you may want to:

• Set pre-defined plates and tubes;

• Set pre-defined assays for each run;
• Set pre-defined controls or standards in each run.

There is one default Template provided with the software. The Myra Demo Kit can be used to evaluate
the performance of the Myra using a kit provided by BMS.

Create a Template
Start a New Run.
Create your run using the process described above.

At least one sample needs to be present in the run in order to be able to allocate the components for
the reactions on the deck layout. In order to able to save the layout in the Template, the first sample
needs to be named, such as ‘Click Here to Start’.

Select the down arrow next to the Save As button, then select Template.
Save the template into the Template library located in Documents/Bio Molecular
Systems/Myra/Templates.

You also have the option of creating subfolders within the library.

Using a Template
Select the Template in the Start page.
The run will open with all the saved parameters, including sample annotation.

Start the run as described above (see Starting the Run).

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During a Run: Execution
Once the run begins, the instrument will first send the head over to the waste tub to ensure there is no
tip attached. It will then commence transfer of liquid based on the programmed run. Typically, all
intermediate mixes are created first with assay master mixes at the top of the list followed by serial
dilutions. During the creation of an intermediate mix the water will be loaded first to avoid
contamination by other reagents. This also allows the instrument to utilise Tip Re-use to speed up the
run and minimise tip usage. The next reagent loaded will always be the one with the highest volume
so that tip re-use can be maximised to save time and tips. All subsequent reagents will use one tip at a
time to avoid contamination of the stock material. Tip reuse will also be applied to loading the assay
intermediate mix into reaction tubes. Templates and serial dilutions will be loaded using one tip at a
time.

In the Run Summary banner, the current pipetting step is displayed to the left side of the banner next
to the instrument icon.

A graphic of the amount progressed through is displayed in blue.

The Time Remaining to complete the run is displayed to the right side of the Run Summary banner.

Pausing or Aborting a Run

You can pause a run by selecting the Pause icon in the run summary banner.

You can stop the run at any point by selecting the Abort function in the summary window.
The head will move to the home position.

Run Status
Liquid Transfer Operations display all the volumes and positions liquid is being transferred during a
run. The operation being conducted in real time is highlighted in blue. A blue arrow on the deck
layout displays the trajectory of the transfer. Completed operations in the list receive a green tick.

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Hovering over an operation in the list brings up a grey trajectory arrow on the deck layout.

During the creation of an intermediate mix or loading of reaction tubes, the well will turn from grey
to a lighter content colour, defined in the legend (see Configuration). On completion of the mix or
reaction the well will turn into the content colour.

Any issues during the run such as running out of liquid will be notified to the user.

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Messages
All actions achieved by the instrument as well as any warnings about the run will be logged and
displayed in Messages along with the time it occurred.

Common messages will include the start time and instrument name and firmware version.
Some messages may be warnings such as:

• Running out of tips;

• Not detecting any volume or low volume;
• Lid open events.

Re-Run Option
The Re-Run option lets you repeat the previous run without needing to setup the software again. This
option is great for repeating experiments.

Select the Re-Run option in the Instrument icon drop down list after a run has completed.
All aspects of the previous run will be used including reagents, templates and reaction numbers.

Only the tip and Mic tube positions will be updated to reflect the previous runs usage.

You can modify any of the run parameters prior to starting the run.

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Reports
View a Pre-run or Post-run report for each run located in the Run Navigator. A preview of the report
will be displayed to the right side of the user interface and can be configured to show only certain
parts.

A Pre-run report will display information about Run Properties, Reactions, Assays, and Deck Layout.

A Post-run report will display the same information along with the additional logs for the run.

Report Configuration
Each report is divided into standard sections; Run Properties, Reactions, Assays and Deck layout. You
can choose which sections to display in the report by ticking or unticking the sections in the report
Configuration.

Report Preview
Each selected section will be displayed in the report Preview. A new page will begin following each
section. Each page will have a number in page footer along with the version of software used. The run
name will be displayed in the page header.

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Run Properties

The Run Properties section will display the following:

Name The name of the run

File The directory location of the run file

Status Completed or not

Operator Name of the individual that completed the run

Notes Any notes regarding the run completed by the user

Started Date and time run began

Completed Date and time run finished

Event Log A report of important messages generated during the run including any
issues such as loss of communication

Reactions

The Samples editor is replicated in the report preview including sample Name, Type, standard
concentrations, and Assay. All samples will be displayed including the second Mic run.

Assays

Assays contain all the information about the targets as well as oligonucleotides and reporter dyes.
The reaction components and volumes are also listed out. All the segments of the run profile are
reported for any Holds, Cycling and Melts. The channels used are reported along with the step at
which fluorescence was acquired.

Deck Layout

A simple representation of the deck layout is displayed in the reports. The names and volumes of
each reagent, mix or reaction is also shown.

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Report Options

Search: find a word or string of characters in the report preview. Enter the search word(s) to find
them in the report. The located words will be highlighted in the preview.

Print: print the report using user defined settings.

Quick Print: print the report using default print settings.

Page Setup: select the paper type and orientation and adjust page margins.

Zoom: Use the zoom in or zoom out to best view the report preview.

Page selection: navigate through the pages using the page selection buttons; First page, Previous page,
Next page and Last page.

Export: export the report using one of the available file formats including PDF, XLS and Text file.
Each export will have a set of options to choose from.

Send: email a report using one of the available file formats. A report generated in the selected file
format will be attached to an email using your default email client, which will open automatically (if
available).

Watermark: add a watermark to your report. The water mark can be either a text or image. This
option can be used to embed text such as Confidential to the report. A list of default text is provided, or
you can enter your own. Alternatively, add an image to the report such as a company logo. The
direction and position of the text or image can be configured as well as which pages to apply the
watermark to.

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Laboratory Information Management System (LIMS) Settings
If the reaction setup is for a Mic qPCR run it is possible to setup connection to a Laboratory
Information Management System (LIMS) that will allow all data from Myra and micPCR run files to
be exported into CSV and XLSX formats. You will find this option in the Information page.

Each Myra (and micPCR) run file contains its own set of key, value meta data that is editable.

Enter the required Key labels and their Values in the table. Any user defined key and value
combinations will be stored in the run file and exported into the export file.

It is possible to automatically save the data from the MicPCR run to a folder that is linked to a LIMS
by clicking on the more icon (three horizontal dots) and selecting the desired folder. The run data can
be auto exported in either CSV or XLSX format by selecting it in the drop-down menu of Auto save mic
run.

There is also the option to have the auto export be cancelled if an error is detected in any auto
generated analysis. If an error is detected a warning should be displayed allowing you to possible
rectify or otherwise process the run file. This can be done by selecting one of the following options in
the auto save mic run menu: Analysis error, Optical Failure, Reportable Warning, Run Failure.

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There is also a common LIMS metadata registry used by both micPCR and Myra which is stored on
the computer.

Save to Registry will overwrite the values in the CommonMetadata.xml file from the run.

Load from Registry will overwrite the values in the run from the CommonMetadata.xml file.

When a new Myra (or Mic) file is created using New file it will load the values from the common
CommonMetadata.xml.

When a new Myra (or Mic) file is created from a Template it will use the meta data values stored in the
template. It will not load the values from the common CommonMetadata.xml.

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Acknowledgement of Registered Trademarks
Adobe® and Reader® are both registered trademarks of Adobe Systems Incorporated, San Jose CA USA

Bluetooth® is a registered trademark of the Bluetooth SIG, Kirkland WA USA

CAL Fluor®, Quasar® and BHQ® are registered trademarks of Biosearch Technologies, Petaluma CA
USA.

Eclipse® is a registered trademark of Epoch Biosciences Inc., Bothwell WA USA.

Eva Green® is a registered trademark of Biotium, Hayward CA USA.

Hex™, NED™, ROX™, Cy™, FAM™, TET™, TAMRA™ and JOE™ are trademarks, and VIC® is a
registered trademark of Applera Corporation, Foster City CA USA.

Iowa Black® is a registered trademark of Integrated DNA Technologies Inc., Coralville IA USA.

LC Green® is a registered trademark of Idaho Technology Inc., Salt Lake City UT USA.

LC® is a registered trademark of Roche Holding AG, Basel Switzerland.

LUX® probes, Texas Red®, SYTO®, SYBR®, PicoGreen®, and RiboGreen® are registered trademarks of
Life Technologies, Carlsbad CA USA

Plexor® is a registered trademark of Promega, Madison WI USA

Scorpion® probes are a registered trademark of Sigma-Aldrich Corporation, St. Louis MO USA.

Windows® is a registered trademark of the Microsoft Corporation, Redmond WA USA

Easy-Fit-Tip™, Smart-Capture-Tip™, and Vector-Drive™ are trademarks of Bio Molecular Systems,

Gold Coast QLD Australia.

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References
1. World Health Organization. Laboratory Biosafety Manual – 3rd ed. Geneva: World Health
Organization; 2004.

111